RetrogeneDB ID: retro_ptro_334

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 1:119164583..119165019(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: VPS25
• Ensembl ID: ENSPTRG00000009220
• Aliases: None
• Description: Pan troglodytes vacuolar protein sorting 25 homolog (S. cerevisiae) (VPS25), mRNA. [Source:RefSeq mRNA;Acc:NM_001252014]

Sequence

>retro_ptro_334
ATGGTGATGAATTTCAAGTGGTTGTGGCAGTATCGCTTTCCCGCCCTTTACATTACAGCTGAACGTGGCCACTTGGCAGA
AGCAGCTGGCCACCTGGTGTTCGTTGGTTCTGTCCATCTGCTGCCTGCACAGACAGTCCAGCATGATGGTTATGGATGCT
CAGGAGATCCTGCTCTTCAGCAACATCAAGCTGTGGAAGCTTCCTGTGGGATCAATCCAGGTTGTATTAGAGGAACTGAG
GAAGAATGGGAACTTACAGTGGCTGGATAAGAGCAAGTCTAGTTTCCTAATCATGTGGCGGAGGCCAGAAGAATGGGGAA
AACTCATCTATCAGTGGGTCTCCAGGAGTGGCCAGAACAACTCCGTACTCAGCCTGTATGAGCTGACCAATGGGGAAGAC
ATAGAGAATGAGGTGTTCCACGGACTAAAGGAGGCC

Alignment

ORF - retro_ptro_334 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.05 %
• Parental protein coverage: 83.52 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAMSFEWPWQYRF-PPFFTLQPNVDTRQKQLAAWCSLVLSFCRLHKQSSMTVMEAQESPLFNNVKLQRKL
          M.M.F.W.WQYRF.PPF.TLQ.NV.T.QKQLA.WCSLVLS.C.LH.QSSM.VM.AQE..LF.N.KL..KL
Retrocopy MVMNFKWLWQYRF>PPF-TLQLNVATWQKQLATWCSLVLSICCLHRQSSMMVMDAQEILLFSNIKLW-KL

Parental  PVESIQIVLEELRKKGNLEWLDKSKSSFLIMWRRPEEWGKLIYQWVSRSGQNNSVFTLYELTNGEDTEDE
          PV.SIQ.VLEELRK.GNL.WLDKSKSSFLIMWRRPEEWGKLIYQWVSRSGQNNSV..LYELTNGED.E.E
Retrocopy PVGSIQVVLEELRKNGNLQWLDKSKSSFLIMWRRPEEWGKLIYQWVSRSGQNNSVLSLYELTNGEDIENE

Parental  EFHGLDEA
          .FHGL.EA
Retrocopy VFHGLKEA

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	0.02 RPM	5.77 RPM
SRP007412_cerebellum	0.00 RPM	3.84 RPM
SRP007412_heart	0.03 RPM	2.89 RPM
SRP007412_kidney	0.00 RPM	9.91 RPM
SRP007412_liver	0.00 RPM	5.92 RPM
SRP007412_testis	0.00 RPM	3.37 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_334 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_334 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_334 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_213
Gorilla gorilla	retro_ggor_284
Pongo abelii	retro_pabe_427
Macaca mulatta	retro_mmul_406

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000013276	1 retrocopy	retro_cjac_2959,
Homo sapiens	ENSG00000131475	1 retrocopy	retro_hsap_213,
Gorilla gorilla	ENSGGOG00000016041	1 retrocopy	retro_ggor_284,
Macropus eugenii	ENSMEUG00000011611	2 retrocopies	retro_meug_1247, retro_meug_1681,
Macaca mulatta	ENSMMUG00000002149	1 retrocopy	retro_mmul_406,
Nomascus leucogenys	ENSNLEG00000011797	1 retrocopy	retro_nleu_1862,
Ochotona princeps	ENSOPRG00000012574	1 retrocopy	retro_opri_1071,
Pongo abelii	ENSPPYG00000008377	1 retrocopy	retro_pabe_427,
Pan troglodytes	ENSPTRG00000009220	2 retrocopies	retro_ptro_1624, retro_ptro_334 ,