RetrogeneDB ID: retro_itri_1084

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393372.1:1588250..1588645(-)
• Located in intron of: ENSSTOG00000003491

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDUFB11
• Ensembl ID: ENSSTOG00000026821
• Aliases: None
• Description: NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 11, 17.3kDa [Source:HGNC Symbol;Acc:20372]

Sequence

>retro_itri_1084
AGTGTCCACGTTTGCTGGGAATCCAGCTCCTCCAGAGCTATGGTTGCCCCATCTGCTTCAGTGAGAAAGAGGAAATAACC
AGAAATAACCACACACTGGTGGGAGGACCCAGATCCTGAGGACAAAAACCTCTATGAGAAGAATCCAGACTCCCATAGTT
ATGACAATGGTCTGCTGTGAGTCTCTGGAACACTCAGGTGATCTTCTCTGGCTTCTCTATCATCCTGGTCTTTGTCAGTT
CCTTTGTGACTTATCTGCCTGACTATGGGATGCAAGAGTGGGCCTGATGGGAAACTGAGAGGCTTGTGAAACACCAAGAG
GCCAACAGCCTCCCAATCTTGGAAGAGGAAGAATATTGTTGCTTTGGCCCCAATGATATTCAGCTATTGGAGGAT

Alignment

ORF - retro_itri_1084 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.7 %
• Parental protein coverage: 84.31 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AARVRWESSSSRAVVAPSAVAGKRP-PEPTMRWQEDPEPEDENLYEKNPDSHGYDKD-PVVDLWNMRVIF
          ...V.WESSSSRA.VAPSA...KR..PE.T..W.EDP.PED.NLYEKNPDSH.YD.....V.LWN..VIF
Retrocopy SVHVCWESSSSRAMVAPSASVRKRK*PEITTHWWEDPDPEDKNLYEKNPDSHSYDNG<SAVSLWNTQVIF

Parental  FFGVSIVLVLGTTFVAYLPDYSMREWARREAERLVKYREANGLPVMESN---CFDPSKIQLPDD
          ..G.SI.LV....FV.YLPDY.M.EWA..E.ERLVK..EAN.LP..E.....CF.P..IQL..D
Retrocopy S-GFSIILVFVSSFVTYLPDYGMQEWA*WETERLVKHQEANSLPILEEEEYCCFGPNDIQLLED

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_1084 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1084 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 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000147123	1 retrocopy	retro_hsap_912,
Macaca mulatta	ENSMMUG00000017422	2 retrocopies	retro_mmul_1116, retro_mmul_830,
Monodelphis domestica	ENSMODG00000018491	1 retrocopy	retro_mdom_1063,
Mus musculus	ENSMUSG00000031059	2 retrocopies	retro_mmus_245, retro_mmus_2602,
Pongo abelii	ENSPPYG00000020284	1 retrocopy	retro_pabe_788,
Pan troglodytes	ENSPTRG00000021836	1 retrocopy	retro_ptro_633,
Rattus norvegicus	ENSRNOG00000008329	1 retrocopy	retro_rnor_151,
Ictidomys tridecemlineatus	ENSSTOG00000026821	1 retrocopy	retro_itri_1084 ,