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 symbol: TRIM6
• Ensembl ID: ENSSTOG00000024836
• Aliases: None
• Description: tripartite motif containing 6 [Source:HGNC Symbol;Acc:16277]

Sequence

>retro_itri_1178
GAAGTGGTGTTGTACCTAGGAAAGCAGCTGAAGATAATTCTTTGTGCACACCATGGAGAGAAGCTCCAGCTCTTCTATAA
GGAGGATGGGAAACTAATTTGCTGGTTTTGTGAACATTCTCAGGAACACTGCGGTTACCATACATTTCTCATGGAGGAGG
TCACCCAGGAGTATCAGGACATGTTCCAGAAGTCTCTGAAGAAGTTGAGGAAAGAGCAGCAGGAAACTGAGAGGCTAAGA
GCTATTATCAGAGAGAAGAGGGCATCTTGGAAGAATCAGATGGAGCCTGAGAGACACAGGATTGAGACAGAGTTTAATCA
GCTGCAAAGGATCCTAAACAAAGAGGAGGAGTAGGAAGTAATGAAGTTGGAGAAGGAAGAGAGGAAGGATCTGAGTATTA
TAGAGAAAGCTGAGGGTGAGCTAATCCACCAGAGCCAGTCACTGGGAGAGCTAATTTCGATCTGGAGAGTTGATGCTGAA
GCTCAGTAGTGGATCTGCTGCAGGTTGTAAGTAATGTCATGGAAAGGAGTAAGTTCTGGACCCTGAGGAAACCCCAAATT
CTCCTGACCAAGCTGAGAAGTATGTTTCAAGTCCAAGATCTGAAAAAAGATGCTACAGATGTTTTGAGATTTGACAGATG
TGCAGAGCTACTGGGTAGACATGACTCTGAATCCCCATATGGCTAATTTAAATCTTGTCCTGTCTAAAAATTGGAGACAG
GTGGGATTCATGGGTACTAAGCTATCTGGACCTTCTGGTTTGGAAGAACATTGTGACTGTAGTGTCCTGGGCTCTTAGCT
CTTCTCCTTAGGAAAATACTACTGAGAGGTAAATGTGACCAGTAAAACTACCTGGATACTGAGGAGTGTGCAATAATTCC
ATGGGACCTACCTTTTCTTTCAAGCCAGTTTGCTAAAAAACCAGAATGCTTATTCCAGACACCACCACAGAATGGATACT
GGGTGATTGGGTTGCAGCATAAATGTGAAGAGGGAGCCTATGAAGAGTCTTCCATTTTCCTACTCCTCTCTAGGACTGTG
CCCACTTGCCACATTGGGATTTTTTAGACTAGGATGACGCTGTCTTATTTTATAATGTCATGAATCATGACTTGCCTATC
TACACTTTCTCTAAATATTACTTTTCTACTGCCATTTGTCTATACTTTAATCTTTACAACAATATAGTCCTAAGGACCCT
A

Alignment

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

Expression

RNA-Seq

Ictidomys tridecemlineatus was not studied using RNA-Seq expression data.

ChIP-Seq

Ictidomys tridecemlineatus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_itri_1178 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1178 was not experimentally validated.

Homology

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.

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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 ,