RetrogeneDB ID: retro_itri_1183

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393395.1:5118073..5118442(+)
• Located in intron of: ENSSTOG00000029077

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPS10
• Ensembl ID: ENSSTOG00000027016
• Aliases: None
• Description: mitochondrial ribosomal protein S10 [Source:HGNC Symbol;Acc:14502]

Sequence

>retro_itri_1183
ATGAAGTGGGCACAGTTTTCAAACCCACACACTGATGTCCCAAAGGATTTGATCAAATGATAACCATATCTGATGAAATG
GATACACTGTATGAATGCCTGTCAATTTTACTAAAAGGCCACAAAAAAGGCTGTAATGAACAGTTATGAATATTTTGCCA
TGCTTGCTGTTAAAGAACTTGATCTCTCTACTAAAGTACATGAACCTCCAAGGAACACAATGATTTTCTTCTCAAATCAG
TGCATATTTTCAAGAAGCAGAGTTCAGTATGAAATGAGAATGCTTTGCAGATGTTTAGAGTTAGAACATCTAACTGGATG
TACAGCAGATGTCTACTTGGAATATTCTCAGCAAAACTTACCTGAAGGT

Alignment

ORF - retro_itri_1183 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.97 %
• Parental protein coverage: 62.69 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MKWVQFSNLHIDV-PKDLTKPTITISDEPDTLYKRLSILVKGHDK-AVLDSYEYFAVLAAKELGISIKVH
          MKW.QFSN.H.DV.PK......ITISDE.DTLY..LSIL.KGH.K.AV..SYEYFA.LA.KEL..S.KVH
Retrocopy MKWAQFSNPHTDV<PKGFDQ-MITISDEMDTLYECLSILLKGHKK>AVMNSYEYFAMLAVKELDLSTKVH

Parental  EPPRKIERFTLLKSVHIFKKHRVQYEMRTLYRCLELEHLTGCTADVYLEYIQRNLPEG
          EPPR....F.......IF...RVQYEMR.L.RCLELEHLTGCTADVYLEY.Q.NLPEG
Retrocopy EPPRNTMIF--FSNQCIFSRSRVQYEMRMLCRCLELEHLTGCTADVYLEYSQQNLPEG

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_1183 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1183 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 12 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000002081	1 retrocopy	retro_dord_412,
Homo sapiens	ENSG00000048544	1 retrocopy	retro_hsap_4157,
Gorilla gorilla	ENSGGOG00000012808	1 retrocopy	retro_ggor_2532,
Microcebus murinus	ENSMICG00000011379	1 retrocopy	retro_mmur_321,
Macaca mulatta	ENSMMUG00000014661	1 retrocopy	retro_mmul_48,
Mus musculus	ENSMUSG00000034729	1 retrocopy	retro_mmus_1654,
Nomascus leucogenys	ENSNLEG00000004800	1 retrocopy	retro_nleu_1385,
Oryctolagus cuniculus	ENSOCUG00000016697	1 retrocopy	retro_ocun_1141,
Pongo abelii	ENSPPYG00000016613	1 retrocopy	retro_pabe_3456,
Pan troglodytes	ENSPTRG00000018169	1 retrocopy	retro_ptro_2826,
Rattus norvegicus	ENSRNOG00000022609	1 retrocopy	retro_rnor_2284,
Ictidomys tridecemlineatus	ENSSTOG00000027016	1 retrocopy	retro_itri_1183 ,