RetrogeneDB ID: retro_itri_1240

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393410.1:3737813..3738079(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATPIF1
• Ensembl ID: ENSSTOG00000020766
• Aliases: None
• Description: ATPase inhibitory factor 1 [Source:HGNC Symbol;Acc:871]

Sequence

>retro_itri_1240
ATGAAAGCCTGGGATTTTTCAAGGCTTGGCTTGGACCAGTTGCAGAATTTGGATAAAGGCACTGGCTCTTTCCAGGAATC
CGGTGGGGACTTCAGAAAGAGAAAACAGTTGAGGAAGAACAATATTTCCCAGAGAAGACTTGAGAATGACTGGCAGACTT
GAAGAAACACCACAAAGATAAGATCGTTTGTCATCATAAGGAGCTTGAACATCTGCAGAAAGAAATTGAGCCACATAAGA
AGATCAAACATCTAAAACATAATGAT

Alignment

ORF - retro_itri_1240 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.95 %
• Parental protein coverage: 83.96 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MRAMQTRGFGSDQSEDGGRSAGAIREAGGAFGKRER-AEEERYFREKTREQLAILKKHHEDEISHHKKEI
          M.A......G.DQ........G...E.GG.F.KR....EEE.YF.EKT.E.LA.LKKHH.D.I..H.KE.
Retrocopy MKAWDFSRLGLDQLQNLDKGTGSFQESGGDFRKRKQ<VEEEQYFPEKT*E*LADLKKHHKDKIVCHHKEL

Parental  ERLQKEIERHKQKIKHL-HND
          E.LQKEIE.HK.KIKHL.HND
Retrocopy EHLQKEIEPHK-KIKHLKHND

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_1240 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1240 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 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000032458	2 retrocopies	retro_cfam_1777, retro_cfam_651,
Callithrix jacchus	ENSCJAG00000009581	1 retrocopy	retro_cjac_1406,
Dasypus novemcinctus	ENSDNOG00000015460	1 retrocopy	retro_dnov_2592,
Myotis lucifugus	ENSMLUG00000000170	1 retrocopy	retro_mluc_363,
Mustela putorius furo	ENSMPUG00000015536	1 retrocopy	retro_mputfur_1570,
Mus musculus	ENSMUSG00000054428	2 retrocopies	retro_mmus_2516, retro_mmus_908,
Otolemur garnettii	ENSOGAG00000010337	2 retrocopies	retro_ogar_116, retro_ogar_268,
Pteropus vampyrus	ENSPVAG00000017615	1 retrocopy	retro_pvam_817,
Rattus norvegicus	ENSRNOG00000013300	1 retrocopy	retro_rnor_2655,
Sorex araneus	ENSSARG00000010860	1 retrocopy	retro_sara_458,
Ictidomys tridecemlineatus	ENSSTOG00000020766	1 retrocopy	retro_itri_1240 ,