RetrogeneDB ID: retro_itri_1441

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393487.1:3020323..3022256(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: TRAF7
• Ensembl ID: ENSSTOG00000013083
• Aliases: None
• Description: TNF receptor-associated factor 7, E3 ubiquitin protein ligase [Source:HGNC Symbol;Acc:20456]

Sequence

>retro_itri_1441
ATGAGCTCAGGCAAGAGTGTCTGCTACAATCGCTTCTCCGGGGAGCCTGCCAACCTTCCGTCCCCAGACCTCAGAACCGG
GACCAGAATGGAAACAACCGTTGGACCCGCCTTCTCGGCTGTCACCACCATCATGAAAGCCGATGGGACCAGTACTTAAA
AGCAGCACCGCAGAATACCTTCCTCTTCCAGCACCCTCGCCTATACCCCACGGGATGAGGGAGACAGCATGCCCCCCCAT
CAGCACCCCTCGTCCCTCTGATTCGGCCATCTCCGTCGGCTCCCTGCATTCTGAGTCCAGCATGTGCTTGCGCTCCACAT
TCTCACTGCCTGAGGAAGAAGAGGAGCCGGAGCCACTGGTATTTGCTGAGCAGCCCTCGGTGAAGTTGTGCCGGCAACTC
TGCTGTGGTGTATTCAAGGACCCTGTGATCACCACCTGTGGCCACACGTTCTGTAGAAGATGCGCCTTGAAGTCAGAAAA
GTGTCCCGTGGACAATGCCAAATTGACAGTGGTGGTGAACAACATCCCAGTGGCCGAACAAATTGGGGAGCTCTTCATCC
ACTGCAGGCAAGGCTGCTGTGTGGTGGGTGCAGGGAAGTCCAGTGTCGTGGAGGTGGACCCCCCGGGGTGTCCTTTCACC
ATCAAGCTTAGTGCCCGAAAGGATCACTAGGTCGCCTGTGACTACAGGCCTGTCCGCTGCCCCAGCAATACGAGCTTCCC
ACCCCTCCTCGAGATGAACCTGGAAGCCCACCTCAAAGAATGGGAGCACATCAAGTGTCCCCACTCCAAGTACGGTGCAC
CTTCATCGGGAACCAGGACACATATGAGACACATCTAGAGACATACAGGTTTGAGGGCCTGAAGGAGTTCTTGCAGCAGA
CAGATGACAACTTCTATGACATGCATGTGGCCCTGGCACAAAAGGACCAGGAGATAGCCTTCCTGCGCTCCATGCTAGGC
AAGCTCTCTGAGATTGACCAGCTAGAGAAGAGCCTCGAGCTCAAGTTTGATGTCCTGGGTGAAAATCAGAGCAAACTCAG
CGAGGACCTCATGGAGTTCCAGAGGGATGCATCCATGTTGAATGATGAGCTGCCCCACATCAACACAAGGCTGAACATGG
GCATCCTAGGATCCCATGACCCTCAGCTGATCTTCAAGTTCAAAAGGACTTTTGTGGCCACCAGGGCCTTGTCTGGTGTC
TCTGTGTCTACTCCATGGGTGACCTGCTCTTCAGTGGTTCCTCTGACAAGACCATCAAGGTATGGGACACCTGTACCACC
TACAAGTGCCAGAAGACACTAGAGGGCCATGACGGCATTGTGCTAGCTCTCTGCATCCAGGGGTGCAAGCCCTATAGTGG
CTCTGCAGATTGCACTATCATTGTGTGGGACATCCAGAACCTGCAGAAGGTGAACACCATCCAGGCCCATGACAACCCTG
TGTGCACACTTGTGTCCTCTCACAACTGCTCTTCAGTGGCTCCCTGAAGGCCATTAAGGTCTGGGACATCGTGGGTACTG
AACTAAAGTTGAAGAAGGAGCTCACAGGCCTCCACCACTGGGTGGGGGCCCTGATGGCAGCCCAGAGCTACTTGTACAGT
GGCTCCTACCAAACAATCAAGATCTGGGACATCCAGACCCTTGATTGCATCCACGTCCTACAGACGTCTGGTGGCAGTGT
CTACTCCATCGCTGTGATGAATCACCACATTGTCTGTGGCACATGTGAGAATCTCATTCATATTTGGGACATCGAGTCCA
AGGAGCAAGTGCAGACCCTAACAGGCCTTGTGGGAACCGTCTATGCCCTGGCAGTCATCTCGACACCAGACCAGACCAAA
GTCTTCAGTGCACCCTACTATCGGTCCCTCAGGGTCTGGAGTATGGATAACATGATCTGCACCCAGACCCTACTGTGCCA
CCAGGGTAGTGTG

Alignment

ORF - retro_itri_1441 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.46 %
• Parental protein coverage: 96.42 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MSSGKSARYNRFSGGPANLPSPDLSTGTRMETTFGPAFSAVTTITKADGTSTYKQHRRTPSSSSTLAYSP
          MSSGKS..YNRFSG.PANLPSPDL.TGTRMETT.GPAFSAVTTI.KADGTST.KQHRR.PSSSSTLAY.P
Retrocopy MSSGKSVCYNRFSGEPANLPSPDLRTGTRMETTVGPAFSAVTTIMKADGTST*KQHRRIPSSSSTLAYTP

Parental  RDEEDTMPP-ISTPRRSDSAISVRSLHSESSMSLRSTFSLPEEEEEPEPLVFAEQPSVKLCCQLCCGVFK
          RDE.D.MPP.ISTPR.SDSAISV.SLHSESSM.LRSTFSLPEEEEEPEPLVFAEQPSVKLC.QLCCGVFK
Retrocopy RDEGDSMPP>ISTPRPSDSAISVGSLHSESSMCLRSTFSLPEEEEEPEPLVFAEQPSVKLCRQLCCGVFK

Parental  DPVITTCGHTFCRRCALKSEKCPVDNAKLTVVVNNIAVAEQIGELFIHCRHGCRVVGAGKPSVFEVDPRG
          DPVITTCGHTFCRRCALKSEKCPVDNAKLTVVVNNI.VAEQIGELFIHCR.GC.VVGAGK.SV.EVDP.G
Retrocopy DPVITTCGHTFCRRCALKSEKCPVDNAKLTVVVNNIPVAEQIGELFIHCRQGCCVVGAGKSSVVEVDPPG

Parental  CPFTIKLSARKDHEGSCDYRPVRCPNNPSCPPLLKMNLEAHLKECEHIKCPHSKYG-CTFIGNQDTYETH
          CPFTIKLSARKDH...CDYRPVRCP.N.S.PPLL.MNLEAHLKE.EHIKCPHSKYG.CTFIGNQDTYETH
Retrocopy CPFTIKLSARKDH*VACDYRPVRCPSNTSFPPLLEMNLEAHLKEWEHIKCPHSKYG<CTFIGNQDTYETH

Parental  LETCRFEGLKEFLQQTDDRFHEMHVALAQKDQEIAFLRSMLGKLSEKIDQLEKSLELKFDVLDENQSKLS
          LET.RFEGLKEFLQQTDD.F..MHVALAQKDQEIAFLRSMLGKLSE.IDQLEKSLELKFDVL.ENQSKLS
Retrocopy LETYRFEGLKEFLQQTDDNFYDMHVALAQKDQEIAFLRSMLGKLSE-IDQLEKSLELKFDVLGENQSKLS

Parental  EDLMEFRRDASMLNDELSHINARLNMGILGSYDPQQIFKCKGTFV-GHQGPVWCLCVYSMGDLLFSGSSD
          EDLMEF.RDASMLNDEL.HIN.RLNMGILGS.DPQ.IFK.K.TFV.GHQG.VWCLCVYSMGDLLFSGSSD
Retrocopy EDLMEFQRDASMLNDELPHINTRLNMGILGSHDPQLIFKFKRTFV<GHQGLVWCLCVYSMGDLLFSGSSD

Parental  KTIKVWDTCTTYKCQKTLEGHDGIVLALCIQGCKLYSGSADCTIIVWDIQNLQKVNTIRAHDNPVCTLVS
          KTIKVWDTCTTYKCQKTLEGHDGIVLALCIQGCK.YSGSADCTIIVWDIQNLQKVNTI.AHDNPVCTLVS
Retrocopy KTIKVWDTCTTYKCQKTLEGHDGIVLALCIQGCKPYSGSADCTIIVWDIQNLQKVNTIQAHDNPVCTLVS

Parental  SHN-MLFSGSLKAIKVWDIVGTELKLKKELTGLNHWVRALVAAQSYLYSGSYQTIKIWDIRTLDCIHVLQ
          SHN..LFSGSLKAIKVWDIVGTELKLKKELTGL.HWV.AL.AAQSYLYSGSYQTIKIWDI.TLDCIHVLQ
Retrocopy SHN<LLFSGSLKAIKVWDIVGTELKLKKELTGLHHWVGALMAAQSYLYSGSYQTIKIWDIQTLDCIHVLQ

Parental  TSGGSVYSIAVTNHHIVCGTYENLIHVWDIESKEQVRTLTGHVGTVYALAVISTPDQTKVFSASYDRSLR
          TSGGSVYSIAV.NHHIVCGT.ENLIH.WDIESKEQV.TLTG.VGTVYALAVISTPDQTKVFSA.Y.RSLR
Retrocopy TSGGSVYSIAVMNHHIVCGTCENLIHIWDIESKEQVQTLTGLVGTVYALAVISTPDQTKVFSAPYYRSLR

Parental  VWSMDNMICTQTLLRHQGSV
          VWSMDNMICTQTLL.HQGSV
Retrocopy VWSMDNMICTQTLLCHQGSV

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_1441 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1441 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Ictidomys tridecemlineatus	ENSSTOG00000013083	1 retrocopy	retro_itri_1441 ,
Tursiops truncatus	ENSTTRG00000008169	1 retrocopy	retro_ttru_1213,