RetrogeneDB ID: retro_itri_1564

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393541.1:263332..263858(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000015610
• Aliases: None
• Description: None

Sequence

>retro_itri_1564
TTTGGACTTACTGCTGAACTTGTAGTGGATAAAACCATGGGGTTAAGGCTTGTGGGTGGCATCTATGGTGGAAACATAAA
ACCAACCCCCTTTTTGTATTTAACCTTGAAGATGCTTCAAATTCAACCCGAGAAGGACATCATTGTAGAATTTATAAAAA
ATGACAACTCCAAATATGTCTGCATATGGGGGGCACTTTACATCAGACCGACAGGTACCACAATTGATTGCTACAAGTAC
TTGGAGCCTTTATACAATGACTATCGAAAAATCAAGAGCCAGAACAGAAATGGGGAGTTTGAACTGATGCATGCAAACGA
GTTTATGATGAACTATTGCACAGTGAGAGGGTCTGTGATATCATTCTGCCCGGCTGCAGAAACACTATGTGCTAGAGAAA
GCTGAGCAACTGGAGCCTTGAGTTAGTGTTCTAGAAGACATGGATGATGTGGAGTCCAGTGAGGAGGAGAAAGAAGAAGA
TGAGAAATTGGGAGGAGTGCCATTATCTGACCACCACAGACAAGCC

Alignment

ORF - retro_itri_1564 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.12 %
• Parental protein coverage: 56.73 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  FGLTAELVVDKAMELRFVGGVYGGNIKPTPFLCLTLKMLQIQPEKDIIVEFIKNEDFKYVRMLGALYMRL
          FGLTAELVVDK.M.LR.VGG.YGGNIKPTPFL.LTLKMLQIQPEKDIIVEFIKN...KYV...GALY.R.
Retrocopy FGLTAELVVDKTMGLRLVGGIYGGNIKPTPFLYLTLKMLQIQPEKDIIVEFIKNDNSKYVCIWGALYIRP

Parental  TGTAIDCYKYLEPLYNDYRKIKSQNRNGEFELMHVDEFI-DELLHSERVCDIILP-RLQKRYVLEEAEQL
          TGT.IDCYKYLEPLYNDYRKIKSQNRNGEFELMH..EF..DELLHSERVCDIILP.RLQK.YVLE.AEQL
Retrocopy TGTTIDCYKYLEPLYNDYRKIKSQNRNGEFELMHANEFM<DELLHSERVCDIILP<RLQKHYVLEKAEQL

Parental  EPRVSALEEDMDDVESSEEEEEEDEKLERVPSPDHRRRS
          EP.VS.L.EDMDDVESSEEE.EEDEKL..VP..DH.R..
Retrocopy EP*VSVL-EDMDDVESSEEEKEEDEKLGGVPLSDHHRQA

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_1564 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1564 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 18 parental genes, and 35 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000021594	1 retrocopy	retro_cjac_2862,
Dasypus novemcinctus	ENSDNOG00000013904	1 retrocopy	retro_dnov_443,
Homo sapiens	ENSG00000134748	2 retrocopies	retro_hsap_541, retro_hsap_545,
Gorilla gorilla	ENSGGOG00000003940	4 retrocopies	retro_ggor_493, retro_ggor_494, retro_ggor_496, retro_ggor_563,
Loxodonta africana	ENSLAFG00000025862	1 retrocopy	retro_lafr_794,
Myotis lucifugus	ENSMLUG00000001053	8 retrocopies	retro_mluc_1105, retro_mluc_1208, retro_mluc_1856, retro_mluc_2016, retro_mluc_2150, retro_mluc_2405, retro_mluc_2576, retro_mluc_828,
Monodelphis domestica	ENSMODG00000000644	1 retrocopy	retro_mdom_184,
Mus musculus	ENSMUSG00000063800	2 retrocopies	retro_mmus_1227, retro_mmus_671,
Nomascus leucogenys	ENSNLEG00000017999	2 retrocopies	retro_nleu_715, retro_nleu_719,
Oryctolagus cuniculus	ENSOCUG00000000963	1 retrocopy	retro_ocun_713,
Otolemur garnettii	ENSOGAG00000005423	1 retrocopy	retro_ogar_3216,
Petromyzon marinus	ENSPMAG00000005561	1 retrocopy	retro_pmar_28,
Pongo abelii	ENSPPYG00000001348	2 retrocopies	retro_pabe_500, retro_pabe_503,
Pan troglodytes	ENSPTRG00000000739	2 retrocopies	retro_ptro_406, retro_ptro_410,
Pteropus vampyrus	ENSPVAG00000009803	1 retrocopy	retro_pvam_967,
Sus scrofa	ENSSSCG00000003858	1 retrocopy	retro_sscr_924,
Ictidomys tridecemlineatus	ENSSTOG00000015610	1 retrocopy	retro_itri_1564 ,
Taeniopygia guttata	ENSTGUG00000008995	3 retrocopies	retro_tgut_12, retro_tgut_13, retro_tgut_14,