RetrogeneDB ID: | retro_itri_1178 | ||
Retrocopy location | Organism: | Squirrel (Ictidomys tridecemlineatus) | |
| Coordinates: | JH393394.1:2222371..2223572(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | TRIM6 | ||
| Ensembl ID: | ENSSTOG00000024836 | ||
| Aliases: | None | ||
| Description: | tripartite motif containing 6 [Source:HGNC Symbol;Acc:16277] |
Retrocopy-Parental alignment summary:
>retro_itri_1178
GAAGTGGTGTTGTACCTAGGAAAGCAGCTGAAGATAATTCTTTGTGCACACCATGGAGAGAAGCTCCAGCTCTTCTATAA
GGAGGATGGGAAACTAATTTGCTGGTTTTGTGAACATTCTCAGGAACACTGCGGTTACCATACATTTCTCATGGAGGAGG
TCACCCAGGAGTATCAGGACATGTTCCAGAAGTCTCTGAAGAAGTTGAGGAAAGAGCAGCAGGAAACTGAGAGGCTAAGA
GCTATTATCAGAGAGAAGAGGGCATCTTGGAAGAATCAGATGGAGCCTGAGAGACACAGGATTGAGACAGAGTTTAATCA
GCTGCAAAGGATCCTAAACAAAGAGGAGGAGTAGGAAGTAATGAAGTTGGAGAAGGAAGAGAGGAAGGATCTGAGTATTA
TAGAGAAAGCTGAGGGTGAGCTAATCCACCAGAGCCAGTCACTGGGAGAGCTAATTTCGATCTGGAGAGTTGATGCTGAA
GCTCAGTAGTGGATCTGCTGCAGGTTGTAAGTAATGTCATGGAAAGGAGTAAGTTCTGGACCCTGAGGAAACCCCAAATT
CTCCTGACCAAGCTGAGAAGTATGTTTCAAGTCCAAGATCTGAAAAAAGATGCTACAGATGTTTTGAGATTTGACAGATG
TGCAGAGCTACTGGGTAGACATGACTCTGAATCCCCATATGGCTAATTTAAATCTTGTCCTGTCTAAAAATTGGAGACAG
GTGGGATTCATGGGTACTAAGCTATCTGGACCTTCTGGTTTGGAAGAACATTGTGACTGTAGTGTCCTGGGCTCTTAGCT
CTTCTCCTTAGGAAAATACTACTGAGAGGTAAATGTGACCAGTAAAACTACCTGGATACTGAGGAGTGTGCAATAATTCC
ATGGGACCTACCTTTTCTTTCAAGCCAGTTTGCTAAAAAACCAGAATGCTTATTCCAGACACCACCACAGAATGGATACT
GGGTGATTGGGTTGCAGCATAAATGTGAAGAGGGAGCCTATGAAGAGTCTTCCATTTTCCTACTCCTCTCTAGGACTGTG
CCCACTTGCCACATTGGGATTTTTTAGACTAGGATGACGCTGTCTTATTTTATAATGTCATGAATCATGACTTGCCTATC
TACACTTTCTCTAAATATTACTTTTCTACTGCCATTTGTCTATACTTTAATCTTTACAACAATATAGTCCTAAGGACCCT
A
ORF - retro_itri_1178 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 69.12 % |
| Parental protein coverage: | 85.5 % |
| Number of stop codons detected: | 7 |
| Number of frameshifts detected: | 7 |
Retrocopy - Parental Gene Alignment:
| Parental | EVVLCPGKQLQVILCAHHGEKLQLFCKEDGKLICWLCERSQEHRGHHTFLMEEVAQEYQEMFQESLKKLR |
| EVVL..GKQL..ILCAHHGEKLQLF.KEDGKLICW.CE.SQEH.G.HTFLMEEV.QEYQ.MFQ.SLKKLR | |
| Retrocopy | EVVLYLGKQLKIILCAHHGEKLQLFYKEDGKLICWFCEHSQEHCGYHTFLMEEVTQEYQDMFQKSLKKLR |
| Parental | KEQQEAEKLRAFIKEKRASWKTQVEPERQRIQTEFSQLRSILDKEEQRELKKLEEEERKGLSIIEKAEEE |
| KEQQE.E.LRA.I.EKRASWK.Q.EPER.RI.TEF.QL..IL.KEE..E..KLE.EERK.LSIIEKAE.E | |
| Retrocopy | KEQQETERLRAIIREKRASWKNQMEPERHRIETEFNQLQRILNKEEE*EVMKLEKEERKDLSIIEKAEGE |
| Parental | VIYQSQSLEELIS-NLEHRCQGSVMDLLQLIMSVLPRSEFWTLRDPPALPTKLRSMFRAPDL-KKMLRVF |
| .I.QSQSL.ELIS..LE..C..SV.DLLQ....V..RS.FWTLR.P..L.TKLRSMF...DL.KKML..F | |
| Retrocopy | LIHQSQSLGELIS<DLES*C*SSVVDLLQVVSNVMERSKFWTLRKPQILLTKLRSMFQVQDL>KKMLQMF |
| Parental | RELTDVQSYWVDVTMNPHTANLNLVLSKNRRQVRFVGTKLSETSCLEEHHDFSVLGSQQFSSGKYYWEVD |
| ..LTDVQSYWVD.T.NPH.ANLNLVLSKN.RQV.F.GTKLS..S.LEEH.D.SVLGS..FS.GKYY.EV. | |
| Retrocopy | *DLTDVQSYWVDMTLNPHMANLNLVLSKNWRQVGFMGTKLSGPSGLEEHCDCSVLGS*LFSLGKYY*EVN |
| Parental | VTRKTAWIL-GVCSNPMGPAFS-GSQFANK-QNAYSRYQ-PQTGYWVIGLQHKHEYRAYEDASTSLLLSM |
| VT.KT.WIL.GVC.N.MGP.FS..SQFA.K.QNAYSR...PQ.GYWVIGLQHK.E..AYE..S..LLLS. | |
| Retrocopy | VTSKTTWIL>GVCNNSMGPTFS>SSQFAKK>QNAYSRHH<PQNGYWVIGLQHKCEEGAYEESSIFLLLSR |
| Parental | TVPPRRVGV-FLDYEAGTVSFYNVTNHGLPIYTFTKYYFPTAVCPYFNPCDCVVPMTL |
| TVP....G..FLD.........NV.NH.LPIYTF.KYYF.TA.C.YFN.....V..TL | |
| Retrocopy | TVPTCHIGI<FLD*DDAVLFY-NVMNHDLPIYTFSKYYFSTAICLYFNLYNNIVLRTL |
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_1178 retrocopy.
Ictidomys tridecemlineatus was not studied using FANTOM5 data.
retro_itri_1178 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 | ENSSTOG00000024836 | 1 retrocopy |
retro_itri_1178 ,
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