RetrogeneDB ID: retro_itri_1706

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393647.1:743089..743967(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF2A
• Ensembl ID: ENSSTOG00000003374
• Aliases: None
• Description: eukaryotic translation initiation factor 2A, 65kDa [Source:HGNC Symbol;Acc:3254]

Sequence

>retro_itri_1706
GAAAGTGAGGTAGTACAATGACTAAAAACTAACCCCATAGAGGATGTAGGTTGGAATTCTAGTTCTACTGAGATTTTTGC
TGTTCTGGTTTTAGACCTGCCAAAGCAACACTTTTCAACTTGAAATGTGACCCTGGGTTTGAGTTTGGAATCCATCCTTA
CAATGAAGCCTACTGCAGCCCTCGTGGACGTGTATTAGTACTAGTTGGATTTGGAAACCTGAGGGAACAAATGGAAACGT
GGAATATTAAAAACTATATATTTTTTTCTAAACTAGTGGTTTCTGATTCTATATGTTTTGTTTGGTGCCCAGATGGGGAG
TGTATTTTAACAGCTGCATTTGCTCCCAGGTACAAGTTAATGATTGGCACAAGATAAAGCATTGCTCTGGCTCTAAATGT
GATGTACCATCAAATGCAAAATCATGGCAGGTCTCTTGGCAGCCAGTTTTGGATGGAATATTTTCAGCAAAACCAATAAT
TTACCAAGCAGTTCCAAGTGAAGTACCCAGTGAGGACCTTTAGGAACCAAAAGTTGCAACAGCTTATAGACCCCCAGCTT
TAGGAAATAAACCAATTACTGATTCCAAATTGCATGAAGAGAACCAGTTCAGAATATGAAACCAGAAGCAGAAAATAAAA
GCCATTACCCCAAACAGACATTAAAAATCAAAGGAAGCATGATTTAAGAAAGCTGCCAAGAGAAAAGCAAGAAGTGACAA
GAGGTCAGATTTGACAGTTACTCTTGCCCTCATAGTATAACATGAAACACCACTCCTCTGTCAACTTCTGGTGACCCTAA
AGTAGACACACAAAAAGAAAGAACTTAAAGAAGACAGTGAAAGCAATCAAAGAATTGAAGGAAAAAGCAGTAGCTGGA

Alignment

ORF - retro_itri_1706 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.28 %
• Parental protein coverage: 51.76 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  ESAVVQLPKSGPIYDVAWNSSSTEFCAVY-GFMPAKATVFNLKCDPVFDFGTGPRNAAYFSPHGHILVLA
          ES.VVQ..K..PI.DV.WNSSSTE..AV..GF.PAKAT.FNLKCDP.F.FG..P.N.AY.SP.G..LVL.
Retrocopy ESEVVQ*LKTNPIEDVGWNSSSTEIFAVL<GFRPAKATLFNLKCDPGFEFGIHPYNEAYCSPRGRVLVLV

Parental  GFGNLRGQMEVWDVKNYKLISKPVASDSTYFAWCPDGEHILTATCAPR-LRVNNGYKVWHYTGSVLHKHD
          GFGNLR.QME.W..KNY...SK.V.SDS..F.WCPDGE.ILTA..APR...VN...K..H..GS...K.D
Retrocopy GFGNLREQMETWNIKNYIFFSKLVVSDSICFVWCPDGECILTAAFAPR<VQVNDWHKIKHCSGS---KCD

Parental  VPSNAELWQVSWQPFLDGIFPAKRITYQAVPSEVPND---EPKVATAYRPPALRNKPITNSKLHEE-EPP
          VPSNA..WQVSWQP.LDGIF.AK.I.YQAVPSEVP.....EPKVATAYRPPAL.NKPIT.SKLHEE.EP.
Retrocopy VPSNAKSWQVSWQPVLDGIFSAKPIIYQAVPSEVPSEDL*EPKVATAYRPPALGNKPITDSKLHEE<EPV

Parental  QNMKPHTGNE-KPLSKTALKNQRKHEA-KKAAKQEAKNDQSPDVAPT-PTPQSTSWNTVSQATSGDPEVD
          QNMKP...N..KPL..T..KNQRKH...KKAAK..A..D...D...T...P.S...NT....TSGDP.VD
Retrocopy QNMKPEAENK<KPLPQTDIKNQRKHDL<KKAAKRKARSDKRSDLTVT<SCPHSIT*NTTPLSTSGDPKVD

Parental  -KKIR-NLKKKLKAIEQLKEQAAAG
          ..K.R.NLKK..KAI..LKE.A.AG
Retrocopy TQKER<NLKKTVKAIKELKEKAVAG

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_1706 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1706 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 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000001199	1 retrocopy	retro_cjac_968,
Dasypus novemcinctus	ENSDNOG00000014002	1 retrocopy	retro_dnov_1148,
Homo sapiens	ENSG00000144895	1 retrocopy	retro_hsap_565,
Gorilla gorilla	ENSGGOG00000015391	1 retrocopy	retro_ggor_509,
Loxodonta africana	ENSLAFG00000003767	1 retrocopy	retro_lafr_502,
Macaca mulatta	ENSMMUG00000017696	1 retrocopy	retro_mmul_2395,
Nomascus leucogenys	ENSNLEG00000003219	1 retrocopy	retro_nleu_2213,
Oryctolagus cuniculus	ENSOCUG00000016095	3 retrocopies	retro_ocun_1771, retro_ocun_1825, retro_ocun_1861,
Pongo abelii	ENSPPYG00000029636	2 retrocopies	retro_pabe_517, retro_pabe_652,
Pan troglodytes	ENSPTRG00000015528	1 retrocopy	retro_ptro_423,
Ictidomys tridecemlineatus	ENSSTOG00000003374	1 retrocopy	retro_itri_1706 ,