RetrogeneDB ID: retro_ptro_15

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 18:20722579..20723290(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000042188
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: WBP2
• Ensembl ID: ENSPTRG00000009660
• Aliases: WBP2, CERS2, LASS2
• Description: WW domain binding protein 2 [Source:HGNC Symbol;Acc:12738]

Sequence

>retro_ptro_15
ATCCCAATGTCCTACGATCATGTGAAACTTACGTTCAGTGACATGAAGAACGTGCCAGAGGCCTCCAAAGGGACCAAGAA
AGGCACCGTCTACCTTACCCCTTTCATCTTTCTGTCCAGGGCGAAGGATGCCATGCAGTCCTTCGTAATGTCATTTTATC
TCTTGAAGGCCTGTGAGATCAAGCAGCCTGTGTTTGACACAAACTGCATCAAGGGAACAGTGAACGCCGAAGCAGGCGGT
GGCTGGGAAGGCTCTGCTTCCGGCAAGTCCGCCTTCACGGCAGGGGGCGCCACTGAATCTGGACAGCAGGTGCTCCAGGT
GACATCTCAAGCGTCCAGGGGTGAAGCCCTCAGTGGAGCCTACGGCCACTCTCACATGCCTGGCAGGACTTGTGTCTTTC
CCCCGCCAGTCACTAGTGGAATGTATCCCTGCCCTCCTGGCTGCCCTTCTCCACCACCTTCCCCTGAGTTCTATCCAGGA
CCTCCCAAGATGGACAGGGCCATGGGGTATGTGCAGCCCCCGCCACCGCCCTATCCTGGGCCCATGGAACCTCCGGTCAG
CGCAGATGTTCCCTGCACTCCTGCAGCCGAAGCCAGGGCCACAAAAGCAGCTGCCAGCACCTATTATAACCCAGGCAAAC
CACACCACGTCTCCATGCCCACGAAGCATCCTCCGCCATCTTACCCGAGGGAAGATAAGAAGACCCAGTAG

Alignment

ORF - retro_ptro_15 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.48 %
• Parental protein coverage: 70.45 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ILMSYDHVELTFNDMKNVPEAFKGTKKGTVYLTPYRVIFLSKGKDAMQSFMMPFYLMKDCEIKQPVFGAN
          I.MSYDHV.LTF.DMKNVPEA.KGTKKGTVYLTP...IFLS..KDAMQSF.M.FYL.K.CEIKQPVF..N
Retrocopy IPMSYDHVKLTFSDMKNVPEASKGTKKGTVYLTPF--IFLSRAKDAMQSFVMSFYLLKACEIKQPVFDTN

Parental  YIKGTVKAEAGGGWEGSASYKLTFTAGGAIEFGQRMLQVASQASRGEVPSGAYGYSYMPSGAYVYPPPVA
          .IKGTV.AEAGGGWEGSAS.K..FTAGGA.E.GQ..LQV.SQASRGE..SGAYG.S.MP....V.PPPV.
Retrocopy CIKGTVNAEAGGGWEGSASGKSAFTAGGATESGQQVLQVTSQASRGEALSGAYGHSHMPGRTCVFPPPVT

Parental  NGMYPCPPGYPYPPP
          .GMYPCPPG.P.PPP
Retrocopy SGMYPCPPGCPSPPP

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	344.42 RPM
SRP007412_cerebellum	4.05 RPM	377.63 RPM
SRP007412_heart	0.26 RPM	110.26 RPM
SRP007412_kidney	1.10 RPM	180.19 RPM
SRP007412_liver	1.41 RPM	165.70 RPM
SRP007412_testis	0.42 RPM	98.32 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_15 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_15 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_15 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1926
Gorilla gorilla	retro_ggor_1404
Pongo abelii	retro_pabe_75

---

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,