RetrogeneDB ID: retro_pabe_2135

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 2b:81778876..81779353(-)
• Located in intron of: ENSPPYG00000013027

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAB1B
• Ensembl ID: ENSPPYG00000012360
• Aliases: None
• Description: ras-related protein Rab-1B [Source:RefSeq peptide;Acc:NP_001127221]

Sequence

>retro_pabe_2135
ATGTCCAGCATGAATCCCAAATATGATTATTTATTCAAATTACTTCTGATTGGCGACTCTGGGATTGGAAAGTCTTGCCT
CCTTCTTAGGTTTGCAGATGATACATATACAGAAAGCTACATCAGCACAATTGGTGTGGATTTCAAAATAAGAACTATAG
AGTTAGACAGGAAAACAATCAAGCTTCAAATATGGAACACAGCAGAACAGGAAAGATTTCGAACAGTCATCTCCAGTTAT
TACAGAGGAGCCAATGGCATCCTAGTTGTGTATGATGTGACAGAACAGGAGTCCTTCAGTAATATTAAACAATGACTGCA
GAAAATAGATCATTATCCCAGTGAAAACGTCAACAAATTGTTGGTAGGGAACAAGTGTGATCTGACCACAAAGAAAGTAG
TAGACTACACAACAGCAAAGGAATTTGCTGATTCCCTTGGAATTCTGTTTTTGGAAACCAGTGTTAAGAATGCAACA

Alignment

ORF - retro_pabe_2135 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.68 %
• Parental protein coverage: 77.56 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSSMNPEYDYLFKLLLIGDSGVGKSCLLLRFADDTYTESYISTIGVDFKIRTIELDGKTIKLQIWDTAGQ
          MSSMNP.YDYLFKLLLIGDSG.GKSCLLLRFADDTYTESYISTIGVDFKIRTIELD.KTIKLQIW.TA.Q
Retrocopy MSSMNPKYDYLFKLLLIGDSGIGKSCLLLRFADDTYTESYISTIGVDFKIRTIELDRKTIKLQIWNTAEQ

Parental  ERFRTITSSYYRGAHGIIVVYDVTDQESFNNVKQWLQEIDRYASENVNKLLVGNKCDLTTKKVVDYTTAK
          ERFRT..SSYYRGA.GI.VVYDVT.QESF.N.KQ.LQ.ID.Y.SENVNKLLVGNKCDLTTKKVVDYTTAK
Retrocopy ERFRTVISSYYRGANGILVVYDVTEQESFSNIKQ*LQKIDHYPSENVNKLLVGNKCDLTTKKVVDYTTAK

Parental  EFADSLGIPFLETSAKNAT
          EFADSLGI.FLETS.KNAT
Retrocopy EFADSLGILFLETSVKNAT

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	0.06 RPM	120.59 RPM
SRP007412_cerebellum	0.00 RPM	108.10 RPM
SRP007412_heart	0.03 RPM	56.81 RPM
SRP007412_kidney	0.07 RPM	127.18 RPM
SRP007412_liver	0.09 RPM	129.26 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2135 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2135 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2135 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2362
Pan troglodytes	retro_ptro_1727
Gorilla gorilla	retro_ggor_1792

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000002205	2 retrocopies	retro_etel_1687, retro_etel_413,
Homo sapiens	ENSG00000138069	2 retrocopies	retro_hsap_2362, retro_hsap_3626,
Macaca mulatta	ENSMMUG00000021721	1 retrocopy	retro_mmul_951,
Oryctolagus cuniculus	ENSOCUG00000017003	1 retrocopy	retro_ocun_800,
Pongo abelii	ENSPPYG00000003031	1 retrocopy	retro_pabe_3386,
Pongo abelii	ENSPPYG00000012360	1 retrocopy	retro_pabe_2135 ,
Pan troglodytes	ENSPTRG00000011989	1 retrocopy	retro_ptro_1727,
Rattus norvegicus	ENSRNOG00000004992	1 retrocopy	retro_rnor_110,
Ictidomys tridecemlineatus	ENSSTOG00000020693	1 retrocopy	retro_itri_1541,
Drosophila melanogaster	FBgn0016700	1 retrocopy	retro_dmel_36,