RetrogeneDB ID: | retro_itri_653 | ||
Retrocopy location | Organism: | Squirrel (Ictidomys tridecemlineatus) | |
| Coordinates: | JH393309.1:11696411..11697707(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | SEC23A | ||
| Ensembl ID: | ENSSTOG00000013426 | ||
| Aliases: | None | ||
| Description: | Sec23 homolog A (S. cerevisiae) [Source:HGNC Symbol;Acc:10701] |
Retrocopy-Parental alignment summary:
>retro_itri_653
AAAATAATTTTGAATCTTTTGTGTCAAGTGGATTATTGAGCAAAGCTCTGGTCTTGCAACTTTTCTTATCAAAATATCAG
TTTCTAACTACTTATGCTGGGATATCTAAACTGAATCAGTATGCTGAACATTTGCCTCAGTTCTCTCGCATTGAATATGT
AGTTCTGTGTGGTCCTCAGAAACCTTTGATATTCCTCTATGTGGTTGATACTTGCATGGAACATGAAGATTTACAAGCCT
TAATAGAATCCATGCAGATATCACTAAGTCTCCTATCACCTAGAGCTTTGATTTGCCTTTGGGGAGGAATGTGCAGGTTC
ATAAACTTGGATGTGAACGTATTTCAAAAAGCTATGTCTTCAAGGGAACAAAAGATGGTTTTCCAAACAACTGTAGGAGA
TGCTGGGACCCTCTAGAGTACCACTTACTCAAGCAACACATGGTCCTCAGGTACAGCAGCCACATGCATCCAATAAATTT
TTTATAGCCACTACAGAATATAGACATGAATCTCCCATATCTTCTGGGAGAACAGCAGTGAGACCCTTGGCCTATATTAC
AGGGAAAGGGACCTTTGTGTACCTCAGAAATGGCACTTTGCATAGCTGTAGGACTAATCAAGTGTATTTTCCCCAACGCT
GGTGCTCATATTATGATGTCCATGGGTGGTCTTGCTATTCAAGCAGCTAGAATGGTGGTTGGAGATGAATTGATGATGCC
TAGAAGATCATGGCATGATATTGAAAAAGACAATGTCAAGTATGTTTAAAAAGGACCCAAGCATTTTGAAGAACTGGCTA
ATCAAGCTGCTACAACTCGTCATGTTATTGACATCTATGCATGTGCATTAGATCAGACAGGTCTCTTGCAGATAAAATGC
TGTTCCAACCTTACTGGTGAAAACATGGTAATGGGAGATTCTTTTAACACTTCCTTATCAAACAAACTTTTCAAACAGTC
TTTCCCAAAGATATTCATGAACAGTTTAAAATGAGCTTTGGTGGTGCATTAGAAATAAACACTTTAAGGGAAATAAAAAT
TTCAGGAGCAATTGGACCCTGTGTGTCTCTCAATTCAAAAGGACCCTGTATGCCTGCAAAATGTGATAGGAATGTGTGGC
ATTTGTCAAGGTAAGTTATGCAGATTCTATCTCACTACAACCTTAGCTATGTATTTTGGTGTTGTTAATCAGCATAATGC
TCCAATTCTTCATGGTGGACATTGTGCAATCCAGTTTGTGACATGGTATCATCATGCAATGGGCAGAGATGCATCAGAGT
GACCACCATTACTAGG
ORF - retro_itri_653 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 71.95 % |
| Parental protein coverage: | 86.83 % |
| Number of stop codons detected: | 5 |
| Number of frameshifts detected: | 7 |
Retrocopy - Parental Gene Alignment:
| Parental | RAVLNPLCQVDYRAKLWACNFCYQ-RNQFPPTYAGISELNQPAELLPQFSSIEYVVLRGPQMPLIFLYVV |
| ...LN.LCQVDY.AKLW.CNF.YQ...QF..TYAGIS.LNQ.AE.LPQFS.IEYVVL.GPQ.PLIFLYVV | |
| Retrocopy | KIILNLLCQVDY*AKLWSCNFSYQ<KYQFLTTYAGISKLNQYAEHLPQFSRIEYVVLCGPQKPLIFLYVV |
| Parental | DTCMEDEDLQALKESMQMSLSLLPPTALVGLITFGRM-VQVHELGCEGISKSYVFRGTKD-LSAKQLQEM |
| DTCME.EDLQAL.ESMQ.SLSLL.P.AL..L...G.M.VQVH.LGCE.ISKSYVF.GTKD....KQL.EM | |
| Retrocopy | DTCMEHEDLQALIESMQISLSLLSPRALICL--WGGM<VQVHKLGCERISKSYVFKGTKD<WFSKQL*EM |
| Parental | LGLSKVPVTQATRGPQVQQPPPSNR-FLQPVQKIDMNLTDLLGELQRDPWPVPQGKRPLRSSGVALSIAV |
| LG.S.VP.TQAT.GPQVQQP..SN..FL.P.Q.IDMNL..LLGE.Q.DPWP..QGK.PL..S..AL.IAV | |
| Retrocopy | LGPSRVPLTQATHGPQVQQPHASNK>FL*PLQNIDMNLPYLLGEQQ*DPWPILQGKGPLCTSEMALCIAV |
| Parental | GLLECTFPNTGARIMMFIGGPATQGPGMVVGDELKTPIRSWHDIEKDNAKYVKKGTKHFEALANRAATTG |
| GL..C.FPN.GA.IMM..GG.A.Q...MVVGDEL..P.RSWHDIEKDN.KYV.KG.KHFE.LAN.AATT. | |
| Retrocopy | GLIKCIFPNAGAHIMMSMGGLAIQAARMVVGDELMMPRRSWHDIEKDNVKYV*KGPKHFEELANQAATTR |
| Parental | HVIDIYACALDQTGLLEMKCCPNLTGGYMVMGDSFNTS-LFKQTFQRVFTKDMHGQFKMGFGGTLEIKTS |
| HVIDIYACALDQTGLL..KCC.NLTG..MVMGDSFNTS.L.KQTFQ.VF.KD.H.QFKM.FGG.LEI.T. | |
| Retrocopy | HVIDIYACALDQTGLLQIKCCSNLTGENMVMGDSFNTS<LIKQTFQTVFPKDIHEQFKMSFGGALEINTL |
| Parental | REIKISGAIGPCVSLNSKGPCVS-ENEIGTGGTCQWKICGLSPTTTLAIYFEVVNQHNAPIPQGGRGAIQ |
| REIKISGAIGPCVSLNSKGPC....N.IG..G.CQ.K.C....TTTLA.YF.VVNQHNAPI..GG..AIQ | |
| Retrocopy | REIKISGAIGPCVSLNSKGPCMP>QNVIGMCGICQGKLCRFYLTTTLAMYFGVVNQHNAPILHGGHCAIQ |
| Parental | FVTQYQHS-SGQRRIRVTTIAR |
| FVT.Y.H...GQR.IRVTTI.R | |
| Retrocopy | FVTWYHHA<NGQRCIRVTTITR |
Legend:
| * | Stop codon |
| > | Forward frameshift by one nucleotide |
| < | Reverse frameshift by one nucleotide |
Ictidomys tridecemlineatus was not studied using RNA-Seq expression data.
Ictidomys tridecemlineatus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_itri_653 retrocopy.
Ictidomys tridecemlineatus was not studied using FANTOM5 data.
retro_itri_653 was not experimentally validated.
Retrocopy orthology:
Ictidomys tridecemlineatus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Ictidomys tridecemlineatus | ENSSTOG00000013426 | 1 retrocopy |
retro_itri_653 ,
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