Table 1.
Top 90 proteins with enriched expression in mouse E14.5 retina and retinal pigment epithelium combined tissue as compared to WB
| Rank | UniProt Gene Name | Uniprot Accession | Primary Protein Name | Associated Retina or Eye Defects | References |
|---|---|---|---|---|---|
| 1 | Aldh1a1 | P24549 | Retinal dehydrogenase 1 (RALDH 1; RalDH1) | Expressed throughout development in dorsal retina; Choroidal hypoplasia in mice | (Fan et al. 2003; Goto et al. 2018; Duester 2022) |
| 2 | Tyr | P11344 | Tyrosinase | Retinal defects; optic chiasmatic abnormality in mice | (Jeffery et al. 1994, 1997) |
| 3 | Kera | O35367 | Keratocan (KTN) | - | |
| 4 | Pmel | Q60696 | Premelanosome protein | RPE melanosome shape defect in mice | (Hellström et al. 2011) |
| 5 | Cryge | Q03740 | Crystallin γE | - | |
| 6 | Crybb3 | Q9JJU9 | Crystallin βB3, N-terminally processed | - | |
| 7 | Fras1 | Q80T14 | Extracellular matrix protein FRAS1 | - | |
| 8 | Hmcn1 | D3YXG0 | Hemicentin-1 | AMD (age-related macular degeneration) in human | (Pras et al. 2015) |
| 9 | Crybb1 | Q9WVJ5 | Cystallin βB1 | - | |
| 10 | Nfatc4 | Q8K120 | Nuclear factor of activated T-cells, cytoplasmic 4 (NF-ATc4; NFATc4) | - | |
| 11 | Mylk | Q6PDN3 | Myosin light chain kinase, smooth muscle, deglutamylated form | - | |
| 12 | Rlbp1 | Q9Z275 | Retinaldehyde-binding protein 1 | Retinitis punctatta albescens in human | (Morimura et al. 1999) |
| 13 | Specc1l | Q2KN98 | Cytospin-A | - | |
| 14 | Igdcc4 | Q9EQS9 | Immunoglobulin superfamily DCC subclass member 4 | - | |
| 15 | Crym | O54983 | Ketimine reductase mu-crystallin | - | |
| 16 | Epb41l5 | Q8BGS1 | Band 4.1-like protein 5 | - | |
| 17 | Lig3 | P97386 | DNA ligase 3 | - | |
| 18 | Champ1 | Q8K327 | Chromosome alignment-maintaining phosphoprotein 1 | - | |
| 19 | Tes | P47226 | Testin | - | |
| 20 | Mdc1 | Q5PSV9 | Mediator of DNA damage checkpoint 1 | - | |
| 21 | Hras | Q61411 | GTPase HRas, N-terminally processed | Retinal dystrophy in human | (Pierpont et al. 2017) |
| 22 | Lama5 | Q61001 | Laminin subunit α-5 | Retinal defects; malformation of retina morphology in mice | (Jones et al. 2020) |
| 23 | Frem2 | Q6NVD0 | FRAS1-related extracellular matrix protein 2 | Detected in outer plexiform layer of the retina; mutations associated with Cryptophthalmos in human | (Zhang et al. 2019) |
| 24 | Mfap2 | P55002 | Microfibrillar-associated protein 2 (MFAP-2) | - | |
| 25 | Smarcd1 | Q61466 | SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1 | - | |
| 26 | Egfr | Q01279 | Epidermal growth factor receptor | Retinal cell fate determination | (Lillien 1995) |
| 27 | Heph | Q9Z0Z4 | Hephaestin | Retinal defects; retinal degeneration in mice | (Hahn et al. 2004) |
| 28 | Rai14 | Q9EP71 | Ankycorbin | - | |
| 29 | Tenm3 | Q9WTS6 | Teneurin-3 (Ten-3) | Retinal defects in mouse and zebrafish | (Leamey et al. 2007) (Antinucci et al. 2013) |
| 30 | Nelfe | P19426 | Negative elongation factor E (NELF-E) | - | |
| 31 | Znf326 | O88291 | Zinc finger protein 326 | - | |
| 32 | Crocc | Q8CJ40 | Rootletin | Retinal defects; retinal degeneration in mice | (Yang et al. 2005) |
| 33 | Cadm1 | Q8R5M8 | Cell adhesion molecule 1 | Retinal defects; retinal photoreceptor synapse defects in mice | (Ribic et al. 2014) |
| 34 | Fbln5 | Q9WVH9 | Fibulin-5 (FIBL-5) | Retinal defects; AMD and cutis laxa in human | (Lotery et al. 2006) (Stone et al. 2004) |
| 35 | Wiz | O88286 | Widely-interspaced zinc finger motifs | - | |
| 36 | Cryaa | P24622 | Crystallin αA chain | Retinal neovascularization defects in mice | (Xu et al. 2015) |
| 37 | Znf219 | Q6IQX8 | Zinc finger protein 219 | - | |
| 38 | Gldc | Q91W43 | Glycine dehydrogenase (decarboxylating), mitochondrial | - | |
| 39 | Mex3a | G3UYU0 | Mex3 RNA-binding family member A | - | |
| 40 | Nub1 | P54729 | NEDD8 ultimate buster 1 | - | |
| 41 | Uncharacterized protein FLJ45252 homolog | Q6PIU9 | Uncharacterized protein FLJ45252 homolog | - | |
| 42 | Kif1a | P33173 | Kinesin-like protein KIF1A | - | |
| 43 | Dync2h1 | Q45VK7 | Cytoplasmic dynein 2 heavy chain 1 | Retinal defects; non-syndromic inherited retinal disease in human | (Vig et al. 2020) |
| 44 | Gja1 | P23242 | Gap junction alpha-1 protein | Retinal defects (optic nerve and retinal dysplasia) and other eye defects in human | (Gabriel et al. 2011) |
| 45 | Fbn2 | Q61555 | Fibrillin-2 C-terminal peptide | AMD | (Ratnapriya et al. 2014) |
| 46 | Pcca | Q91ZA3 | Propionyl-CoA carboxylase alpha chain, mitochondrial (PCCase subunit alpha) | - | |
| 47 | Zmym4 | A2A791 | Zinc finger MYM-type protein 4 | - | |
| 48 | Emilin3 | P59900 | EMILIN-3 | - | |
| 49 | Tbl1x | Q9QXE7 | Transducin (beta)-like 1 X-linked | - | |
| 50 | Bcat1 | P24288 | Branched-chain-amino-acid aminotransferase, cytosolic (BCAT(c)) | - | |
| 51 | Niban1 | Q3UW53 | Protein Niban 1 | - | |
| 52 | Ehmt2 | Q9Z148 | Histone-lysine N-methyltransferase EHMT2 | - | |
| 53 | Brd7 | O88665 | Bromodomain-containing protein 7 | - | |
| 54 | Taf15 | Q8BQ46 | TAF15 RNA polymerase II, TATA box binding protein (TBP)-associated factor | - | |
| 55 | Hspa4l | P48722 | Heat shock 70 kDa protein 4L | - | |
| 56 | Msi1 | Q61474 | RNA-binding protein Musashi homolog 1 (Musashi-1) | Retinal defects; defects in photoreceptor morphogenesis in mice | (Sundar et al. 2020) |
| 57 | Aldh5a1 | Q8BWF0 | Succinate-semialdehyde dehydrogenase, mitochondrial | - | |
| 58 | Strn | O55106 | Striatin | - | |
| 59 | Dido1 | Q8C9B9 | Death-inducer obliterator 1 (DIO-1) | - | |
| 60 | Ctcf | Q61164 | Transcriptional repressor CTCF | Retinal defects; loss of anterior retina in mice; involved in control of chromosome structure | (Watson et al. 2014) |
| 61 | Sptbn2 | Q68FG2 | Spectrin beta chain | - | |
| 62 | Rnmt | Q9D0L8 | mRNA cap guanine-N7 methyltransferase | - | |
| 63 | Cux1 | P53564 | Homeobox protein cut-like 1 | Controls RPGRIP1L, which is associated with loss of photoreceptors and is a modifier of retinal degeneration in cilipathies | (Khanna et al. 2009; Stratigopoulos et al. 2011) |
| 64 | Ephb2 | P54763 | EphB2/CTF2 | Retinal defects; loss of axons in retina/optic nerve in mice | (Fu and Sretavan 2012) |
| 65 | Golga5 | Q9QYE6 | Golgin subfamily A member 5 | - | |
| 66 | Golgb1 | E9PVZ8 | Golgi autoantigen, golgin subfamily b, macrogolgin 1 | - | |
| 67 | Ank2 | Q8C8R3 | Ankyrin-2 (ANK-2) | Retinal defects; defects in the Na/K-ATPase and Na/Ca exchanger in the inner segment of rod photoreceptors in mice | (Kizhatil et al. 2009b) |
| 68 | Snx6 | Q6P8X1 | Sorting nexin-6, N-terminally processed | - | |
| 69 | Srsf2 | Q62093 | Serine/arginine-rich splicing factor 2 | Upregulated in the vitreous in human cases of glaucoma; mutations in 5% patients with Uveal melanoma | (Mirzaei et al. 2017; Akin-Bali 2021) |
| 70 | Smarce1 | O54941 | SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1 | - | |
| 71 | Hmgn1 | P18608 | Non-histone chromosomal protein HMG-14 | - | |
| 72 | Ptprf | A2A8L5 | Receptor-type tyrosine-protein phosphatase F | - | |
| 73 | Dnajc7 | Q9QYI3 | DnaJ homolog subfamily C member 7 | - | |
| 74 | Pnn | O35691 | Pinin | - | |
| 75 | Mccc2 | Q3ULD5 | Methylcrotonoyl-CoA carboxylase beta chain, mitochondrial (MCCase subunit beta) | - | |
| 76 | Nipbl | Q6KCD5 | Nipped-B-like protein | - | |
| 77 | Ank3 | G5E8K5 | Ankyrin-3 (ANK-3) | Retinal defects; transport of cyclic nucleotide-gated channels to the plasma membrane of rod outer segments in frog | (Kizhatil et al. 2009a) |
| 78 | Rbp1 | Q00915 | Retinol-binding protein 1 | Retinal defects; defects in organization of nascent outer segment membranes in frog | (Wang et al. 2010) |
| 79 | Yap1 | P46938 | Transcriptional coactivator YAP1 (Yes-associated protein 1) | Retinal defects; retinal pigment epithelium differentiation defects in mice | (Lu et al. 2020) |
| 80 | Smarcc1 | P97496 | SWI/SNF complex subunit SMARCC1 | - | |
| 81 | Utrn | E9Q6R7 | Utrophin | - | |
| 82 | Cald1 | E9QA15 | Caldesmon 1 | - | |
| 83 | Ccar1 | Q8CH18 | Cell division cycle and apoptosis regulator protein 1 | - | |
| 84 | Cttn | Q60598 | Src substrate cortactin | - | |
| 85 | Prrc2c | Q3TLH4 | Protein PRRC2C | - | |
| 86 | Arid1a | A2BH40 | AT-rich interactive domain-containing protein 1A (ARID domain-containing protein 1A) | - | |
| 87 | Cbx1 | P83917 | Chromobox protein homolog 1 | - | |
| 88 | Dcn | P28654 | Decorin | Retinal defects; retinal angiogenic disease including neuronal and vascular defects in mice | (Lim et al. 2018) |
| 89 | Mif | P34884 | Macrophage migration inhibitory factor (MIF) | Associated with proliferative retinopathy in mice | (Wang et al. 2017) |
| 90 | Igf2bp1 | O88477 | Insulin-like growth factor 2 mRNA-binding protein 1 (IGF2 mRNA-binding protein 1; IMP-1) | Retinal defects; retinal ganglion axonal outgrowth and tectal coverage, and retinal cell survival defects in Zebrafish | (Gaynes et al. 2015) |