RetrogeneDB ID: retro_itri_309

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393283.1:10145667..10146196(-)
• Located in intron of: ENSSTOG00000028034

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATAD1
• Ensembl ID: ENSSTOG00000006563
• Aliases: None
• Description: ATPase family, AAA domain containing 1 [Source:HGNC Symbol;Acc:25903]

Sequence

>retro_itri_309
ATGTATGGGACTTGGAGTGGTTTAGCAGTTTTAGGTGATGTCATTTATGGATCTGAAAAACAGTCATATTATCTATAGAA
GAAGTATATGAGAATTTCAGGCTTCTTGCAGCCTCCAATAAGATATTATTTATGATCCTCTAGCCTCTGGTAAAACATTG
ATTGTCAAGGCTACAGCCAAGAAAGCAAGTCATCAATTTATTAACCTTCAGCCTTGTAAGTATTATACAGAATCTCAAAA
TTTGGCTGCTGCTGTTTCCTCCCTTGTCATAAAGCCACAGCTTTCCATCCTCTGAATAGATGAAATATATTCCTTCCTAT
GAAACTGCTCACATTCTAACTATGAAGTTACAGCTTTGGCTAAGCTCAACTTATGAGTCTCTAGGATTATTTTGAATACT
GACCACAACTGCCAAGTCATAGTAATGGGAGCTACTGAGTGTCCTTAGGACCTTGACTTGACTATAAGAAGGATGATTCT
TATAGTATTCCACATTTACCTGCTTGCTCTAAAATAGAGAGAAACAATA

Alignment

ORF - retro_itri_309 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.61 %
• Parental protein coverage: 66.3 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MHVTWSDIAGLDDVITDLKD-TVILPIKKKHLFENSRLLQPPKGVL-LYGPPGCGKTLIAKATAKEAGCR
          M..TWS..A.L.DVI......TVIL.I......EN.RLL......L..Y.P...GKTLI.KATAK.A...
Retrocopy MYGTWSGLAVLGDVIYGSEK<TVILSIEE--VYENFRLLAASNKIL<IYDPLASGKTLIVKATAKKASHQ

Parental  FINLQPSTLTDKWYGESQKLAAAVFSLAIKLQPSIIFIDEIDSFLRNRSSSDHEATAMMK-AQFMSLWDG
          FINLQP.....K.Y.ESQ.LAAAV.SL.IK.Q.SI..IDEI.SFL.N.S.S..E.TA..K.AQ.MSL.D.
Retrocopy FINLQPC----KYYTESQNLAAAVSSLVIKPQLSIL*IDEIYSFL*NCSHSNYEVTALAK<AQLMSL*DY

Parental  -LDTDHSCQVIVMGATNRPQDLDSAIMRRMPTRFHINQPALKQREAI
          .L.TDH.CQVIVMGAT..P.DLD..I.R.....FHI...ALK.RE.I
Retrocopy >LNTDHNCQVIVMGATECP*DLDLTIRRMILIVFHIYLLALK*RETI

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_309 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_309 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 10 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000005296	1 retrocopy	retro_cjac_1101,
Homo sapiens	ENSG00000138138	1 retrocopy	retro_hsap_1900,
Gorilla gorilla	ENSGGOG00000026651	1 retrocopy	retro_ggor_1393,
Macaca mulatta	ENSMMUG00000006414	1 retrocopy	retro_mmul_608,
Nomascus leucogenys	ENSNLEG00000012135	1 retrocopy	retro_nleu_1231,
Oryctolagus cuniculus	ENSOCUG00000012082	1 retrocopy	retro_ocun_1634,
Pan troglodytes	ENSPTRG00000002717	1 retrocopy	retro_ptro_1255,
Pteropus vampyrus	ENSPVAG00000014020	1 retrocopy	retro_pvam_1080,
Rattus norvegicus	ENSRNOG00000010861	1 retrocopy	retro_rnor_2752,
Ictidomys tridecemlineatus	ENSSTOG00000006563	1 retrocopy	retro_itri_309 ,