RetrogeneDB ID: retro_ggor_2182

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 5:74326853..74327413(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSGGOG00000027562
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RAB5C
• Ensembl ID: ENSGGOG00000005472
• Aliases: None
• Description: None

Sequence

>retro_ggor_2182
TCTGCAGTGGGCAAATCTAACCTGTCCTCTGCCTTGTGAAGGGACAATTTCATGCGTACTAGGAGAGCACACTCGGAGCA
GCCTTCCTCACACAGAATGTCTGCTTGGACAACACAACAGTTAGGTTTGAGATCTGGGACACGGTTGGACAGCAGTGGTA
TCACAGCCTGGCCCCCATGTACTCTTGGGGGGGCCCAGGCTGCCATCATGGTCTATGACATCACCAATACAGATACATTT
GCCGGAGCCAGGGACTGAGTGAAGGAGCTACCAAGCAGGCCAGCCCCAACATGGTCCTTGCGCTCATGAGTAACAAGGCA
GACCTGGCCAGCAAGAGACCCCTGGAATTCCAGGAAGCACAAGCCTATGCAGACGACGACAGTTGGCTGTTCATGGAGAC
ATCAGCAAAGGGTGCAATGAATGTGAATGAAATTTTCATGGCAATAGCTGAGAAACTTCCCAAGAGCAAGCCCCAGAATG
CAGCTGGTGCTCCAGACAGAAACCAAGCTGTGGACCTCCAGGAGAACCACCCGGCCAGCCCCAACCAGTGTTGCAGCAAT

Alignment

ORF - retro_ggor_2182 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.37 %
• Parental protein coverage: 86.57 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SAVGKSSL-VLRFVKGQFHEYQESTIGAAFLTQTVCLDDTTVKFEIWDTAGQERYHSLAPMY-YRGAQAA
          SAVGKS.L.VL..VKGQFH.Y.EST.GAAFLTQ.VCLD.TTV.FEIWDT.GQ..YHSLAPMY...GAQAA
Retrocopy SAVGKSNL<VLCLVKGQFHAY*ESTLGAAFLTQNVCLDNTTVRFEIWDTVGQQWYHSLAPMY>LGGAQAA

Parental  IVVYDITNTDTFARAKNWVKEL-QRQASPNIVIALAGNKADLASKRAVEFQEAQAYADDNSLLFMETSAK
          I.VYDITNTDTFA.A...VKEL...QASPN.V.AL..NKADLASKR..EFQEAQAYADD.S.LFMETSAK
Retrocopy IMVYDITNTDTFAGARD*VKEL<TKQASPNMVLALMSNKADLASKRPLEFQEAQAYADDDSWLFMETSAK

Parental  TAMNVNEIFMAIAKKLPKNEPQNATGAPGRNRGVDLQENNPASRSQCCSN
          .AMNVNEIFMAIA.KLPK..PQNA.GAP.RN..VDLQEN.PAS..QCCSN
Retrocopy GAMNVNEIFMAIAEKLPKSKPQNAAGAPDRNQAVDLQENHPASPNQCCSN

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	0.05 RPM	80.27 RPM
SRP007412_cerebellum	0.00 RPM	67.57 RPM
SRP007412_heart	0.03 RPM	24.55 RPM
SRP007412_kidney	0.00 RPM	133.34 RPM
SRP007412_liver	0.00 RPM	48.64 RPM
SRP007412_testis	0.21 RPM	54.91 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_2182 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2182 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000000472	2 retrocopies	retro_cjac_189, retro_cjac_1948,
Gorilla gorilla	ENSGGOG00000005472	1 retrocopy	retro_ggor_2182 ,
Gorilla gorilla	ENSGGOG00000015981	1 retrocopy	retro_ggor_848,
Macropus eugenii	ENSMEUG00000005614	1 retrocopy	retro_meug_2118,
Macaca mulatta	ENSMMUG00000014761	1 retrocopy	retro_mmul_2022,
Monodelphis domestica	ENSMODG00000014792	1 retrocopy	retro_mdom_1399,
Pongo abelii	ENSPPYG00000008398	1 retrocopy	retro_pabe_2664,
Pan troglodytes	ENSPTRG00000009194	1 retrocopy	retro_ptro_2237,
Tupaia belangeri	ENSTBEG00000007092	1 retrocopy	retro_tbel_4668,