RetrogeneDB ID: retro_ggor_1259

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 16:28502602..28503121(-)
• Located in intron of: ENSGGOG00000017086

Retrocopy information

• Ensembl ID: ENSGGOG00000009325
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: VHL
• Ensembl ID: ENSGGOG00000010456
• Aliases: None
• Description: None

Sequence

>retro_ggor_1259
CAGGCGGGCACCCAGGAGGCAGGCCCAGAAGAGTACTGCCAGGAAGAGTTCGGCGCCGAGGAGGAGATGGCAGCCGGAGC
AGCATGGCCTGTGCTGCGCTCTGTGAACTCACACGAGCTCTCCCGGATCATCATCTGCAATCACAGCCCACGAATCGTGC
TGCCTGTGTGGCTCAACTACTATGGCGAGCTGCTGCCCTACCTGACGCTGCTGCCCGGCAGGGACTTCCGCATCCACAAC
TTCCGAAGCCACCCTTGGCTCTTCAGAGATGCAAGGATACATGGTAAGCTTCTGGTTAACCAAACTGAATTGTTTGTGCC
ATCTTCCAATGTTATTGGACAGCCTGTTTTTGCCAACATCACACTGCAGTGTATACCCTGAAAGAGCAATGCCTCCAGGT
TGTCGGAAGCCTAGTCAAGCCCAAGAATTACAGGAGACTGGACATCGTCAGATCACTCTGTGATGATCTGGAAGATCATC
CAAATGTGCTTGAAAGACCTGGAGCGGCTGACGCAGGAG

Alignment

ORF - retro_ggor_1259 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.43 %
• Parental protein coverage: 81.22 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ESSAEESGPEESGPEELGAEEEMEAGRPRPVLRSVNSREPSQVIFCNRSPRVVLPVWLNFDGEPQPYPTL
          .....E.GPEE...EE.GAEEEM.AG...PVLRSVNS.E.S..I.CN.SPR.VLPVWLN..GE..PY.TL
Retrocopy QAGTQEAGPEEYCQEEFGAEEEMAAGAAWPVLRSVNSHELSRIIICNHSPRIVLPVWLNYYGELLPYLTL

Parental  PPGTGRRIHSYRGHLWLFRDAGTHDGLLVNQTELFVPSLNVDGQPIFANITL-PVYTLKERCLQVVRSLV
          .PG...RIH..R.H.WLFRDA..H..LLVNQTELFVPS.NV.GQP.FANITL..VYTLKE.CLQVV.SLV
Retrocopy LPGRDFRIHNFRSHPWLFRDARIHGKLLVNQTELFVPSSNVIGQPVFANITL<AVYTLKEQCLQVVGSLV

Parental  KPENYRRLDIVRSLYEDLEDHPNV-QKDLERLTQE
          KP.NYRRLDIVRSL..DLEDHPNV..KDLERLTQE
Retrocopy KPKNYRRLDIVRSLCDDLEDHPNV>LKDLERLTQE

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	26.81 RPM
SRP007412_cerebellum	0.04 RPM	33.69 RPM
SRP007412_heart	0.00 RPM	3.78 RPM
SRP007412_kidney	0.00 RPM	22.49 RPM
SRP007412_liver	0.00 RPM	14.30 RPM
SRP007412_testis	0.00 RPM	42.37 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_1259 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1259 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,