RetrogeneDB ID: retro_ptro_1255

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 18:15345425..15346127(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATAD1
• Ensembl ID: ENSPTRG00000002717
• Aliases: None
• Description: None

Sequence

>retro_ptro_1255
ACAGTCATCTTACCTATCAAAAAGAAACATTTGTTTGAGAATTCCAGGCTTCTGCAGCCTCCAAAAGGTGTTCTTCTCTA
TGACCCTCCCCAGGCTGTGGTGAAACGTTGATTGCCAAGGCCACAGCCAAAGAAGCAGGCTGTCGATTTATTAACCTTGA
GCCTTCGACACTGACCAATAAGTGGTATGGAGAATCTCAAACACTGGCTGCTGCTGTCTTCTCCCTTGCCATGAAGCTAC
AACTGTCCATCATCATTTAGACGAAATAGACTCCTTTCTACGAAACCGTTCGGAGTTCTGACCATGAAGCTACAGCCATA
ATGAAAGCTCAGTTTATGAGTCTCTGGGATGGACTGGATACTGATCACAGCTCCCAGGTCATAGTAATGGGAGCTACCAT
TCATCCTCAGGACCTTGACACGGCTATAACGAGAAGAATTCCTACAAGATTTCATATCAACCAGCCTGCTTTAAAACAGA
AAGAAGCAATCCTGAAACTCATCTTGAAAAATGAAAATGTGGATAGGCATGTAGACCTGCTAGAAGTTGCCCAGGAAACT
GATGCGTTTTCAGGAAGGGACCTAAATGCGATGTGTTGAGATGCTGCCCTCCTCTGTGTTAGAGAATGTTAATTCTACAT
CAGAAGAAAGCCATGATGAAGATGAAATTCGGCCTGTTCAACAGCAGGACCTGCATCGGGCA

Alignment

ORF - retro_ptro_1255 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.92 %
• Parental protein coverage: 64.82 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  TVILPIKKKHLFENSR-LLQPPKGVLLYGP-PGCGKTLIAKATAKEAGCRFINLQPSTLTDKWYGESQKL
          TVILPIKKKHLFENSR.L..P....L...P.PGCG.TLIAKATAKEAGCRFINL.PSTLT.KWYGESQ.L
Retrocopy TVILPIKKKHLFENSRLLQPPKGVLLYDPP<PGCGETLIAKATAKEAGCRFINLEPSTLTNKWYGESQTL

Parental  AAAVFSLAIKLQPSIIF-IDEIDSFLRNRS-SSDHEATAMMKAQFMSLWDGLDTDHSCQVIVMGATNRPQ
          AAAVFSLA.KLQ.SII...DEIDSFLRNRS.SSDHEATA.MKAQFMSLWDGLDTDHS.QVIVMGAT..PQ
Retrocopy AAAVFSLAMKLQLSIII<LDEIDSFLRNRS>SSDHEATAIMKAQFMSLWDGLDTDHSSQVIVMGATIHPQ

Parental  DLDSAIMRRMPTRFHINQPALKQREAILKLILKNENVDRHVDLLEVAQETDGFSGSDLKEMCRDAALLCV
          DLD.AI.RR.PTRFHINQPALKQ.EAILKLILKNENVDRHVDLLEVAQETD.FSG.DL..MC.DAALLCV
Retrocopy DLDTAITRRIPTRFHINQPALKQKEAILKLILKNENVDRHVDLLEVAQETDAFSGRDLNAMC*DAALLCV

Parental  RE-YVNSTSEESHDEDEIRPVQQQDLHRA
          RE.......E.......IRPVQQQDLHRA
Retrocopy RE>VNSTSEESHDEDE-IRPVQQQDLHRA

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain_prefrontal_cortex	0.02 RPM	31.53 RPM
SRP007412_cerebellum	0.04 RPM	37.21 RPM
SRP007412_heart	0.00 RPM	91.31 RPM
SRP007412_kidney	0.00 RPM	34.02 RPM
SRP007412_liver	0.13 RPM	20.46 RPM
SRP007412_testis	0.11 RPM	124.98 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1255 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1255 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1255 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1900
Gorilla gorilla	retro_ggor_1393
Callithrix jacchus	retro_cjac_1101

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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,