RetrogeneDB ID: retro_itri_1730

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393684.1:343286..343751(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CNOT7
• Ensembl ID: ENSSTOG00000009175
• Aliases: None
• Description: CCR4-NOT transcription complex, subunit 7 [Source:HGNC Symbol;Acc:14101]

Sequence

>retro_itri_1730
ATACAGACCCAGTACTTTGCAGAACTTCTTGTGACTTTCAGAGTGGTCCTCTATAAAGAGGTCAAATGATAATCATTTCT
CAGTGGTTAGGACTTTGGCAATTTAATCAAAATCCCAACCAACTATAATTTGCCCAAAGAAGAACTTGACTTCTTTGAGA
GTCTTTTGATTATTCTTCTCCTGCCGTTTATGATGTGACTACCTCAAGAAGAGCTGAAAAAATCTTAACAGTGGATTACA
ACGAGTTTCTGAACAGCTAGAGATGAAAAAAAATAGGACATAGCATCAGGCAAGATCAAATTTGTTGTTTTCAGCAATGG
CCTTATTCAAAAAGAGAGAAATGTTCTTTGAAGATTATGTCAATGATGTCAAATATTATGGTCATTTCTGTGTCTATGAT
TCTAGTTCATCCTAGTACAGAGTGGCATAGGGAATGCATAGGAAGAGGAAGCCAACAAGCAGTCA

Alignment

ORF - retro_itri_1730 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.26 %
• Parental protein coverage: 54.39 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  IETQYFAELLMTSGVVLCEGVKWLSFHSGYDFGYLIKILTNSNLPEEELDFFEILR-LFF-PVIYDVK-Y
          I.TQYFAELL.T..VVL...VK..SF.SG.DFG.LIKI.TN.NLP.EELDFFE.L..LFF.P..YDV..Y
Retrocopy IQTQYFAELLVTFRVVLYKEVK**SFLSG*DFGNLIKIPTNYNLPKEELDFFESLL>LFF>PAVYDVT<Y

Parental  LMKSCKNLKGGLQEVAEQLELERIGPQHQAGSDSLLTGMAFFKMREMFFEDHIDDAKYCGHLYGLGSGSS
          L.KS.KNL..GLQ.V.EQLE.......HQA.S..L...MA.FK.REMFFED...D.KY.GH.....S.SS
Retrocopy LKKS*KNLNSGLQRVSEQLEMXXXRT*HQARSNLLFSAMALFKKREMFFEDYVNDVKYYGHFCVYDSSSS

Parental  -YVQNGTGNAYEEEANKQS
          ..VQ.G.GNA.EEEANKQS
Retrocopy <LVQSGIGNA*EEEANKQS

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_1730 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1730 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 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000677	4 retrocopies	retro_chof_1431, retro_chof_1581, retro_chof_822, retro_chof_963,
Callithrix jacchus	ENSCJAG00000011795	1 retrocopy	retro_cjac_720,
Felis catus	ENSFCAG00000000591	1 retrocopy	retro_fcat_1889,
Homo sapiens	ENSG00000198791	2 retrocopies	retro_hsap_211, retro_hsap_4851,
Macaca mulatta	ENSMMUG00000001873	1 retrocopy	retro_mmul_2592,
Mustela putorius furo	ENSMPUG00000017972	1 retrocopy	retro_mputfur_1596,
Nomascus leucogenys	ENSNLEG00000002489	2 retrocopies	retro_nleu_1860, retro_nleu_2373,
Oryctolagus cuniculus	ENSOCUG00000014589	1 retrocopy	retro_ocun_118,
Otolemur garnettii	ENSOGAG00000006324	2 retrocopies	retro_ogar_1883, retro_ogar_505,
Pongo abelii	ENSPPYG00000018385	2 retrocopies	retro_pabe_3771, retro_pabe_428,
Sarcophilus harrisii	ENSSHAG00000011828	2 retrocopies	retro_shar_103, retro_shar_631,
Ictidomys tridecemlineatus	ENSSTOG00000009175	2 retrocopies	retro_itri_1729, retro_itri_1730 ,