RetrogeneDB ID: retro_pabe_18

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 17:20152237..20153020(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPPYG00000008067
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: RNASEH1
• Ensembl ID: ENSPPYG00000025873
• Aliases: None
• Description: ribonuclease H1 [Source:HGNC Symbol;Acc:18466]

Sequence

>retro_pabe_18
ATGAGCTGGCTTCTGTTCCTGGCCCACGGAGTCGCCTTGGCCGCCGTGCCCTGCCGCCGCGGCTCTCGCGGGTTCGGGAT
GTTCTATGCCCTGAGGAGGCGCCGCAAGACCGGGGTCTTTCTGACCTGGAATGAGTGCAAAGCACAGGTGGACCGGTTTC
CTGCTGCCAGATTTAAGAAGTTTGGCACCGAGGATGAGGCCTGGGACTTTGTCAGGAAATCTGCAAGCCCGGAAGTTTCA
GAAGGGCAGGAAAATCAACATGGACAAGAATCGGAGACGAAAGCCCCCAAGCGACTCCGTGAGCCACTGGATGAAGATGG
AGATGAAAGCGCAGAGCCGTATGCAAAGCACATGAAGCCGAGCGTGGAGCCGGAGCATCCAGTTAGCAGAGACACGTTTT
CCTACATGGGAGACTTCGTCGTCGTCTACACTGATGGCTGCTGCTCCAGTAATGGGCGTAGAAGGTCACGAGCAGGAATC
CGCTTTTACTGGGGGCCGGGCCATCCTTTAGATGTAGGCATTAGACTTCCTGGGCGGCAGACAAACCAAAGAGCGGAAAT
TCATGCAGCCTGCAAAGCCATTGAACAAGCAAAGACTCAGAACATCAATAAACTGGTTCTGTATACAGACAGTATGTTTA
CGATAAATGGTATAACTAACTGGGTTCCAGGTTGGAAGAAAAATGGGTGGAAGACAAGTGCAGGGAAAGAGGTGATCAAC
AGAGAGGACTTCCCGGCACTGGAGAGGCTGACCCAGGGGATGGACATTCAGTGGGCAAGTGTC

Alignment

ORF - retro_pabe_18 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.44 %
• Parental protein coverage: 53.97 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSWLLFLAHRVVLAAVSCRRGSRGFGMFYAVRRGRKTGVFLTWNECRAQVDRFPAARFKKFATEDEAWAF
          MSWLLFLAH.V.LAAV.CRRGSRGFGMFYA.RR.RKTGVFLTWNEC.AQVDRFPAARFKKF.TEDEAW.F
Retrocopy MSWLLFLAHGVALAAVPCRRGSRGFGMFYALRRRRKTGVFLTWNECKAQVDRFPAARFKKFGTEDEAWDF

Parental  VRKSASPEVSEGQENQHGQESETKASKRLREPLDGDGDESTEPYAKHMKPSVEPVPPVSRDTFSYM
          VRKSASPEVSEGQENQHGQESETKA.KRLREPLD.DGDES.EPYAKHMKPSVEP..PVSRDTFSYM
Retrocopy VRKSASPEVSEGQENQHGQESETKAPKRLREPLDEDGDESAEPYAKHMKPSVEPEHPVSRDTFSYM

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	0.94 RPM	7.57 RPM
SRP007412_cerebellum	0.85 RPM	4.74 RPM
SRP007412_heart	0.42 RPM	4.88 RPM
SRP007412_kidney	0.73 RPM	8.75 RPM
SRP007412_liver	0.31 RPM	5.02 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_18 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_18 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_18 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_2175

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000008547	6 retrocopies	retro_chof_158, retro_chof_1653, retro_chof_1836, retro_chof_2224, retro_chof_485, retro_chof_843,
Callithrix jacchus	ENSCJAG00000035450	1 retrocopy	retro_cjac_3811,
Echinops telfairi	ENSETEG00000012674	1 retrocopy	retro_etel_1286,
Homo sapiens	ENSG00000171865	2 retrocopies	retro_hsap_1814, retro_hsap_300,
Gorilla gorilla	ENSGGOG00000034822	2 retrocopies	retro_ggor_2175, retro_ggor_336,
Macropus eugenii	ENSMEUG00000003610	1 retrocopy	retro_meug_1172,
Macaca mulatta	ENSMMUG00000014475	2 retrocopies	retro_mmul_544, retro_mmul_799,
Monodelphis domestica	ENSMODG00000014491	1 retrocopy	retro_mdom_593,
Nomascus leucogenys	ENSNLEG00000015400	2 retrocopies	retro_nleu_2399, retro_nleu_2959,
Pongo abelii	ENSPPYG00000025873	1 retrocopy	retro_pabe_18 ,
Pan troglodytes	ENSPTRG00000011614	1 retrocopy	retro_ptro_244,
Pteropus vampyrus	ENSPVAG00000002070	1 retrocopy	retro_pvam_144,
Sarcophilus harrisii	ENSSHAG00000013051	1 retrocopy	retro_shar_245,