RetrogeneDB ID: retro_pabe_913

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 12:33268301..33268693(-)
• Located in intron of: ENSPPYG00000004403

Retrocopy information

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

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_913
CAGTTTGGACAATGAATGCTCAAGGTGGACATTTCAAGCCTCCAGGGGCGAGGCCCCCAACGGAGCCTATGGGTACTCTT
ACATACCCAACAGAGCCTGTCTTTCCTCTACCAGTTGCCAATGCAATGTACCTTTGCCCTCCTGGCTGCCCCAATCCACA
GTCCCCATCTGAGTTCTAGCCAGGACCTCCCATGGTGGATGGAGCTATGGGATGCCTGCAATCCCTGCCACTGCCCTATC
TGGGCTCATGGAACCTCTGGTCCGTGGCCCCATTGGCCCCTCTGCTCTGGCAGCCAAAGCCAGAGCTGCAGAAGCAGTTG
TCAGTGCCAGGCAACCCACACAACACCTACATACCTAGGAACCAGCCTCTGCCACTACACTATTACAGCCCC

Alignment

ORF - retro_pabe_913 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.68 %
• Parental protein coverage: 51.72 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  EFGQRMLQV-ASQASRGEV-PSGAYGYSYMPSGAYVYPPPVANGMYPCPPGYPYPPPPPEFYPGPPMMDG
          .FGQ.ML.V...QASRGE..P....G....P....V.P.PVAN.MY.CPPG.P.P..P.EF.PGPPM.DG
Retrocopy QFGQ*MLKV>TFQASRGEA>PTEPMGTLTYPTEP-VFPLPVANAMYLCPPGCPNPQSPSEF*PGPPMVDG

Parental  AMGYVQPPPPPYPGP-MEPPVSGPDVPSTPAAEAKAAEAAASAYYN-PGNPHNVYMPTSQPPPPPYYPP
          AMG..Q..P.PY.G..MEP.V.GP..PS..A..AKA...AA.A....PGNPHN.Y.P..QP.P..YY.P
Retrocopy AMGCLQSLPLPYLGS<MEPLVRGPIGPS--ALAAKAR--AAEAVVS>PGNPHNTYIPRNQPLPLHYYSP

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	0.06 RPM	436.63 RPM
SRP007412_cerebellum	0.49 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_913 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_913 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_913 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Macaca mulatta	retro_mmul_854

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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,