RetrogeneDB ID: retro_itri_60

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393790.1:61953..64413(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000021364
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: ZXDC
• Ensembl ID: ENSSTOG00000007207
• Aliases: None
• Description: ZXD family zinc finger C [Source:HGNC Symbol;Acc:28160]

Sequence

>retro_itri_60
ATGGAAATCCCGAGGCTGCTCCCGGCTCGCGGGACAAGACAGGGCAGCGGCGGTTATTGCCCCGCGGGCGGCGGCGGGGT
CCACCGAGGCCCTGACCCGCCGGCTGGTCAGGCCCCCGCGCGGCGCCTTCTACTGCTCCGGGGGGCCCAAGATGGCGGGC
CCGTGCCGCGGAGCGAGGAGGCCCGCAGGGCCTCACGGGGCCGGGGCCCGGGCCCAAGCCCGAGCCCGTTGGCGCCGAGG
CCGAATCACCCGAGCGGCGGCGGCGACGACTTCTTCCTGGTGCTGCTTGACCCGGTGGGTGGCGACGTGGAGACCTCGGG
CACCGATCAGGCCGAAGGGCCCGTGTGGAGGGAGGAGGCCGAAGCGGGCCTGGGGCCCCAGGGGGACGAGAGCGGCGCGA
ACCCCGCGGGCCGCCCTGCGCTGGGCCCCCGCTGCCTGTCCGCGGCCCCGGGCCCGGCCCCGGTCCCGGTCCCCGTCCCG
GTCCCGATCCCGATCCCGATCCCGGCTCCAGCCTCAGGCCCGGGCCACGGGGCGGCCTTCGCAGGCACCATCACTATCCA
TAACCAGGACCTGCTGTTGCGTTTTGAGAACGGCGTCCTCACCCTGACCACGCCCCCGCTGCCGGCCTGGGAGCCGGGGG
TCGCGCCTTTCCCGCAGCCTGGGGGTCTAACTGCCCCGCCGCCAGCTGGGTTCCCGCACACCGCGCAGTTGGGTGACTGC
CCAGAGCTGCCGCCTGAGCTCCTGCTGGCCGAGCCGGCGGAACCTGCGCCGGCCCCGGCTCCTGAGGAGGAGGCTGAGGG
CCGGGCCGCCGCCCAGAGCCCTCGCGGGCCGCTGGGCCCGGCCCCAGGCGTGGTGCTGTACCTGTGCCCCGAGGCGCAGT
GCGGACAAACCTTCGCCAAGAAACACCAGCTGAAGGTGCACCTGCTGACGCACAGCAGCAGCCAGGGTCAGAGGCCCTTC
AAGTGCCCCCTGGGCGGCTGCGGCTGGACCTTCACCACGTCTTACAAGCTCAAGAGGCACCTGCAGTCGCATGACAAACT
AAGGCCTTTCGGCTGCCCGGTGGAGGGCTGTGGAAAGAGCTTCACCACTGTGTACAACCTCAAAGCACACATGAAGGGCC
ATGAGCAGGAGAACTCCTTCAAATGTGAGGTGTGCGAGGAGAGCTTCCCCACGCAGGCTAAGCTCAGTGCCCACCAGCGC
AGCCACTTCGAGCCAGAGAGGCCCTACCAATGTGCGTTTTCCGGCTGCAAGAAGACGTTTATTACCGTGAGTGCCCTGTT
TTCCCATAACCGCGCCCATTTCAGGGAACAGGAACTCTTTGCCTGCTCTTTCCCTGGCTGCAGTAAACAGTATGACAAGG
CTTGTAGGCTGAAAATTCACCTGCGGAGCCACACAGGCGAGAGACCTTTCCTTTGTGACTTTGAGGGCTGTGGCTGGAAT
TTCACCAGCATGTCCAAACTCTTAAGGCACAAAAGGAAGCATGATGATGACCGGAGGTTCACGTGCCCTGTAGAAGGCTG
TGGGAAATCTTTCACAAGGGCCGAGCATCTGAAAGGCCACAGCATAACCCACCTGGGCACAAAACCTTTCGTGTGTCCTG
TGGAAGGCTGCTGTGCCAGGTTTTCTGCTCGTAGTAGTCTCTACATTCACTCCAAGAAACACCTGCAGGATGTGGAGACT
TGGAAGAGTCGTTGCCCTGTCTCCACCTGTAATAAACTCTTCACATCCAAGCACAGCATGAAGACCCACATGGCCAAAAG
GCACAACCTTGGCCAGGATCTCTTAGCTCAGCTCGAAGCTGCAAATTCTCTCACGCCCAGCAGTGAGCTTACCAGCCAGG
GACAGAATGATCTCAGCGATGCAGAGATAGTGTCTTTCTTCTCTGATGTGCCTGGCAAGAGTTCTGCTGCAGTGCTGGAC
ACCGCATTGGTCAATTCTGGAATCCTGACTATTGATGTGGCTTCTGTGAGCTCCACTCTGGCAGGGAATCTGCCTGCCAA
CAATAATAATTCTCTAGGGCAGGCTGTGGACCCTCGGGCCTTGATGGCCACCAGTGACCTTCCTCAGAGCCTGGATACCT
CTCTCTTTTTTGGAACGACAGCTGCTGCTTTTCAGCAGGGTCCCTTAGATATGGATGATGTCTCCAGTGTAAGCGTGGGG
CCACTGGGGTCTCTGGGTTCTTTGGCAATGAAAAACTCGAGTCCAGAGCCCCAGACTTTGACACCCAGCAATAAGTTAAC
AGTCGACACAGAAGCTCTGACTCCTTCAAGCACCCTTTGTGAAAACAGTGTTTCAGAACTACTGACACCAACCAAAGCGG
ATTGGAATGTACATCCTGACTCCGACTTCTTTGGACAGGAGGAAGAAACCCAGTTTGGATTCCCCAATCCAGCAGGAAAC
CATGGTTCTCAGAAAGAAACAGATCTTATCACAGTGACTGGCAGCCCATTTTTGGTATGA

Alignment

ORF - retro_itri_60 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.78 %
• Parental protein coverage: 71.49 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  YRCPEPQCALAFAKKQQLQVHLLTHGGPQARRPFKCPLDGCGWAFTTSYKLKRHLQSHDKLRPFGCPVGG
          Y.CPE.QC...FAKK.QL.VHLLTH...Q..RPFKCPL.GCGW.FTTSYKLKRHLQSHDKLRPFGCPV.G
Retrocopy YLCPEAQCGQTFAKKHQLKVHLLTHSSSQGQRPFKCPLGGCGWTFTTSYKLKRHLQSHDKLRPFGCPVEG

Parental  CGKKFTTVYNLKAHMRGHEQESLFKCEVCAERFPTHAKLSSHQRSHFEPERPYKCDFPGCEKTFITVSAL
          CGK.FTTVYNLKAHM.GHEQE..FKCEVC.E.FPT.AKLS.HQRSHFEPERPY.C.F.GC.KTFITVSAL
Retrocopy CGKSFTTVYNLKAHMKGHEQENSFKCEVCEESFPTQAKLSAHQRSHFEPERPYQCAFSGCKKTFITVSAL

Parental  FSHSRAHFREQELFPCSFPGCSKQYDKACRLKIHLRSHTEGERPFICDSDSCGWTFTSMSKLLRHKRKHD
          FSH.RAHFREQELF.CSFPGCSKQYDKACRLKIHLRSHT.GERPF.CD...CGW.FTSMSKLLRHKRKHD
Retrocopy FSHNRAHFREQELFACSFPGCSKQYDKACRLKIHLRSHT-GERPFLCDFEGCGWNFTSMSKLLRHKRKHD

Parental  DDRRFTCPVEGCGKSFTRAEHLKGHSITHLGTKPFECPVEGCCARFSARSSLYIHSKKHLQDVGAPKSRC
          DDRRFTCPVEGCGKSFTRAEHLKGHSITHLGTKPF.CPVEGCCARFSARSSLYIHSKKHLQDV...KSRC
Retrocopy DDRRFTCPVEGCGKSFTRAEHLKGHSITHLGTKPFVCPVEGCCARFSARSSLYIHSKKHLQDVETWKSRC

Parental  PVSSCNRLFTSKHSMKAHVVRQHSQRPDLVPPLEAPSSLTPSSELSGPGQSELSSLDLAALFSEPPASGG
          PVS.CN.LFTSKHSMK.H....H....DL...LEA..SLTPSSEL...GQ..LS.......FS..P....
Retrocopy PVSTCNKLFTSKHSMKTHMAKRHNLGQDLLAQLEAANSLTPSSELTSQGQNDLSDAEIVSFFSDVPGKSS

Parental  AAAAGSEEALSSGILTIDVTSVSSSLGGTLPA-NSSSLG-PMDPLVLVAHSDLPPSLESPLILGTAATVL
          AA.........SGILTIDV.SVSS.L.G.LPA.N..SLG...DP..L.A.SDLP.SL...L..GT.A...
Retrocopy AAVLDT-ALVNSGILTIDVASVSSTLAGNLPANNNNSLGQAVDPRALMATSDLPQSLDTSLFFGTTAAAF

Parental  PPGSFSVEDVHAVTTGPVGCLVALPV---GQDPGALTSSGNLA--AHATTPAC----SSVPELPAPVKVE
          ..G.....DV..V..GP.G.L..L........P..LT.S..L.....A.TP.......SV.EL..P.K..
Retrocopy QQGPLDMDDVSSVSVGPLGSLGSLAMKNSSPEPQTLTPSNKLTVDTEALTPSSTLCENSVSELLTPTKAD

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_60 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_60 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 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006438	1 retrocopy	retro_amel_1830,
Equus caballus	ENSECAG00000026954	2 retrocopies	retro_ecab_1064, retro_ecab_1107,
Mus musculus	ENSMUSG00000034430	1 retrocopy	retro_mmus_44,
Rattus norvegicus	ENSRNOG00000025818	1 retrocopy	retro_rnor_2933,
Sus scrofa	ENSSSCG00000001824	1 retrocopy	retro_sscr_50,
Ictidomys tridecemlineatus	ENSSTOG00000007207	1 retrocopy	retro_itri_60 ,