Chr	Model start	Model end	Strand	Number of PhyloCSF regions	PhyloCSF region Ids	Top rank	GENCODEv22 annotation	HumanGENCODEv28 gene ID	Human contemporary RefSeq model	Transcribed?	Mouse GENCODE M18 gene ID	Mouse GENCODE M18 gene biotype	Current MGI symbol	Mouse contemporary RefSeq model	Point of pseudogenisation	Non-murine representative coding model	Disablement event	Notes
1	9951231	9960832	-1	4	chr1:9951232-9951291-, chr1:9952339-9952470-, chr1:9955834-9955902-, chr1:9960725-9960787-	384	absent	ENSG00000283611	/	No	ENSMUSG00000087198	protein-coding	Gm13097	ncRNA XR_001784505.1	human	coelacanth PLAR LongAUGORFlinc|3P|XLOC_005457|TCONS_00005606:1.86419|166AA|136AA|	exon loss and PTC	Uncharacterised protein. While syntenic conservation is currently defined by the human / coelacanth clade, potential homologies for this CDS extend beyond vertebrates (see legend to Figure 3b).
1	21950735	21951578	-1	4	chr1:21950738-21950881-, chr1:21951083-21951142-, chr1:21951161-21951205-, chr1:21951297-21951365-	280	absent	ENSG00000283234	/	Yes	ENSMUSG00000041399	protein-coding	1700013G24Rik	protein coding NM_027063.2	primates	/	PTC and frameshift	Uncharacterised protein.
1	248692152	248698932	1	2	chr1:248692176-248692208+, chr1:248697030-248697161+	5148	two lincRNA	ENSG00000229703	ncRNA NR_125950.1	Yes	ENSMUSG00000052642	protein-coding	4930504O13Rik	protein coding NM_207527.3	apes	/	loss of ATG	Protein containing a u-PAR / Ly-6 domain. The human is locus is transcribed and could theoretically encode a CDS that is 5' truncated.
1	230138601	230138783	1	1	chr2:230138601-230138765+	569	absent	ENSG00000283451	/	No	ENSMUSG00000062783	protein-coding	Csprs	protein coding NM_033616.3	primates	/	multiple exon loss	Characterised as component of Sp100-rs (Csprs) in mouse, a putative G-protein coupled receptor
2	112440396	112440601	-1	2	chr2:112440419-112440472-, chr2:112440491-112440583-	803	absent	ENSG00000283698	/	Yes	ENSMUSG00000079051	protein-coding	Gm14025	protein coding XM_006500514.2	primates	/	loss of ATG and multiple exons	Vinculin superfamily domain containing protein.
3	141660536	141729405	1	5	chr3:141713327-141713374+, chr3:141721005-141721052+, chr3:141721068-141721094+, chr3:141729293-141729376+, chr3:141738332-141738361+	281	lincRNA	ENSG00000242104	ncRNA NR_136190.1	Yes	ENSMUSG00000099564	protein-coding	Gm28729	protein coding XM_006511608.3	human	/	PTC	The mouse gene is unofficially known as NACHT, LRR and PYD domains-containing protein 5.
3	46719749	46736388	-1	2	chr3:46719752-46719787-, chr3:46719827-46719997-	462	protein coding	ENSG00000261603	pseudo NR_147121.1	Yes	ENSMUSG00000049719	protein-coding	Prss46	protein coding NM_183103.2	apes	/	exon loss linked to frameshift	Protease, serine 46 was re-annotated as a pseudogene in human after PhyloCSF indicated that the locus is significantly truncated.
3	58180009	58183978	1	2	chr3:58180356-58180451+, chr3:58180482-58180517+	64	absent	ENSG00000283511	protein coding XM_017007608.1	Yes	ENSMUSG00000109649	protein-coding	Gm45521	protein coding XM_017316351.1	primates	xenopus LOC105947030	PTC	Protein containing a FAM183 domain
3	167903304	167920676	1	4	chr3:167912863-167912901+, chr3:167915073-167915105+, chr3:167915124-167915201+, chr3:167917330-167917494+	287	two lincRNA	ENSG00000244227	pseudo NR_033843.2	Yes	ENSMUSG00000100962	protein-coding	/	/	apes	eagle LOC104324177	indel linked to frameshift and PTC	Protein containing leucine rich repeat 7 domains.
3	100185687	100211766	1	4	chr3:100208048-100208074+, chr3:100208090-100208179+, chr3:100208198-100208245+, chr3:100211575-100211682+	486	protein coding (TMEM30C)	ENSG00000235156	pseudo NR_028357.1	Yes	ENSMUSG00000022753	protein-coding	Tmem30c	protein coding NM_027651.1	human / chimp	/	two splice site mutations	Transmembrane protein 30C was converted to a transcribed unitary pseudogene in human as the loss of splice sites is coupled with the lack of expression data for the final 4 exons. However, as speculated in PMID:17258408, the production of a shorter protein isoform is theoretically possible.
3	195701618	195711643	1	2	chr3:195708133-195708165+, chr3:195711593-195711628+	5786	lincRNA	ENSG00000283426	ncRNA NR_122105.1	Yes	ENSMUSG00000094430	protein-coding	Gm933	protein coding NM_001256309.1	primates	/	multiple PTCs	Certain other mammalian RefSeq models have been unofficially named novel somatomedin-B and thrombospondin type-1 domain-containing protein-like.
3	112321140	112321443	1	1	chr3:112321220-112321279+	1395	absent	ENSG00000283669	/	No	ENSMUSG00000053182	protein-coding	Gm609	protein coding NM_001005854.2	primates	/	multiple exon loss	Immunoglobulin V-set domain containing protein.
3	44421316	44421811	-1	2	chr3:44421325-44421354-, chr3:44421725-44421772-	2995	lincRNA	ENSG00000225873	ncRNA XR_171376.1 (LINC00694)	Yes	ENSMUSG00000107504	protein-coding	Gm35549	protein coding XM_017313737.1	apes	/	indel linked to frameshift and PTC	The coding potential of this locus was initially suggested by weak mass spectrometry evidence, and it briefly existed as a protein-coding gene in GENCODEv24. Subsequent PhyloCSF analysis made it apparent that the human CDS is truncated by 70aa, which is nearly 50% of the protein. The locus was converted to pseudogene on this basis, while high-confidence peptide evidence has yet to be found. Nonetheless, this locus remains an edge case, and RefSeq have recently annotate the truncated CDS as NM_001351479.1.
3	120357754	120367874	1	7	chr3:120366477-120366563+, chr3:120366639-120366722+, chr3:120366732-120366758+, chr3:120366780-120366827+, chr3:120367884-120367967+, chr3:120367974-120368024+, chr3:120368031-120368084+	11	antisense	ENSG00000240661	ncRNA XR_001740865.1	Yes	ENSMUSG00000108763	protein-coding	Gm36028	protein coding XM_006522825.2	primates	/	loss of ATG and multiple splice sites, multiple PTCs	V-set domain containing protein.
3	48997221	48999442	-1	/	found by re-ranking	/	absent	ENSG00000285416	/	No	ENSMUSG00000115688	unitary pseudogene	/	/	mammals	chicken LOC395991	loss of 5' sequence, splice site mutation	Ortholog of chicken avian secreted frizzled-related protein 5.
4	82285053	82340013	1	4	chr4:82285065-82285130+; chr4:82285263-82285295+; chr4:82290504-82290551+; chr4:82295689-82295757+	819	absent	ENSG00000284516	ncRNA XR_938934.2	Yes	ENSMUSG00000105078	protein-coding	Gm35911	protein coding XM_017321222.1	primates	/	multiple PTCs	Vesicle-associated membrane protein family member. While homologies are found beyond vertebrates, syntenic conservation is apparently limited to mammals.
5	140569962	140594570	-1	5	chr5:140590883-140590909-, chr5:140591081-140591131-, chr5:140591663-140591701-, chr5:140592018-140592047-, chr5:140594242-140594367-	66	5' UTR of APBB3	ENSG00000283602	/	Yes	ENSMUSG00000044719	protein-coding	E230025N22Rik	protein coding NM_172831.2	primates	/	loss of ATG, multiple PTCs, splice site mutation	Uncharacterised protein. The human model was identified within the 5' UTR of APBB3.
5	151173981	151180617	1	/	found by re-ranking	/	absent	ENSG00000285420	/	No	/	absent	/	/	primate / rodent	myotis brandtii LOC102242364	exon loss, splice site mutation	Mammalian RefSeq models are typically named unofficially as novel platelet-derived growth factor receptor-like protein. Conservation potentially extends across vertebrates - e.g. fugu ENSTRUT00000033722 – although without synteny beyond mammalian genomes.
6	30056965	30058612	-1	5	chr6:30056989-30057018-, chr6:30057112-30057156-, chr6:30057241-30057297-, chr6:30057580-30057663-, chr6:30058118-30058171-	93	antisense	ENSG00000204623	pseudo NR_026751.2	Yes	ENSMUSG00000036214	protein-coding	Znrd1as	protein coding NM_029602.1	apes	/	multiple frameshifts linked to indels and PTCs	Uncharacterised protein, named as zinc ribbon domain containing 1, antisense in mouse.
7	37796058	37796888	1	6	chr7:37796070-37796132+, chr7:37796163-37796255+, chr7:37796281-37796406+, chr7:37796513-37796542+, chr7:37796595-37796783+, chr7:37796802-37796888+	35	absent	ENSG00000283444	/	No	ENSMUSG00000047462	protein-coding	A530099J19Rik	protein coding NM_175688.4	primates	/	multiple frameshifts linked indels	G-protein receptor coupled protein fmaily member.
7	2383698	2388652	1	2	chr7:2384592-2384675+, chr7:2388551-2388658+	304	lincRNA	ENSG00000230914	/	Yes	ENSMUSG00000106350	protein-coding	Gm4869	/	primates	/	loss of multiple exons, non-canonical splicing, PTC	Similar to kinesin-like protein KIF19.
7	81489472	81608710	-1	10	chr7:81560120-81560206-, chr7:81560743-81560862-, chr7:81570270-81570329-, chr7:81570403-81570444-, chr7:81574077-81574166-, chr7:81581744-81581842-, chr7:81586891-81586944-, chr7:81590981-81591064-, chr7:81597741-81597815-, chr7:81607525-81607572-	904	two lincRNA	ENSG00000233491	ncRNA NR_126025.1/	Yes	ENSMUSG00000109903	protein-coding	/	/	apes	/	multiple indels linked to frameshifts and PTCs	Cadherin-related family member 3-like protein. The mouse gene has 21 exons, though its structure was previously not apparent as it is not supported by Sanger-sequenced transcript evidence. PacBio data allowed for the correct structure to be resolved.
7	73735407	73736073	1	4	chr7:73735456-73735500+, chr7:73735729-73735848+, chr7:73735924-73735983+, chr7:73743038-73743100+	140	antisense	ENSG00000225969	ncRNA NR_026690.1	Yes	ENSMUSG00000085042	transcribed unitary pseudogene	Abhd11os	ncRNA NR_026688.1	primate / rodent	pig: XP_013851001.1 (bicaudal D-related protein homolog isoform X2)	loss of first exon	Certain RefSeq models in other mammals have been named bicaudal D-related protein.
8	8719536	8714055	-1	5	chr8:8714226-8714285-, chr8:8714879-8714917-, chr8:8715416-8715499-, chr8:8715532-8715576-, chr8:8719469-8719546-	167	absent	ENSG00000284717	/	No	ENSMUSG00000109372	protein-coding	Gm19410	protein-coding XM_006509234.3	primates	/	multple exon loss	Lipoprotein receptor-like protein.
8	144049079	144051203	1	9	chr8:144049161-144049202+, chr8:144049291-144049581+, chr8:144049636-144049896+, chr8:144050020-144050055+, chr8:144050302-144050370+, chr8:144050386-144050448+, chr8:144050794-144050856+, chr8:144051015-144051050+, chr8:144051114-144051191+	902	antisense	ENSG00000204791	protein coding XM_017014128.1	Yes	ENSMUSG00000071724	protein-coding	Smpd5	protein coding NM_001195537.1	primates	/	multiple frameshifts linked to indels and PTCs	Long established as sphingomyelin phosphodiesterase 5 in mouse. The frameshift and PTC in ape genomes are shortly downstream of the ancestral ATG. Translation from the next in-frame ATG would give a very small CDS, as it is found in exon 5. The RefSeq model uses an upstream ATG that is poorly conserved and has little evidence for transcription.
9	120847294	120851339	1	1	chr9:120847295-120847354+	1125	antisense	ENSG00000226752	ncRNA NR_024408.1	Yes	ENSMUSG00000026870	protein-coding	Cutal	protein coding NM_001308024.1	primates	/	multiple exon loss	Approximately half of the cutA divalent cation tolerance homolog-like protein-coding gene has been lost in primates.
10	100105754	100140151	-1	8	chr10:100105748-100105804-, chr10:100108360-100108389-, chr10:100108448-100108504-, chr10:100117267-100117368-, chr10:100117406-100117438-, chr10:100121044-100121079-, chr10:100122506-100122571-, chr10:100122574-100122651-	105	absent	ENSG00000283232	/	No	ENSMUSG00000025197	protein-coding	Cyp2c44	protein coding NM_001001446.3	primates	/	multiple exon loss linked to frameshifts and PTCs	Cytochrome P450, family 2, subfamily c, polypeptide 44 is highly degraded in primates.
10	26664336	26697295	-1	2	chr10:26664276-26664392-, chr10:26667561-26667644-	1751	lincRNA	ENSG00000227932	ncRNA XR_930765.1	Yes	/	absent	/	/	primate / rodent	PLAR model from ferret: EnsCodingFull|3P|XLOC_025805|TCONS_00068935:4.5679 (LOC101691422 in RefSeq)	multiple exon loss linked to frameshifts and PTCs	Certain protein-coding RefSeq models from other mammals are known unofficially as selenoprotein O-like.
10	26379034	26387374	-1	/	found by re-ranking	/	absent	ENSG00000284951	/	No	/	absent	/	/	placental mammals	opossum LOC103093635	exon loss, multiple PTCs, splice site mutation	Protein containing a TNFR / NGFR cysteine-rich region. Conservation without synteny apparently extends across vertebrates, e.g. Larimichthys crocea LOC104936695.
11	111448450	111473381	1	37	chr11:111447053-111447100+, chr11:111448458-111448505+, chr11:111448581-111448643+, chr11:111449336-111449365+, chr11:111449437-111449472+, chr11:111449753-111449803+, chr11:111450349-111450399+, chr11:111450415-111450444+, chr11:111451043-111451141+, chr11:111451248-111451313+, chr11:111451338-111451409+, chr11:111452409-111452501+, chr11:111453424-111453489+, chr11:111454244-111454366+, chr11:111454984-111455016+, chr11:111455382-111455477+, chr11:111455806-111455871+, chr11:111456553-111456738+, chr11:111457066-111457335+, chr11:111457329-111457391+, chr11:111457847-111457927+, chr11:111457988-111458044+, chr11:111458117-111458194+, chr11:111459630-111459725+, chr11:111459756-111459782+, chr11:111460211-111460348+, chr11:111461911-111461937+, chr11:111462322-111462393+, chr11:111462672-111462710+, chr11:111463102-111463155+, chr11:111463318-111463368+, chr11:111463396-111463428+, chr11:111466815-111466889+, chr11:111469225-111469287+, chr11:111469784-111469840+, chr11:111469916-111469942+, chr11:111473319-111473375+	394	two lincRNA	ENSG00000255093	ncRNA XR_001748381.1/ncRNA XR_001748382.1	Yes	ENSMUSG00000110266	protein-coding	Gm32742	protein coding XM_017313740.1	primates	/	multiple frameshifts linked to indels and PTCs, multiple splice site mutations	Uncharacterised protein.
12	22116629	22134851	-1	6	chr12:22116633-22116662-, chr12:22116662-22116733-, chr12:22126639-22126758-, chr12:22130471-22130527-, chr12:22134804-22134851-, chr12:22134869-22134940-	65	absent	ENSG00000283582	ncRNA XR_001749042.1	No	ENSMUSG00000048473	protein-coding	Sult6b2	protein coding NM_001145390.1	apes	/	missing exon linked to frameshift	Sulfotransferase family 6B, member 2.
12	95311312	95416098	-1	4	chr12:95405372-95405443-, chr12:95405471-95405503-, chr12:95407918-95407956-, chr12:95408086-95408124-	1638	three lincRNA	ENSG00000257943	ncRNA XR_001749266.1/ncRNA XR_001749265.1	Yes	ENSMUSG00000114757	unitary pseudogene	/	/	primate / rodent	xenopus XP_008109055	exon loss, multiple splice site mutations, multiple PTCs and frameshifts.	Protein containing a FAM194 domain.
12	2761200	2775658	-1	3	chr12:2767965-2768021-, chr12:2770415-2770456-, chr12:2775566-2775661-	2025	lincRNA	ENSG00000255669	ncRNA NR_033958.1	Yes	/	absent	/	/	primate / rodent	dog PLAR model: EnsCodingFull|3P|XLOC_033065|TCONS_00081178|n/a:8.02699 (XP_005637371.1)	multiple PTCs and splice site mutations	Maestro heat-like repeat-containing protein family member.
12	121053732	121059670	-1	7	chr12:121053768-121053842-, chr12:121053873-121053899-, chr12:121053950-121054006-, chr12:121054019-121054045-, chr12:121059440-121059478-, chr12:121059542-121059586-, chr12:121059614-121059655-	1742	absent	ENSG00000283542	/	No	ENSMUSG00000029561	protein-coding	Oasl2	protein coding NM_011854.2	primates	/	multiple exon loss linked to frameshifts, multiple PTCs	2'-5' oligoadenylate synthetase-like 2.
13	24611966	24613983	1	2	chr13:24611978-24612046+, chr13:24613945-24613986+	1873	absent	ENSG00000285228	ncRNA XR_001749794.1	No	/	absent	/	/	primate / rodent	cat: XP_019681345	loss of most exons	Just two exons remain of a large protein-coding gene found in non primate / non-rodent mammals. The cat model is unofficially known as zonadhesin and has a 3,514aa CDS.
14	62117346	62128397	1	3	chr14:62127829-62127903+, chr14:62127863-62127889+, chr14:62128023-62128391+	275	lincRNA	ENSG00000186369	ncRNA NR_015358.2	Yes	ENSMUSG00000071265	unitary pseudogene	1700086L19Rik	ncRNA NR_030733.1	primate / rodent	dog PLAR model: LongAUGORFlinc|3P|XLOC_055903|TCONS_00135715:5.66804|194AA|103AA||Pfam_1_doms|RNACode|HSS_1991_9.6E-10	indels linked to frameshifts and PTCs	Uncharacterised protein.
14	34954859	34982526	-1	1	chr14:34982422-34982517-	353	antisense	ENSG00000258704	ncRNA XR_943744.2	Yes	ENSMUSG00000062198	protein-coding	2700097O09Rik	protein coding NM_028314.2	base of primates (CDS intact in bushbaby but not in new or old world monkey genomes)	/	multiple exon loss, ATG loss, splice site mutation	Protein containing a AdoMet_Mtase superfamily domain.
15	82711246	82711877	-1	4	chr15:82711282-82711380-, chr15:82711677-82711727-, chr15:82711740-82711784-, chr15:82711806-82711838-	594	lincRNA	ENSG00000228141	pseudo NR_034139.1	Yes	ENSMUSG00000061877	protein-coding	BC048679	protein coding NM_001193274.1	primates	/	exon loss linked to frameshift, multiple PTCs	Protein containing a NLPC_P60 superfamily domain.
15	75226401	75234014	-1	2	chr15:75229590-75229646-; chr15:75228852-75228920-	22059	antisense	ENSG00000260660	protein coding  NM_001321990.1	Yes	ENSMUSG00000070298	protein-coding	Trcg1	protein coding NM_001014398.2	primates	/	multiple indels linked to frameshifts and PTCs	Taste receptor cell gene 1. The RefSeq CDS starts downstream of the reading frame disruption, and it is highly 5' truncated.
17	68691809	68716064	-1	1	chr17:68693973-68694062-	839	absent	ENSG00000283376	/	No	ENSMUSG00000020617	protein-coding	1700012B07Rik	protein coding NM_001162428.1	primates	/	multiple indels linked to frameshifts and PTCs	Uncharacterised protein.
19	6396380	6412338	1	8	chr19:6411742-6411786+, chr19:6411844-6411915+, chr19:6412270-6412332+, chr19:6414855-6414923+, chr19:6414920-6414964+, chr19:6424412-6424450+, chr19:6424801-6424848+, chr19:6424859-6424885+	18	lincRNA	ENSG00000214347	protein coding NM_001321601.1	Yes	ENSMUSG00000109739	protein-coding	Gm17949	inferred pseudogene Gm17949	primates	/	exon loss linked to PTC	Adenylate kinase isoenzyme 1-like. The RefSeq pseuodgene in mouse has an incorrect structure.
19	50812707	50808145	-1	2	chr19:50808166-50808204-, chr19:50808655-50808759-	99	absent	ENSG00000284711	/	Yes	ENSMUSG00000108622	protien-coding	Gm36864	protein-coding XM_006541343.3	primates	/	exon loss	Uncharacterised  protein
22	21657811	21661021	1	3	chr22:21657814-21658014+, chr22:21658266-21658385+, chr22:21660896-21660946+	82	absent	ENSG00000284630	/	Yes	ENSMUSG00000049916	protein-coding	2610318N02Rik	protein coding NM_183287.2	base of primates (CDS intact in bushbaby but not in new or old world monkey genomes)	/	multiple exon loss	Uncharacterised protein. The locus has undergone rearrangement in human, leaving a complex distribution of fragments.
X	64405660	64406074	1	1	chrX:64405660-64406073+	335	absent	ENSG00000283349	/	Yes	ENSMUSG00000109858	protein-coding	Gm45800	/	apes	/	PTC	Profilin 2 family-like protein, since named as profilin 5 (Pfn5) by the Mouse Genome Informatics resource based on this annotation. The single exon structure suggests it originated through retrotransposition.