RetrogeneDB ID: retro_itri_1462

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393494.1:1407149..1407955(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HCCS
• Ensembl ID: ENSSTOG00000014037
• Aliases: None
• Description: holocytochrome c synthase [Source:HGNC Symbol;Acc:4837]

Sequence

>retro_itri_1462
ATGGGTTTGTCAGCCTCTACTCCTGCTGTTCCAGTTCAGACCTCAAGTGCTTCAGATCATCAGACAGCATCACTGCCTCA
GGATGCCCAATGCATGAAGGAAAAATGAAAGGCTGTCCAATGAATACAGAACCCTCTAGTCCAACCTGTGAGAGCAAAAC
ACTCTGTGCCTGCCCACAAAGATCGTGCCTATGAGTATGTGGAGTGTCCTGTTACAGGCACTGCTGTTAAGGAGAACCTG
GATCCTTCAAATCTGATGCCACCACCTATTCAAACACCAGCTCCAGGTAAGCCCTTTGCATTGTCTACCATCAGAGAGGA
GTCATCCATTCCATGGGCAGATTCAGAGAAAAAGTGGGTTTATTCTTCCGAATAGATGTTCTGGAATGCAATGTTAAGGA
AAGCGTGGAAGTGGAAGGATGAGGATATTAGTCAGAAAGCTATGTATAATATCATTAAAATTCACAATCAGAACAATGAA
CAGGCCTGGAAGGAGACATTGAAGTGGGAAGCTCTTCATGCTGTGGAGTGCCCTTGTGGTCCATCCTTGATCCGATTTGG
AGAGAAAGCAAAACAATATTCACCAAGAGCAAGAATTCGTTCCTGGATGGGCTATGAGCTGCATTTCGATAGAAACGATT
GGATCATCAACCATTGTGGCAGGAACTTAGATATGTAATAGATTTTTACTATGGTAGCAAAGTCAACAAGGACTACAAGT
TCACCATCCTGGACTTCTGCCCTGCCTTGGATTCGCTTTTAGCAGTATGGAACAGAATGAAAGTTGCTTGTTGGTGCTCG
ACATCA

Alignment

ORF - retro_itri_1462 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.29 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MGLSASTPAVPVQTSNASDHQTASPPSGCPMHEGKMKGCPMNAEPSGPTCESKAYSVPAHQDRAYEYVEC
          MGLSASTPAVPVQTS.ASDHQTAS.P........K.K.......P.......K..SVPAH.DRAYEYVEC
Retrocopy MGLSASTPAVPVQTSSASDHQTASLPQDAQCMKEK*KAVQ*IQNPLVQPVRAK-HSVPAHKDRAYEYVEC

Parental  PVTGGAAKNKENLDPSNLMPPPNQTPAPDQPFALSTVREESSIPRADSEKKWVYPSEQMFWNAMLRKGWK
          PVTG.A.K..ENLDPSNLMPPP.QTPAP..PFALST.REESSIP.ADSEKKWVY.SE.MFWNAMLRK.WK
Retrocopy PVTGTAVK--ENLDPSNLMPPPIQTPAPGKPFALSTIREESSIPWADSEKKWVYSSE*MFWNAMLRKAWK

Parental  WKDEDISQKDMYNIIKIHNQNNEQAWKEILKWEALHAAECPCGPSLIRFGGKAKQYSPRARIRSWMGYEL
          WKDEDISQK.MYNIIKIHNQNNEQAWKE.LKWEALHA.ECPCGPSLIRFG.KAKQYSPRARIRSWMGYEL
Retrocopy WKDEDISQKAMYNIIKIHNQNNEQAWKETLKWEALHAVECPCGPSLIRFGEKAKQYSPRARIRSWMGYEL

Parental  PFDRHDWIINRCG-TEVRYVIDYYDGGEVNKDYQFTILDVRPALDSLSAVWDRMKVAWWRWTS
          .FDR.DWIIN.CG..E.RYVID.Y.G..VNKDY.FTILD..PALDSL.AVW.RMKVA.W..TS
Retrocopy HFDRNDWIINHCG<QELRYVIDFYYGSKVNKDYKFTILDFCPALDSLLAVWNRMKVACWCSTS

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_1462 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1462 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 4 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000022393	1 retrocopy	retro_fcat_1706,
Myotis lucifugus	ENSMLUG00000003569	1 retrocopy	retro_mluc_1621,
Ictidomys tridecemlineatus	ENSSTOG00000014037	6 retrocopies	retro_itri_1277, retro_itri_1462 , retro_itri_1594, retro_itri_1700, retro_itri_242, retro_itri_745,
Tupaia belangeri	ENSTBEG00000002670	1 retrocopy	retro_tbel_1503,