RetrogeneDB ID: retro_ggor_2850

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 9:38432700..38433288(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSGGOG00000023637
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RAB1B
• Ensembl ID: ENSGGOG00000009755
• Aliases: None
• Description: None

Sequence

>retro_ggor_2850
GACCGCCTGTTTAAGCTGCTTTTGATTGGCGACTCAGGCGTGGGCAAGTCATGCCTGCTCCTGCGGTTTGCTGATGACCC
GTACACAGAGAGCTACATCAGCACCATCGGGGTGGACTTCAAGATCCAAACCATCGAGCTGGATGGCAAAACTATCAAAC
TTCAGATCTGGGACACGGCGGGCCAGGAACGGTTCTGGACCATCACTTCCAGCTACTACCGGGGGGCTCATGGCTTCCTC
GTGGTATATGACGTCACTGACCGGGAATCCTATGCCAACGTGAAGCAGTGGCTGCAGGAGATTGACCGCTATGCCAGCGA
GAACGTCAATAAGCTCCTGGTGGGCAACAAGAGCAACCTCACCACCAAGAAGGTGGTGGACAACACCACAGCCAAGGAGT
TTGCAGACTCTTTGGGCATCCCCTTCTTGGAGACGAGTGCCAAGAATGCCACCAATGTCGAGCAGGTGTTCATGACCATG
GCTGCTGAGATCACAAAGCAGATGGGGCCCGGAGCAGCCTCCGGGGGCGAGTGGCCCGATCTCAAGATCGACAGCACCCC
TGTAAAGCCGGCTGGCGGTGGTTGTTGC

Alignment

ORF - retro_ggor_2850 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.37 %
• Parental protein coverage: 97.03 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DYLFKLLLIGDSGVGKSCLLLRFADDTYTESYISTIGVDFKIRTIELDGKTIKLQIWDTAGQERFRTITS
          D.LFKLLLIGDSGVGKSCLLLRFADD.YTESYISTIGVDFKI.TIELDGKTIKLQIWDTAGQERF.TITS
Retrocopy DRLFKLLLIGDSGVGKSCLLLRFADDPYTESYISTIGVDFKIQTIELDGKTIKLQIWDTAGQERFWTITS

Parental  SYYRGAHGIIVVYDVTDQESYANVKQWLQEIDRYASENVNKLLVGNKSDLTTKKVVDNTTAKEFADSLGI
          SYYRGAHG..VVYDVTD.ESYANVKQWLQEIDRYASENVNKLLVGNKS.LTTKKVVDNTTAKEFADSLGI
Retrocopy SYYRGAHGFLVVYDVTDRESYANVKQWLQEIDRYASENVNKLLVGNKSNLTTKKVVDNTTAKEFADSLGI

Parental  PFLETSAKNATNVEQAFMTMAAEIKKRMGPGAASGGERPNLKIDSTPVKPAGGGCC
          PFLETSAKNATNVEQ.FMTMAAEI.K.MGPGAASGGE.P.LKIDSTPVKPAGGGCC
Retrocopy PFLETSAKNATNVEQVFMTMAAEITKQMGPGAASGGEWPDLKIDSTPVKPAGGGCC

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	110.58 RPM
SRP007412_cerebellum	0.20 RPM	96.21 RPM
SRP007412_heart	0.06 RPM	73.95 RPM
SRP007412_kidney	0.00 RPM	86.28 RPM
SRP007412_liver	0.08 RPM	70.01 RPM
SRP007412_testis	0.00 RPM	103.50 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_2850 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2850 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4252
Pan troglodytes	retro_ptro_2892
Pongo abelii	retro_pabe_3386

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000001599	1 retrocopy	retro_cjac_931,
Homo sapiens	ENSG00000174903	1 retrocopy	retro_hsap_4252,
Gorilla gorilla	ENSGGOG00000009755	2 retrocopies	retro_ggor_1792, retro_ggor_2850 ,
Macropus eugenii	ENSMEUG00000000023	1 retrocopy	retro_meug_1985,
Monodelphis domestica	ENSMODG00000008371	1 retrocopy	retro_mdom_196,
Pongo abelii	ENSPPYG00000003031	1 retrocopy	retro_pabe_3386,
Pan troglodytes	ENSPTRG00000003915	1 retrocopy	retro_ptro_2892,
Sarcophilus harrisii	ENSSHAG00000010376	1 retrocopy	retro_shar_68,
Ictidomys tridecemlineatus	ENSSTOG00000011052	1 retrocopy	retro_itri_1677,
Drosophila melanogaster	FBgn0016700	1 retrocopy	retro_dmel_36,