RetrogeneDB ID: retro_ptro_2917

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 9:120274316..120275095(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATP6V1B2
• Ensembl ID: ENSPTRG00000020040
• Aliases: None
• Description: None

Sequence

>retro_ptro_2917
ACTGGGGATATTCTCCAAACATCAGTGTCTGAGGATATGCTTTGTTGGGTATTAGTTGGATCGGGAAAAACCCATTGACA
GAGGTCCTCTTGTACTGGCTGAAGATTTCTTTGATATCATGGGATGGCCAACCAATCCTTAACGTCAAATCTACCCAGAG
GACATGATTCGGACCAGCATTTCAGCCATAGTTGTTATGAACAGTATTGCCGGGGCAGAAAATTTTTATCTTCTCTGCTG
CTGGGTTACTACACAAAGATTGCAGCTCAAATCTGCCACCAGACTGGTTTGCTAAATGAATCCAAAGACGTAGACTACAC
TGAGGAAAATTTTCCAATTGTATTTGCTGCTAAGGATGTAAACATGGAAACTGCCTGGTTCTTCAAATCTGGTGTTGAAG
AAAATGGCTCAATGGACAACATCTGCCTGTTTTTGAACTTGGCTAATGACCCAACTATTGGGTAGATTGTCATCCCTCAC
CTGGTTCTAACCACAGCCGAATTTCTGGCATACCAATATGAGAAACATGTATTGGTTATCCTAACAGATAGGAGTTCATC
TACTGAAGCACTTCAAGAGGTTTCTACAGCCAGAGAAGAGATTCCTGGTTGACGAGGCTTCACAGGTTACACTTATACAG
ACTTAGCCACTTTATATGAACATGCAGGTCGAGGAGAAGGTAGAAATGGCTCGATTACTCAAATTCCTACTCTTACCACG
CCTGCCAACGATATCATTCACCCATCTCTGAACTGACTGGGACAGATCTATGTGGACAG

Alignment

ORF - retro_ptro_2917 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.57 %
• Parental protein coverage: 51.27 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  TGDILRTPVSEDMLGRVFNGSGK-PIDRGPVVLAEDFLDIMGQPINPQCRIYPEEMIQTGISAIDGMNSI
          TGDIL.T.VSEDML..V..GSGK.PIDRGP.VLAEDF.DIMG.P.NP...IYPE.MI.T.ISAI..MNSI
Retrocopy TGDILQTSVSEDMLCWVLVGSGK>PIDRGPLVLAEDFFDIMGWPTNP*RQIYPEDMIRTSISAIVVMNSI

Parental  A-RGQKIPIFSAAGLPHNEIAAQICRQAGLVKKSKDVVDYSEENFAIVFAAMGVNMETARFFKSDFEENG
          A.RG.K.......G.....IAAQIC.Q.GL...SKDV.DY.EENF.IVFAA..VNMETA.FFKS..EENG
Retrocopy A<RGRKFLSSLLLGY-YTKIAAQICHQTGLLNESKDV-DYTEENFPIVFAAKDVNMETAWFFKSGVEENG

Parental  SMDNVCLFLNLANDPTIERIITPRLALTTAEFLAYQCEKHVLVILTDMSSYAEALREVSAAREEVPGRRG
          SMDN.CLFLNLANDPTI..I..P.L.LTTAEFLAYQ.EKHVLVILTD.SS..EAL.EVS.AREE.PG.RG
Retrocopy SMDNICLFLNLANDPTIG*IVIPHLVLTTAEFLAYQYEKHVLVILTDRSSSTEALQEVSTAREEIPG*RG

Parental  FPGYMYTDLATIYERAGRVEGRNGSITQIPILTMPNDDITH-PIPDLTGYITEGQ
          F.GY.YTDLAT.YE.AGR.EGRNGSITQIP.LT.P..DI.H.PI..LTG....GQ
Retrocopy FTGYTYTDLATLYEHAGRGEGRNGSITQIPTLTTPANDIIH<PISELTGTDLCGQ

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	313.37 RPM
SRP007412_cerebellum	0.11 RPM	278.61 RPM
SRP007412_heart	0.06 RPM	28.77 RPM
SRP007412_kidney	0.05 RPM	182.28 RPM
SRP007412_liver	0.00 RPM	37.58 RPM
SRP007412_testis	0.00 RPM	245.44 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2917 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2917 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2917 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4308
Gorilla gorilla	retro_ggor_2879

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003668	1 retrocopy	retro_chof_2287,
Homo sapiens	ENSG00000147416	1 retrocopy	retro_hsap_4308,
Gorilla gorilla	ENSGGOG00000003888	1 retrocopy	retro_ggor_2879,
Microcebus murinus	ENSMICG00000001791	1 retrocopy	retro_mmur_854,
Nomascus leucogenys	ENSNLEG00000000794	1 retrocopy	retro_nleu_1460,
Pan troglodytes	ENSPTRG00000020040	1 retrocopy	retro_ptro_2917 ,
Tarsius syrichta	ENSTSYG00000010477	1 retrocopy	retro_tsyr_2096,
Tursiops truncatus	ENSTTRG00000013650	1 retrocopy	retro_ttru_1845,