Table 2. Genomic Structure of Chicken MUC2.

Exon	cDNA		Exon	UCSC Alignment1		Intron	Splice Junctions
#	Start	Stop	length	Start	Stop	length	5′ Splice acceptor	3′ Splice donor
1a	1	94	94	14368918	14368825	1490	cagtggtattCACAGTTCAC	ATAAGAAAAGgtaagctcta
2	95	359	265	14367335	14367071	2588	aacttaacagGAAGGACAAG	ATGGGCGGATgtaagtacat
3	360	474	115	14364483	14364369	698	ttcttcctagTGTCAAGACA	TGCACTGATGgtatgtaaaa
4	475	565	91	14363671	14363581	411	cattacctagGTGGAGCTGG	ATTAGTGGAGgtgagtcata
5	566	675	110	14363170	14363061	237	tttctcacagTTGCAAGCTA	TAATGAGCATgtgagtaagc
5b	566	744	179	14363060	14362992	168	taatgagcatGTGAGTAAGC	TGAGATGTTAgtgtgtgaag
6	745	961	217	14362824	14362608	450	tccttcccagCGTGAGGAAT	AACTTTTGCTgtaagcagct
7	962	1087	126	14362158	14362033	260	tttttttcagACAAAACATG	TGCCCCGAAGgcaagtgtat
8	1088	1205	118	14361773	14361656	318	tgctttacagGGACTGTGTA	GTGAAGAATGgtaaggatca
9	1206	1344	139	14361338	14361200	663	ttgtttatagCACCTGTGAT	GTTGGCCAAGgtactgtata
10	1345	1455	111	14360537	14360427	1040	gtgattgtagAGTGCTGTGA	CAAAAAAAATgtaagtgttg
11	1456	1525	70	14359387	14359318	1334	ttttatacagGTGGTGGTTT	CATGTGTCAGgtaaggacca
12	1526	1660	135	14357984	14357850	527	tgtttttcagCTAGCTTCTC	GACATTCAAGgcaagtgtcc
12b	1526	1735	210	14357849	14357774	451	acattcaaggCAAGTGTCCA	ACATGGGTGGtaattcatag
13	1736	1900	165	14357323	14357159	608	tttttgatagGTCTTTGTGG	ATTGAAAGTGgtaagcttgc
14	1901	1995	95	14356551	14356457	623	ttttttgcagCAAATTATGC	ATACTATAAGgtatggtaat
15	1996	2122	127	14355834	14355708	578	gctttttcagAGATGTAAAT	AGTGTCTGCTgtaagtaatg
16	2123	2378	256	14355130	14354875	854	tcccctccagCTGATGAAGT	GAGAACGTTGgtatgtgtta
17	2379	2431	53	14354021	14353969	289	tctttcctagTGTTTGCCGA	AGAATGAAAAgtaagtgaca
18	2432	2541	110	14353680	14353571	435	taactttcagGTATAACAGA	AACTGATCTTgtatgtattc
19	2542	2693	152	14353136	14352985	433	tgctccttagTATCAAGGTG	GCAACACCTGgtatgctggt
20	2694	2832	139	14352552	14352414	543	tctcttctagTACCTGCCAG	GGCTACTCAGgtaatgctca
21	2833	2943	111	14351871	14351761	342	ttatccacagGATTATTGCG	GTTTATAGGGgtgagtaatg
22	2944	3123	180	14351419	14351240	995	taccatttagAAAACTGAAC	TGACTATAAAgtaagttaga
23	3124	3363	240	14350245	14350006	1149	ccttttgcagGGGAAAGTGT	TCATTCCAAGgtttgtagat
24	3364	3520	157	14348857	14348701	1075	tttccaacagGTGAACCCAT	GATATATGCCgtgagtaaca
25	3521	3649	129	14347626	14347498	1713	ttctcatcagCAATATTCTG	TACCTGGAAGgtaataaatt
26	3650	3797	148	14345785	14345638	911	gcatcaatagGTTGCTACCC	GTACAAAATGgtatgtaaaa
27	3798	3841	44	14344727	14344684	473	ttgcttttagTATCTGTCGC	CCAATTCCAGgtaaatagtg
28	3842	4039	198	14344211	14344014	354	tttcttgcagGATGTCCTTG	ACCACCATAGgtaagttttc
29	4040	4066	27	14343660	14343634	350	tctatttcagTTACCACAAG	GTACCTACAAgtaagttttg
30	4067	4543	477	14343284	14342808	852	tttcttgcagCTCCATGCCT	GGCTCCACAGgtatttagca
31	4544	4735	192	14341956	14341765	1072	tctcttccagTATCAACCAC	TCGCAACCAGgtgattaatt
32	4736	5338	603	14340693	14340091	1025	tgtctctcagTAGGAAATTG	TCGACAGAAGgtaattgtct
33	5339	5577	239	14339066	14338828		ttttccacagGTCCCACTCC	GACAACTGAAggtaatgtct
34c	5578	5775	198				nnnnnnnnnnATAGTCTGCA	AGAAGATCTAnnnnnnnnnn
35	5776	5786	11	14338698	14338688		tgtttgtcttGGGCA	GAAAGTcccttagtc
36d	5787	6209	423				nnnnnnnnnnGGAATGCGAT	CGTCGACAGAnnnnnnnnnn
37	6210	6453	244	14336621	14336378		gtgttatcccAGGTCCCACT	GACAGAAGGTaattgtctgg
38c	6454	6497	44				nnnnnnnnnnCCCACTTCCC	CGAGTCCAAGnnnnnnnnnn
39e	6498	6675	178	14335163	14334986		cacgtacgacTGTGTCAAGT	ACCCACCACCnnnnnnnnnn
40d	6676	6704	29				nnnnnnnnnnTCCGTAACAC	CGTCGACAGAnnnnnnnnnn
41	6705	6946	242	14313408	14313167	1173	gtgttatcccAGGTCCCACT	TCGACAGAAGgtaattgtct
42	6947	7203	257	14311994	14311738		gttttcccagGTCCCACTTC	GACAGAAGGTaattgtctgg
43c	7204	8072	869				nnnnnnnnnnCCCACTCCTG	CGTCGACAGAnnnnnnnnnn
44	8073	8359	287	14310552	14310266	1463	gtgttatcccAGGTCCCACT	TTGAGGGAGAggtgaaggcc
45	8360	8363	4	14308803	14308800		gagctcccttAC	TTtgtgcttttt
46	8364	8823	460	14308740	14308281	1002	ttttctcaggAACTTCTTCG	AACTCATGCGgttagtgaat
47	8824	8998	175	14307279	14307105	566	ccaaatacagCCGGGTGAGT	GAGTGTGATTgtaagtatat
48	8999	9246	248	14306539	14306292	888	gtttttgcagGCTACTGCAC	GGAAGTAGAGgtattggaga
49	9247	9430	184	14305404	14305221	134	tatttactagGTGACTGTAA	GGACAGTGTGgtaaggctta
50	9431	9635	205	14305087	14304883	644	cccattttagGCATTTGCAA	TTTGGGGAAGgtaggcatgc
51	9636	9814	179	14304239	14304061	176	ctgtttttagTGTGTTTGAG	GGTGTTTGCTgtaagtattt
52f	9815	9817	3	14303885	14303883	1879	ccgctctctgGC	Tgtgtgtgtgg
53	9818	9887	70	14302004	14301935	315	cccattccagCTTATGAATG	GCAAGTCAAGgtaaagaatt
54b , f	9888	9988	101	14301620	14301520	157	tctcatacagTCCACAAAA	AATACCTGTGgtgagtttta
55	9989	10020	32	14301363	14301332	157	attttcacagGCTGTGTTGG	ACCAAGAGAGgtacgctgcc
56	10021	10198	178	14301175	14300998	707	ttaatgacagTTTGGAGAAA	GTCACTTGCAgtgagttaat
57	10199	10303	105	14300291	14300187	576	tttttttcagAATGCAACAC	TACAAGTGTGgtaagtcctt
58	10304	10344	41	14299611	14299571	644	ttgttaacagTTCCCAAGAA	TGAGTTCTTGgtaagttaat
59	10345	10467	123	14298927	14298805	452	aaatttatagCCTAATTCCT	TTGTGAACCAgtaagtgatg
60	10468	10566	99	14298353	14298255	625	taatatctagGGATATGAAC	CATACTGAATgtaagtatgc
61	10567	10695	129	14297630	14297502	665	tcacttgcagCCTGGAGAGT	CTGCAAACCTgtaagtagat
62	10696	10735	40	14296837	14296798	289	gttcttttagGGAACTGTTA	TGCAAAACCTgtaagtatgt
63	10736	10865	130	14296509	14296380	1513	ttccctttagGTATACCTCT	CTTTCTCACTgtaagtaaac
64g	10866	11359	494	14294867	14294374		atcttaacagGTACTCTGTT	ATTAAAAAAAaaaacatggg

¹Nov 2011 Build (ICGSC Gallus_gallus-4.0/galGal4).

^aTranslational start site at nucleotide 25.

^bPredicted alternate splicing events (exons 5b & 12b) or exons (exon 55) from reference [3] that were not cloned in this study.

^cAssembly error—Exon is missing from the current assembly.

^dAssembly error—Exon located in Gap.

^eAssembly error—Exon ends in Gap.

^fSequence was found in cerebrum and in primordial germ cells in the embyronic gondal, but not cloned in intestine in this study.

^gTranslational stop site at nucleotide 11117.