RetrogeneDB ID: retro_ptro_2385

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 6:119734404..119734970(+)
• Located in intron of: ENSPTRG00000018549

Retrocopy information

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

Parental gene information

• Parental gene symbol: SSX9
• Ensembl ID: ENSPTRG00000021857
• Aliases: None
• Description: synovial sarcoma, X breakpoint 9 [Source:HGNC Symbol;Acc:19655]

Sequence

>retro_ptro_2385
ATGAACGGAGACAGCACCTTTGCAAAGAGACCCAGGGATGATGCTCAGATATCAGAGAAGAGACACAAGGCCTTCAATGA
TATTGCCAGATACTTATCTAATAAAGAGTGGGGAAAGCTGAAAAACTCAGAGAAAATCACCCATGTGTATATGAAGAGAA
ACTATGAGACCATGACTAAACTAGGTCTCTAGGCCACCCTCCCAACTTTCATGTATAATACATGGGCTGCAGAATTCCAG
GGGAATGATTCTGATATAGACTAAAACTGCAGGAATCAGGATGAATATCCTCAGATGGCTTTCGGCATGCTACAAGGGAA
CTTTCCAAAGATGATGCCCAAGAAGCCAGCAGAGGAAGGAAATGATTTGAAGGGAGTGCCAGAAGCATCTGGCTCACAAA
ACAATGGGAAACAGCGGTGTCCCCTGGGAAAAGAAAGTACCTCTGAGAAGACTAACAAGACATCTAGACCCAAGAAAAGG
GGGAACATGTCTGGACCCACAGACTGCGAGAGAGAAAGTATCTAGTGATTTATGAAGAGATCAGAGACCCTGAGGAAGAT
GACAAA

Alignment

ORF - retro_ptro_2385 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70. %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MNGDDAFARRPKAGAQIPEKIQKAFDDIAKYFSKKEWEKMKSSEKISYVYMKRKYEAMTKLGFKATLPPF
          MNGD..FA.RP...AQI.EK..KAF.DIA.Y.S.KEW.K.K.SEKI..VYMKR.YE.MTKLG..ATLP.F
Retrocopy MNGDSTFAKRPRDDAQISEKRHKAFNDIARYLSNKEWGKLKNSEKITHVYMKRNYETMTKLGL*ATLPTF

Parental  MRNTGATDLQGNDFDNDRNHRNQVERPQMTFGRLQGIFPKIMPKKPAEVGNDSK-VPEASGSQNNGKQLC
          M.NT.A...QGND.D.D.N.RNQ.E.PQM.FG.LQG.FPK.MPKKPAE.GND.K.VPEASGSQNNGKQ.C
Retrocopy MYNTWAAEFQGNDSDID*NCRNQDEYPQMAFGMLQGNFPKMMPKKPAEEGNDLKGVPEASGSQNNGKQRC

Parental  PPGKRTTSEKINKASGP-KRG-KHAWTHRLSERKQLVIYEEISDPEEDNE
          P.GK..TSEK.NK.S.P.KRG..H.WTHRL.ERK.LVIYEEI.DPEED..
Retrocopy PLGKESTSEKTNKTSRPKKRG<EHVWTHRLRERKYLVIYEEIRDPEEDDK

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	0.07 RPM	0.00 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.12 RPM	0.00 RPM
SRP007412_kidney	1.31 RPM	0.00 RPM
SRP007412_liver	0.16 RPM	0.00 RPM
SRP007412_testis	0.00 RPM	1.05 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2385 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2385 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2385 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3512
Gorilla gorilla	retro_ggor_2374
Pongo abelii	retro_pabe_2903
Macaca mulatta	retro_mmul_1862
Callithrix jacchus	retro_cjac_2373

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000014776	1 retrocopy	retro_cjac_2373,
Pan troglodytes	ENSPTRG00000021857	1 retrocopy	retro_ptro_2385 ,
Ictidomys tridecemlineatus	ENSSTOG00000015375	3 retrocopies	retro_itri_1394, retro_itri_1855, retro_itri_746,