RetrogeneDB ID: retro_pabe_427

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1:110582749..110583181(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: VPS25
• Ensembl ID: ENSPPYG00000008377
• Aliases: None
• Description: vacuolar protein sorting 25 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:28122]

Sequence

>retro_pabe_427
ATGGTGATGAATTTCAAGTGGTTGTGGCAGTATTGCTTCCCACCCTTTACATTACAGCTGAACGTGGCCACTTGGCAGAA
GCAGCTGGCCACCTGGTGTTCGTTGGTTCTGTCCGTTTGCTGCCTGCACAAACAGTCCAGCATGATGGTGATGGATGCTC
AGGAGATCCTGCTCTTTGGCAACATCAAGCTGTGGAAGCTTCCTGTGGGATCAATCCAGGTTGTATTAGAGGAACTGAGG
AATGGGAACTTACAGTGGCTGGATGAGAGCAAGTCTAGTTTCCTAATCATGTGGCAGAGGCCAGAAGAATGGGGAAAACT
CATCTATCAGTGGGTCTCCAGGAGTGGCCAGAACAACTCCATACTTAGCCTGTATGAGCTGACCAATGGGGAAGACATAG
AGAATGAGGTGTTCCATGGACTAAAGAAGGCC

Alignment

ORF - retro_pabe_427 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.86 %
• Parental protein coverage: 83.33 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAMSFEWPWQYRFPPFFTLQPNVDTRQKQLAAWCSLVLSFCRLHKQSSMTVMEAQESPLFNNVKLQRKLP
          M.M.F.W.WQY.FPPF.TLQ.NV.T.QKQLA.WCSLVLS.C.LHKQSSM.VM.AQE..LF.N.KL..KLP
Retrocopy MVMNFKWLWQYCFPPF-TLQLNVATWQKQLATWCSLVLSVCCLHKQSSMMVMDAQEILLFGNIKLW-KLP

Parental  VESIQIVLEELRKKGPRVVDKSKSSFLIMW-RSQKMGELIYQWVSRSGQNNSVFTLYELTNGEDTEDEEF
          V.SIQ.VLEELR.......D.SKSSFLIMW.R....G.LIYQWVSRSGQNNS...LYELTNGED.E.E.F
Retrocopy VGSIQVVLEELRNGNLQWLDESKSSFLIMWQRPEEWGKLIYQWVSRSGQNNSILSLYELTNGEDIENEVF

Parental  HGLDEA
          HGL..A
Retrocopy HGLKKA

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	0.17 RPM	8.46 RPM
SRP007412_cerebellum	0.00 RPM	6.69 RPM
SRP007412_heart	0.09 RPM	6.44 RPM
SRP007412_kidney	0.40 RPM	23.17 RPM
SRP007412_liver	0.15 RPM	17.81 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_427 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_427 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_427 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_213
Pan troglodytes	retro_ptro_334
Gorilla gorilla	retro_ggor_284
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,