RetrogeneDB ID: retro_itri_1005

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393358.1:2303443..2303697(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MED21
• Ensembl ID: ENSSTOG00000008391
• Aliases: None
• Description: mediator complex subunit 21 [Source:HGNC Symbol;Acc:11473]

Sequence

>retro_itri_1005
CTGAACTTGCTTGCAGATCAGTTTTGTAATGCCACTGGAGTGAAATGTGGTCCTCCTGCCTTTCTTAATAATGTACAGAC
AGTAATTAACAAAGACAACCAGCTAATCTTACAGAAGAATATACCCAGCTTTTTGCAGCACTGATTGCATGAACAGCAAA
AGACACTGATGTTTTGATAGATTCCTTACCCAGTGAAGAACCTACAGCTGCTTTACAGGCTGCTAGTTAGAAGAAAATCC
TGAGTCGGCTTCAT

Alignment

ORF - retro_itri_1005 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.86 %
• Parental protein coverage: 60.42 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VNSLADQFCNAIGVLQQCGPPASFNNIQTAINKD-QPANPTEEYAQLFAALIARTAKDIDVLIDSLPSEE
          .N.LADQFCNA.GV...CGPPA..NN.QT.INKD.QPAN.TEEY.QLFAALIA.TAKD.DVLIDSLPSEE
Retrocopy LNLLADQFCNATGV--KCGPPAFLNNVQTVINKD<QPANLTEEYTQLFAALIA*TAKDTDVLIDSLPSEE

Parental  STAALQAASLYKLEEENH
          .TAALQAAS..K.....H
Retrocopy PTAALQAAS*KKILSRLH

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_1005 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1005 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 13 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011670	1 retrocopy	retro_amel_108,
Dasypus novemcinctus	ENSDNOG00000010041	1 retrocopy	retro_dnov_998,
Echinops telfairi	ENSETEG00000006223	1 retrocopy	retro_etel_1141,
Felis catus	ENSFCAG00000030691	1 retrocopy	retro_fcat_1101,
Homo sapiens	ENSG00000152944	1 retrocopy	retro_hsap_4105,
Gorilla gorilla	ENSGGOG00000016313	1 retrocopy	retro_ggor_2756,
Myotis lucifugus	ENSMLUG00000007678	1 retrocopy	retro_mluc_229,
Macaca mulatta	ENSMMUG00000003218	1 retrocopy	retro_mmul_2365,
Nomascus leucogenys	ENSNLEG00000005431	1 retrocopy	retro_nleu_573,
Pongo abelii	ENSPPYG00000004377	1 retrocopy	retro_pabe_3361,
Pan troglodytes	ENSPTRG00000004785	1 retrocopy	retro_ptro_2786,
Pteropus vampyrus	ENSPVAG00000013357	1 retrocopy	retro_pvam_449,
Ictidomys tridecemlineatus	ENSSTOG00000008391	2 retrocopies	retro_itri_1005 , retro_itri_1057,