RetrogeneDB ID: retro_ptro_462

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 10:119064721..119065374(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAD1
• Ensembl ID: ENSPTRG00000016783
• Aliases: None
• Description: None

Sequence

>retro_ptro_462
ATGCCCCTCCTGACCCAACAGATCCAAGACGAGCATGATCAATACAGTCTTGTGGCCAGCCTTGACAATGTTAGGAATCT
CTCCACTATCTTAAAAGCTATTCATTTCCGAAAATGTGCCGTGTGTTTCGCAACTAAAAATGGAATCAAAGTAACAATGG
AAAACGCAAAGTGTGTGCAAGCAAATGCTTTTATTCAGGCTGGAATATTTCAAGAGCTTAAAGTTCAGGAAGAGTCTGTT
ACTTTTTGAATTAATTTCATTGTCCTTTTAGACTGTTTATCTATTTTTGGATCAAGTCCTATGCCAGGGACTTGAACTGC
ACTTCGGATGTGTTACCAAGGTTATGGTTACCCTTTGATGCTCTTCCTGGAAGAAGCAGGAGAGGTGGCAGTCTGCAAAA
TCAATACACAGGAACCTGAAGGGACCTGGACTTTAATTTCTACAGCACTAATGTTATTGATAAAATTCTGCAGTCAGAGG
GGCTCTGTGAAGCTTTTTCTGAATTGGATATGACGAGTGAGGTCCTACAAATTACCATGTCTCCTGACAAGCCTTATTTC
AGGTTATCTACTTTTGGAAATGTAGGAAGTTCCCACCTTGACCGCCCCAAAGATTCTGATTTGATGGAAGCATTATAATC
AGACCCAAGTCAA

Alignment

ORF - retro_ptro_462 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.27 %
• Parental protein coverage: 77.66 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPLLTQQIQDEDDQYSLVASLDNVRNLSTILKAIHFREHATCFATKNGIKVTVENAKCVQANAFIQAGIF
          MPLLTQQIQDE.DQYSLVASLDNVRNLSTILKAIHFR..A.CFATKNGIKVT.ENAKCVQANAFIQAGIF
Retrocopy MPLLTQQIQDEHDQYSLVASLDNVRNLSTILKAIHFRKCAVCFATKNGIKVTMENAKCVQANAFIQAGIF

Parental  QEFKVQEESVTFRINLTVLLDCLSIFGSSPMPGTLTALRMCYQGYGYPLMLFLEEGGVVTVCKINTQEPE
          QE.KVQEESVTF.IN..VLLDCLSIFGSSPMPGT.TALRMCYQGYGYPLMLFLEE.G.V.VCKINTQEPE
Retrocopy QELKVQEESVTF*INFIVLLDCLSIFGSSPMPGT*TALRMCYQGYGYPLMLFLEEAGEVAVCKINTQEPE

Parental  ET-LDFDFCSTNVINKIILQSEGLREAFSELDMTSEVLQITMSPDKPYFRLSTFGNAGSSHLDYPKDSDL
          .T.LDF.F.STNVI.K.ILQSEGL.EAFSELDMTSEVLQITMSPDKPYFRLSTFGN.GSSHLD.PKDSDL
Retrocopy GT<LDFNFYSTNVIDK-ILQSEGLCEAFSELDMTSEVLQITMSPDKPYFRLSTFGNVGSSHLDRPKDSDL

Parental  MEAFHCNQTQ
          MEA......Q
Retrocopy MEAL*SDPSQ

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	0.04 RPM	5.22 RPM
SRP007412_cerebellum	0.00 RPM	6.38 RPM
SRP007412_heart	0.00 RPM	7.61 RPM
SRP007412_kidney	0.00 RPM	7.48 RPM
SRP007412_liver	0.00 RPM	5.47 RPM
SRP007412_testis	0.00 RPM	11.80 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_462 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_462 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_462 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_634
Gorilla gorilla	retro_ggor_555
Pongo abelii	retro_pabe_564
Callithrix jacchus	retro_cjac_1004

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018514	1 retrocopy	retro_cjac_1004,
Homo sapiens	ENSG00000113456	1 retrocopy	retro_hsap_634,
Gorilla gorilla	ENSGGOG00000004219	1 retrocopy	retro_ggor_555,
Macaca mulatta	ENSMMUG00000030184	1 retrocopy	retro_mmul_54,
Nomascus leucogenys	ENSNLEG00000014437	1 retrocopy	retro_nleu_455,
Otolemur garnettii	ENSOGAG00000014822	2 retrocopies	retro_ogar_2296, retro_ogar_2726,
Pongo abelii	ENSPPYG00000015389	1 retrocopy	retro_pabe_564,
Pan troglodytes	ENSPTRG00000016783	1 retrocopy	retro_ptro_462 ,
Tarsius syrichta	ENSTSYG00000002894	1 retrocopy	retro_tsyr_738,