RetrogeneDB ID: retro_ptro_2971

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: GL389466.1:10619..11189(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000011894
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RHOJ
• Ensembl ID: ENSPTRG00000006424
• Aliases: None
• Description: None

Sequence

>retro_ptro_2971
ATGCTCAAGTGCGTGGTGGTCGGCGACGGGGCGGTGGGCAAGACGTGCCCACTCATGAGCTATGCCAACGAAGCCTTCCC
GGAGGAGTATGTGCCCACCGTCTTCCACCACTAAGCAGTCAGCGTCACCGTGGGGGGCAAGCAGTACCTCCTAGGACTCT
ATGACACGGCCGGACAGGAAGACTATGACTGTCTGAGGCCTTCATCTTACCCAGTGACCGACGTCTTCCTTATATGCTTC
TCGGTGGTAAATCCAGCCTCATTTCAAAATGTGAAAGAGGAGTGGGTACCGGAACTTAAGGAATACGCACCAAATGTACC
CTTTTTATTAATAGGAACTCAGATTGATCTCCGAGATGACCCCAAAAGTTTAGCAAGACTGAAGGATATGAAAGAAAAAC
CTATATGTGTGGAACAAGGACAGAAACTAGCAAAAGAGATAGGAGCATGCTGCTATGTGGAATGTTCAGCTTTAACCCAG
AAGGGATTGAAGACTGTTTTTGATGAGGCTGTCATAGCCATTTTAACTCCAAAGAAACACACTGTAAAAAAAAGAATAGG
ATCAAGATGT

Alignment

ORF - retro_ptro_2971 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.32 %
• Parental protein coverage: 88.79 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MLKCVVVGDGAVGKTCLLMSYANDAFPEEYVPTVFDHYAVTVTVGGKQHLLGLYDTAGQEDYNQLRPLSY
          MLKCVVVGDGAVGKTC.LMSYAN.AFPEEYVPTVF.H.AV.VTVGGKQ.LLGLYDTAGQEDY..LRP.SY
Retrocopy MLKCVVVGDGAVGKTCPLMSYANEAFPEEYVPTVFHH*AVSVTVGGKQYLLGLYDTAGQEDYDCLRPSSY

Parental  PNTDVFLICFSVVNPASYHNVQEEWVPELKDCMPHVPYVLIGTQIDLRDDPKTLARLLYMKEKPLTYEHG
          P.TDVFLICFSVVNPAS..NV.EEWVPELK...P.VP..LIGTQIDLRDDPK.LARL..MKEKP...E.G
Retrocopy PVTDVFLICFSVVNPASFQNVKEEWVPELKEYAPNVPFLLIGTQIDLRDDPKSLARLKDMKEKPICVEQG

Parental  VKLAKAIGAQCYLECSALTQKGLKAVFDEAILTIFHPKKKKKRCSEGHSC
          .KLAK.IGA.CY.ECSALTQKGLK.VFDEA...I..PKK.......G..C
Retrocopy QKLAKEIGACCYVECSALTQKGLKTVFDEAVIAILTPKKHTXXXXIGSRC

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	0.11 RPM	2.47 RPM
SRP007412_cerebellum	0.00 RPM	3.73 RPM
SRP007412_heart	0.03 RPM	9.65 RPM
SRP007412_kidney	0.00 RPM	6.01 RPM
SRP007412_liver	0.00 RPM	4.78 RPM
SRP007412_testis	0.00 RPM	2.32 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2971 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2971 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2971 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2158

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000001761	2 retrocopies	retro_dnov_192, retro_dnov_927,
Gorilla gorilla	ENSGGOG00000007948	1 retrocopy	retro_ggor_22,
Pan troglodytes	ENSPTRG00000006424	4 retrocopies	retro_ptro_1643, retro_ptro_2091, retro_ptro_2971 , retro_ptro_910,
Pan troglodytes	ENSPTRG00000018910	4 retrocopies	retro_ptro_1288, retro_ptro_3044, retro_ptro_3274, retro_ptro_36,
Vicugna pacos	ENSVPAG00000004859	2 retrocopies	retro_vpac_574, retro_vpac_588,