RetrogeneDB ID: retro_pabe_275

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1:95196508..95196947(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: VHL
• Ensembl ID: ENSPPYG00000013663
• Aliases: None
• Description: von Hippel-Lindau disease tumor suppressor [Source:RefSeq peptide;Acc:NP_001126390]

Sequence

>retro_pabe_275
AAGGCGGGCACCCAGGAGGCAGGCCCAGAAGAGTACTGCCAGGAAGAGTTGGGCACCGAGGAGGAGATGGCAGCCAGAGC
AGCATGGCCTGTGCTGCGCTCTGTGAACTCGCGCGAGCTCTCCCGGATCATCATCTGCAATCACAGCCCACGAATCGTGC
TGCCTGTGTGGCTCAACTACTATGGCGAGCTGCTGCCCTACCTGACGCTGCTGCCTGCAGGGACTTCCGCATCCACAACT
TCTAAAGCCACGCTTGGCTCTTCAGAGATGCAAGGACACACGATAAGCTTCTGGTTAACCAAACTGAATTATTTGTGCCA
TCTTCCAATGTTAACGGACAGCCTATTTTTGCCAACATCACACTGCAGTGTATACCCTGAAAGAGCAATGCCTCCAGGTT
GTCGGAAGCCTAGTCAAGCCCAAGAATTACAGGAGACTG

Alignment

ORF - retro_pabe_275 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.8 %
• Parental protein coverage: 69.01 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ESGAEESGPEESGPEELGAEEEMEAGRPRPVLRSVNSREPSQVIFCNRSPRVVLPVWLNFDGEPQPYPTL
          ..G..E.GPEE...EELG.EEEM.A....PVLRSVNSRE.S..I.CN.SPR.VLPVWLN..GE..PY.TL
Retrocopy KAGTQEAGPEEYCQEELGTEEEMAARAAWPVLRSVNSRELSRIIICNHSPRIVLPVWLNYYGELLPYLTL

Parental  PPG-TGRRIHSYRGHLWLFRDAGTHDGLLVNQTELFVPSLNVDGQPIFANITL-PVYTLKERCLQVVRSL
          .P.....RIH....H.WLFRDA.THD.LLVNQTELFVPS.NV.GQPIFANITL..VYTLKE.CLQVV.SL
Retrocopy LPA<RDFRIHNF*SHAWLFRDARTHDKLLVNQTELFVPSSNVNGQPIFANITL<AVYTLKEQCLQVVGSL

Parental  VKPENYRRL
          VKP.NYRRL
Retrocopy VKPKNYRRL

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	35.11 RPM
SRP007412_cerebellum	0.12 RPM	47.42 RPM
SRP007412_heart	0.00 RPM	5.84 RPM
SRP007412_kidney	0.03 RPM	17.47 RPM
SRP007412_liver	0.00 RPM	9.64 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_275 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_275 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_275 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Gorilla gorilla	ENSGGOG00000010456	1 retrocopy	retro_ggor_1259,
Otolemur garnettii	ENSOGAG00000007587	1 retrocopy	retro_ogar_2307,
Pongo abelii	ENSPPYG00000013663	1 retrocopy	retro_pabe_275 ,
Ictidomys tridecemlineatus	ENSSTOG00000013959	1 retrocopy	retro_itri_1624,