RetrogeneDB ID: retro_pabe_3738

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: X:41461552..41462443(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DKFZP459C0145
• Ensembl ID: ENSPPYG00000018612
• Aliases: None
• Description: syntenin-1 [Source:RefSeq peptide;Acc:NP_001125892]

Sequence

>retro_pabe_3738
ATGTCTCTCTATCTATCTCTTGAAGACTTGAAGGTAGACAAAGTAATTGGGGCTCAAACTACTTTTTCTGCAAACTCTGC
CAATCCAGCAATTTTGTCAGAAGCTTCTGCTCCCATCTCTCAAAATGGAAATCTGTATCCCAAATTATATCCGGAGCTCT
CTCAATACATGGGCCTGAGTTTAAATGAAGAAGAAATATGTGCAAATGTGGCCATGGTTTCTGGTGCACCAATTCAAGGG
CAGTTGGTAGCAAGACCTTCCAGTATGAACTATATGGTGGCTCCTGTAACTTGTAATGATGTTGGAATTCACAGAACAGA
AATTAAGCAAGGGATTCGTGAAGTCATTTTGTGTAACGATCAAGATGGAAAAATTGGACTCAGGCTTAAATCAATAGATA
ATGGTATATTTGTTCAGCTAGTCCAGGCTAATTCTCCAGCCTCATTGGTTGGTCTGACAATTGAGGACCAAGTACTCCAG
ATTAATAGTGAAAACTGTGCAGGGTAGAGCTCTGATAAAGCGCACAAGGTGCTCAAACAGGATTTTGGAGAGATTACCAT
GACCATTCATGACAGGCCCTTTGAACGGACGATTACCATGCATAAGGATAGCACTGGACATGTTGGTTTTATCTTTAAAA
ACGGAAAAATAACATCCATAGTGAAAGATAGCTCTGCAGCCAGAAGTGGTCTTCTCACAGAACATAACATCTGTGAAATC
AATGGACACAATGTCATTGAATTGAAGGACTCTCAAATTGCAGACATACTGTCAACATCTGGGACTGTAGTTACTATTAC
AATTATGCCTGCTTTTATCTTTGAACATATTATTAAGCGGATGGTACCAAGCATTATGAAAAGCCTAACGGACCACACCA
TTTCTGAGGTT

Alignment

ORF - retro_pabe_3738 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.26 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSLYPSLEDLKVDKVIQAQTAFSANPANPAILSEASAPIPHDGNLYPRLYPELSQYMGLSLNEEEIRANM
          MSLY.SLEDLKVDKVI.AQT.FSAN.ANPAILSEASAPI...GNLYP.LYPELSQYMGLSLNEEEI.AN.
Retrocopy MSLYLSLEDLKVDKVIGAQTTFSANSANPAILSEASAPISQNGNLYPKLYPELSQYMGLSLNEEEICANV

Parental  AVVSGAPLQG-LVARPSSMNYMVAPVTGNDAGIRRAEIKQGIREVILCKDQDGKIGLRLKSIDNGIFVQL
          A.VSGAP.QG.LVARPSSMNYMVAPVT.ND.GI.R.EIKQGIREVILC.DQDGKIGLRLKSIDNGIFVQL
Retrocopy AMVSGAPIQGQLVARPSSMNYMVAPVTCNDVGIHRTEIKQGIREVILCNDQDGKIGLRLKSIDNGIFVQL

Parental  VQANSPASLVGLRFGDQVLQINGENCAGWSSDKAHKVLKQAFGEKITMTIRDRPFERTITMHKDSTGHVG
          VQANSPASLVGL...DQVLQIN.ENCAG.SSDKAHKVLKQ.FGE.ITMTI.DRPFERTITMHKDSTGHVG
Retrocopy VQANSPASLVGLTIEDQVLQINSENCAG*SSDKAHKVLKQDFGE-ITMTIHDRPFERTITMHKDSTGHVG

Parental  FIFKNGKITSIVKDSSAARNGLLTEHNICEINGQNVIGLKDSQIADILSTSGTVVTITIMPAFIFEHIIK
          FIFKNGKITSIVKDSSAAR.GLLTEHNICEING.NVI.LKDSQIADILSTSGTVVTITIMPAFIFEHIIK
Retrocopy FIFKNGKITSIVKDSSAARSGLLTEHNICEINGHNVIELKDSQIADILSTSGTVVTITIMPAFIFEHIIK

Parental  RMAPSIMKSLMDHTIPEV
          RM.PSIMKSL.DHTI.EV
Retrocopy RMVPSIMKSLTDHTISEV

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	1.99 RPM	101.24 RPM
SRP007412_cerebellum	0.61 RPM	69.80 RPM
SRP007412_heart	0.60 RPM	52.50 RPM
SRP007412_kidney	1.92 RPM	151.51 RPM
SRP007412_liver	1.35 RPM	98.97 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3738 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3738 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3738 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4810
Pan troglodytes	retro_ptro_3200
Gorilla gorilla	retro_ggor_2995
Macaca mulatta	retro_mmul_2564

---

Parental genes homology:

Parental genes homology involve 18 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006161	1 retrocopy	retro_amel_654,
Bos taurus	ENSBTAG00000019910	2 retrocopies	retro_btau_1035, retro_btau_383,
Canis familiaris	ENSCAFG00000007112	1 retrocopy	retro_cfam_112,
Choloepus hoffmanni	ENSCHOG00000003565	5 retrocopies	retro_chof_1063, retro_chof_1151, retro_chof_1910, retro_chof_713, retro_chof_970,
Equus caballus	ENSECAG00000015053	1 retrocopy	retro_ecab_439,
Homo sapiens	ENSG00000137575	2 retrocopies	retro_hsap_3971, retro_hsap_4810,
Gorilla gorilla	ENSGGOG00000009019	2 retrocopies	retro_ggor_2666, retro_ggor_2995,
Loxodonta africana	ENSLAFG00000010757	1 retrocopy	retro_lafr_1044,
Microcebus murinus	ENSMICG00000003968	1 retrocopy	retro_mmur_170,
Myotis lucifugus	ENSMLUG00000004807	1 retrocopy	retro_mluc_12,
Macaca mulatta	ENSMMUG00000017296	1 retrocopy	retro_mmul_2564,
Mustela putorius furo	ENSMPUG00000010339	5 retrocopies	retro_mputfur_1055, retro_mputfur_1340, retro_mputfur_292, retro_mputfur_829, retro_mputfur_933,
Nomascus leucogenys	ENSNLEG00000001408	2 retrocopies	retro_nleu_2185, retro_nleu_2525,
Otolemur garnettii	ENSOGAG00000013462	1 retrocopy	retro_ogar_3259,
Procavia capensis	ENSPCAG00000016432	1 retrocopy	retro_pcap_186,
Pongo abelii	ENSPPYG00000018612	3 retrocopies	retro_pabe_3265, retro_pabe_3266, retro_pabe_3738 ,
Pan troglodytes	ENSPTRG00000020277	2 retrocopies	retro_ptro_2696, retro_ptro_3200,
Tupaia belangeri	ENSTBEG00000013965	1 retrocopy	retro_tbel_2142,