RetrogeneDB ID: retro_pabe_75

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 18:36717487..36718258(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPPYG00000009073
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: WBP2
• Ensembl ID: ENSPPYG00000008640
• Aliases: None
• Description: WW domain binding protein 2 [Source:HGNC Symbol;Acc:12738]

Sequence

>retro_pabe_75
ATGGTGCTCAACGAGAGTCACTCAGAGGGCAGCAGAATGATTGCCAACAACACTGAGAGCATCCCAATGTCCTACGATCT
TGTGAAACTTACGTTCAGTGACATGAAGAACGTGCCAGAGGCCTCCAAAGGGACCAAGAAAGGCACCATCTACCTTACCT
CTTTCATCTTTCTGTACAGGGCGAAGGATGCTATGCAGTCCTTCGTAATGTCATTTTATCTCGTGAAGACCTGTGAGATC
AAGCAGCCTGTGTTTGATACAAACTACATCAAGGGAACAGTGAACGCCGAAGCAGGCGGTGGCTGGGAAGGCTCTGCTTC
CGGCAAGTCCGCCTGCACGGCAGGGGGCGCCACTGAATCTGGACAGCAGGTGCTCCAGGTGACATCTCAAGCGTCCAGGG
GTGAAGCCCTCAGTGGAGCCTACGGCCACTCTCACATGCCTGGCAGGACTTGTGTCTTTCCCCTGCCAGTCACTAGTGGA
ATGTATCCCTGCCCTCCTGGCTGCCCTTCTCCACCACCTTCGCCTGAGTTCTATCCAGGACCTCCCAAGATGGACAGGGC
CGTGGGGTATGTGCAGCCCCCACCACCGCCCTATCCTGGGCCCATGGAACCTCCGGTCAGCCCAGATGTTCCCTGCAGTC
CTGCAGCCGAAGCCAGGGCCACAGAAGTAGCTGCCAGCACCTATTATAACCCAGGCAAACCACACCACGTCTCCATGCCC
ACGAAGCAGCCTCCGCCATCTTACCCGAGGGAAGATAAGAAGACCCAGTAG

Alignment

ORF - retro_pabe_75 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.56 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MALNKNHSEGGGVIVNNTESILMSYDHVELTFNDMKNVPEAFKGTKKGTVYLTPYRVIFLSKGKDAMQSF
          M.LN..HSEG...I.NNTESI.MSYD.V.LTF.DMKNVPEA.KGTKKGT.YLT....IFL...KDAMQSF
Retrocopy MVLNESHSEGSRMIANNTESIPMSYDLVKLTFSDMKNVPEASKGTKKGTIYLTSF--IFLYRAKDAMQSF

Parental  MMPFYLMKDCEIKQPVFGANYIKGTVKAEAGGGWEGSASYKLTFTAGGAIEFGQRMLQVASQASRGEVPS
          .M.FYL.K.CEIKQPVF..NYIKGTV.AEAGGGWEGSAS.K...TAGGA.E.GQ..LQV.SQASRGE..S
Retrocopy VMSFYLVKTCEIKQPVFDTNYIKGTVNAEAGGGWEGSASGKSACTAGGATESGQQVLQVTSQASRGEALS

Parental  GAYGYSYMPSGAYVYPPPVANGMYPCPPGYPYPPPPPEFYPGPPMMDGAMGYVQPPPPPYPGPMEPPVSG
          GAYG.S.MP....V.P.PV..GMYPCPPG.P.PPP.PEFYPGPP.MD.A.GYVQPPPPPYPGPMEPPVS.
Retrocopy GAYGHSHMPGRTCVFPLPVTSGMYPCPPGCPSPPPSPEFYPGPPKMDRAVGYVQPPPPPYPGPMEPPVS-

Parental  PDVPSTPAAEAKAAEAAASAYYNPGNPHNVYMPTSQPPPPPYYPPEDKKTQ
          PDVP..PAAEA.A.E.AAS.YYNPG.PH.V.MPT.QPPP...YP.EDKKTQ
Retrocopy PDVPCSPAAEARATEVAASTYYNPGKPHHVSMPTKQPPPS--YPREDKKTQ

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	436.63 RPM
SRP007412_cerebellum	0.00 RPM	132.55 RPM
SRP007412_heart	0.00 RPM	51.30 RPM
SRP007412_kidney	0.00 RPM	117.54 RPM
SRP007412_liver	0.00 RPM	42.72 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_75 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_75 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_75 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1926
Pan troglodytes	retro_ptro_15
Gorilla gorilla	retro_ggor_1404

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000004946	1 retrocopy	retro_cfam_1038,
Callithrix jacchus	ENSCJAG00000037619	1 retrocopy	retro_cjac_575,
Felis catus	ENSFCAG00000005760	1 retrocopy	retro_fcat_1454,
Homo sapiens	ENSG00000132471	1 retrocopy	retro_hsap_1926,
Gorilla gorilla	ENSGGOG00000009241	2 retrocopies	retro_ggor_1404, retro_ggor_698,
Macropus eugenii	ENSMEUG00000000070	1 retrocopy	retro_meug_579,
Macaca mulatta	ENSMMUG00000009381	2 retrocopies	retro_mmul_1062, retro_mmul_854,
Monodelphis domestica	ENSMODG00000007725	3 retrocopies	retro_mdom_1410, retro_mdom_1847, retro_mdom_375,
Mustela putorius furo	ENSMPUG00000013775	1 retrocopy	retro_mputfur_645,
Nomascus leucogenys	ENSNLEG00000001625	1 retrocopy	retro_nleu_1214,
Ochotona princeps	ENSOPRG00000006045	2 retrocopies	retro_opri_301, retro_opri_851,
Pongo abelii	ENSPPYG00000008640	3 retrocopies	retro_pabe_693, retro_pabe_75 , retro_pabe_913,
Pan troglodytes	ENSPTRG00000009660	1 retrocopy	retro_ptro_15,
Ictidomys tridecemlineatus	ENSSTOG00000021421	2 retrocopies	retro_itri_1585, retro_itri_660,