RetrogeneDB ID: retro_ptro_2353

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 6:53377932..53378277(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SH3BGRL3
• Ensembl ID: ENSPTRG00000000379
• Aliases: None
• Description: SH3 domain-binding glutamic acid-rich-like protein [Source:UniProtKB/TrEMBL;Acc:K7CEW1]

Sequence

>retro_ptro_2353
TCTCCTCATAGTGCAGGTGCCATTACCGCCGCCCTCTGCCCTCTGGCCTGTCAATCTACCTGCAGCATGAGCAGCCTGCA
CCTCTACAGCACATCAGTCACTGGCTCCCACAAAATCAAGTCCCAGCAGAGTGAGGTGACCTGAATCCTGGATAGGAAGT
GCATCTAATACCAACTAGTGGACATCTCCCAGGACAACGCCCTGAGGGATGAGATGCGAGTCTTGGTGGGCAACTCCAAG
GCTGCCCCACCCCGGATTGTCAATGGGGACCACTACCGTGGAGGCTTTGAGCTCTTCATGGAGGCTGTGGAACAAAACAT
GCTGCAGGAGTTCTTGAAACCGGCC

Alignment

ORF - retro_ptro_2353 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.65 %
• Parental protein coverage: 50.88 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SPGSAAAATAALCPPARLSTPSMSGLRVYSTSVTGSREIKSQQSEVTRILDGKRIQYQLVDISQDNALRD
          SP.SA.A.TAALCP.A..ST.SMS.L..YSTSVTGS..IKSQQSEVT.ILD.K.I.YQLVDISQDNALRD
Retrocopy SPHSAGAITAALCPLACQSTCSMSSLHLYSTSVTGSHKIKSQQSEVT*ILDRKCI*YQLVDISQDNALRD

Parental  EMRALAGNPKATPPQIVNGDQYCGDYELFVEAVEQNTLQEFLKLA
          EMR.L.GN.KA.PP.IVNGD.Y.G..ELF.EAVEQN.LQEFLK.A
Retrocopy EMRVLVGNSKAAPPRIVNGDHYRGGFELFMEAVEQNMLQEFLKPA

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	69.16 RPM
SRP007412_cerebellum	0.00 RPM	31.58 RPM
SRP007412_heart	0.00 RPM	18.07 RPM
SRP007412_kidney	0.00 RPM	45.37 RPM
SRP007412_liver	0.00 RPM	58.14 RPM
SRP007412_testis	0.00 RPM	13.59 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2353 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2353 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2353 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3470

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000012567	1 retrocopy	retro_cfam_1539,
Homo sapiens	ENSG00000142669	1 retrocopy	retro_hsap_3470,
Macropus eugenii	ENSMEUG00000007201	1 retrocopy	retro_meug_388,
Nomascus leucogenys	ENSNLEG00000009265	1 retrocopy	retro_nleu_341,
Pan troglodytes	ENSPTRG00000000379	1 retrocopy	retro_ptro_2353 ,