RetrogeneDB ID: retro_pabe_3386

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 9:23996907..23997506(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPPYG00000019058
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RAB1B
• Ensembl ID: ENSPPYG00000003031
• Aliases: None
• Description: RAB1B, member RAS oncogene family [Source:HGNC Symbol;Acc:18370]

Sequence

>retro_pabe_3386
AACCCCGGATATGACTACCTGTTTAAGCTGCTTTTGATTGGCGACTCAGGCGTGGGCAAGTCACGCCTGCTCCTGCGGTT
TGCTGATGACACGTACACAGAGAGCTACATCGGCACCATCGGGGTGGACTTCAAGATCCAAACCATCGAGCTGGATGGCA
AAACTATCAAACTTCAGATCTGGGACACGGCAGGCCAGGAACGGTTCTGGACCATCACTTCCAGCTACTACCGGGGGGCT
CATGGCATCCTCGTGGTATGTGACGTCAGTGACCAGGAATCCTAGGCCAGCGCGAAGCAGTGGCTGCAGGAGATTGACCG
CTATGCCAGCGAGAACGTCAATAAGCTCCTGGTGGGCAAGAAGAGAGACCTCACCACCAAGAAGGTGGTGGACAACACCA
CAGCCAAGGAGTTTTCAGACTTTTTGGGCATCCCCTTCTTGGAGACGAGTGCCAAGAACGCCACCAATGTCGAGCAGGCG
TTCGTGACCATGGCCGCTGAGATCAAAAAGCAGATGGGGCCCGGAGCAGCCTCCGGGGCCAGCGGCCCAATCTCAAGATC
GACAGCACCCCTGTAAAGCCGGCTGGAGGTGGTTGTTGC

Alignment

ORF - retro_pabe_3386 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.62 %
• Parental protein coverage: 99.5 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NPEYDYLFKLLLIGDSGVGKSCLLLRFADDTYTESYISTIRGWDFK-ESIELD-KTIKLQIWDTAGQERF
          NP.YDYLFKLLLIGDSGVGKS.LLLRFADDTYTESYI.TI.G.DFK...IELD.KTIKLQIWDTAGQERF
Retrocopy NPGYDYLFKLLLIGDSGVGKSRLLLRFADDTYTESYIGTI-GVDFKIQTIELDGKTIKLQIWDTAGQERF

Parental  RTITSSYYRGAHGIIVVYDVTDQESYANVKQWLQEIDRYASENVNKLLVGNKSDLTTKKVVDNTTAKEFA
          .TITSSYYRGAHGI.VV.DV.DQES.A..KQWLQEIDRYASENVNKLLVG.K.DLTTKKVVDNTTAKEF.
Retrocopy WTITSSYYRGAHGILVVCDVSDQES*ASAKQWLQEIDRYASENVNKLLVGKKRDLTTKKVVDNTTAKEFS

Parental  DSLGIPFLETSAKNATNVEQAFMTMAAEIKKRMGPGAASG-GERPNLKIDSTP-KPAGGGCC
          D.LGIPFLETSAKNATNVEQAF.TMAAEIKK.MGPGAASG.G.RPNLKIDSTP.KPAGGGCC
Retrocopy DFLGIPFLETSAKNATNVEQAFVTMAAEIKKQMGPGAASG<GQRPNLKIDSTPVKPAGGGCC

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	4.48 RPM	44.84 RPM
SRP007412_cerebellum	2.92 RPM	25.66 RPM
SRP007412_heart	1.48 RPM	16.95 RPM
SRP007412_kidney	3.71 RPM	37.39 RPM
SRP007412_liver	2.39 RPM	19.31 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3386 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3386 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3386 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4252
Pan troglodytes	retro_ptro_2892
Gorilla gorilla	retro_ggor_2850

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 12 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 ,
Pongo abelii	ENSPPYG00000012360	1 retrocopy	retro_pabe_2135,
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,