RetrogeneDB ID: retro_pabe_564

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 10:119114600..119115247(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAD1
• Ensembl ID: ENSPPYG00000015389
• Aliases: None
• Description: Cell cycle checkpoint protein RAD1 [Source:UniProtKB/Swiss-Prot;Acc:Q5R7X9]

Sequence

>retro_pabe_564
ATGCCCCTCCTGACCCAACAGATCCAAGACAAGAATGATCAATACAGTCTTGTGGCCAGCCTTGACAACGTTAGGAATCT
CTCCATTATCTTAAAAGCTATTCATTTCCAAAAATGTGCCGTGTGTTTCGCAACTAAAAATGGAATCAAAGTAACAATGG
AAATTGCAAAGTGTGTGCAAGCAAATGCTTTTATTCAGGCTGGAATATTTCAAGAGCTTAAAGTTCAGGAAGAGTCTGTT
ACTTTTTGAATTAATTTAATTGTCCTTTTAGACTGTTTATCTATTTTTGGATCAAGTCCCGTGCCAGGGACTTGAACTGC
ACTTCGGATGTGTTACCAAGGTTATAGTTACCCTTTGTTCCTGGAAGAAGAAGGAGTGGTGGCAGTCTGCAAAATCAATA
CACAGGAACCTGAAGTGACCTGGACTTTAATTTCTACAGCACTAATGTTATTGATAAAATTCTGCAGTCAGAGGGGCTCT
GTGAAGCTTTTTCTGAGTTGGATATGATAAGTGAGGTCCTACAAGTTACCATGTCTCCTGACAAGCCTTATTTCAGGTTA
TCTACTTTTGGAAATGTAGGAAGTTCCCACCTTGACGGCCCCAAAGATTCTGATCAGATGGAAGCATTATAATCAGACCC
AAGTCAA

Alignment

ORF - retro_pabe_564 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.18 %
• Parental protein coverage: 77.66 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPLLTQQIQDEDDQYSLVASLDNVRNLSTILKAIHFREHATCFATKNGIKVTVENAKCVQANAFIQAGIF
          MPLLTQQIQD..DQYSLVASLDNVRNLS.ILKAIHF...A.CFATKNGIKVT.E.AKCVQANAFIQAGIF
Retrocopy MPLLTQQIQDKNDQYSLVASLDNVRNLSIILKAIHFQKCAVCFATKNGIKVTMEIAKCVQANAFIQAGIF

Parental  QEFKVQEESVTFRINLTVLLDCLSIFGSSPMPGTLTALRMCYQGYGYPLMLFLEEGGVVTVCKINTQEPE
          QE.KVQEESVTF.INL.VLLDCLSIFGSSP.PGT.TALRMCYQGY.YP..LFLEE.GVV.VCKINTQEPE
Retrocopy QELKVQEESVTF*INLIVLLDCLSIFGSSPVPGT*TALRMCYQGYSYP--LFLEEEGVVAVCKINTQEPE

Parental  ET-LDFDFCSTNVINKIILQSEGLREAFSELDMTSEVLQITMSPDKPYFRLSTFGNAGSSHLDYPKDSDL
          .T.LDF.F.STNVI.K.ILQSEGL.EAFSELDM.SEVLQ.TMSPDKPYFRLSTFGN.GSSHLD.PKDSD.
Retrocopy VT<LDFNFYSTNVIDK-ILQSEGLCEAFSELDMISEVLQVTMSPDKPYFRLSTFGNVGSSHLDGPKDSDQ

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	0.00 RPM	13.21 RPM
SRP007412_cerebellum	0.00 RPM	26.75 RPM
SRP007412_heart	0.00 RPM	7.04 RPM
SRP007412_kidney	0.00 RPM	8.45 RPM
SRP007412_liver	0.00 RPM	7.50 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_564 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_564 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_564 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_634
Pan troglodytes	retro_ptro_462
Gorilla gorilla	retro_ggor_555
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,