RetrogeneDB ID: retro_pabe_1912

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 22:37383710..37384413(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: OLA1
• Ensembl ID: ENSPPYG00000012943
• Aliases: None
• Description: obg-like ATPase 1 [Source:RefSeq peptide;Acc:NP_001127505]

Sequence

>retro_pabe_1912
ATACCCCCTAAAAAGGGAGGTGATGGAATTAAACCACCCCCAATTATTGGAAGATTTGGAAACTCACTGAAAATTGGTAT
TGTTGGATTGCCAAATGTTGGGAAATCTACTTTCTTCAATGTATTAACCAATAGTCAGACTTCAGCAGAAAACTTCCATT
CTGCACTATTGATCCTAATGAGAGCAGAGTACCTGTGCCAGATGAAAGGTTTGACTTTCTTTGCCAACATTACAAACCAG
CAAGCAAAATTCCTACCTTTCTAAATGTAGTGGATATTGCTGGCCTTGTGAAAGGAGCTCACAATGGGCAGGGCCTGGGG
AATGCTTTTTTATCTCATTTTAGTGCTTGTGATGGCATCTTTCATCTAACACGTGCTTTTCAAGAGATGATATCACGCAT
GTTGAAGAAAGTGTAGATCCTGTTCGAGATATAGAAATAATACATGAAGAGCTTCAGCTTAAAGATGAGGAAATGATTAG
GTCCATTATAGATAAACTAGAAAAGGTGGCTGTGAGAGGAGGAGATAAAAAACTAAAACCTAAATACGATATAATGTGCA
AAGTAAAATCCTGGGTTATAGATCAAAAGAAACCTGTTCACTTCTATCATGATTGGAATGACAAAGAGATTGAAGTGTTG
AATAAACACTTATTTTTGACTTCAAAACCAATGGTCTACTTGGTTAATCTTTCTGAAAAAGAA

Alignment

ORF - retro_pabe_1912 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.41 %
• Parental protein coverage: 59.34 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MPPKKGGDGIKPPPIIGRFGTSLKIGIVGLPNVGKSTFFNVLTNSQASAENF-PFCTIDPNESRVPVPDE
          .PPKKGGDGIKPPPIIGRFG.SLKIGIVGLPNVGKSTFFNVLTNSQ.SAENF.PFCTIDPNESRVPVPDE
Retrocopy IPPKKGGDGIKPPPIIGRFGNSLKIGIVGLPNVGKSTFFNVLTNSQTSAENF<PFCTIDPNESRVPVPDE

Parental  RFDFLCQYHKPASKIPAFLNVVDIAGLVKGAHNGQGLGNAFLSHISACDGIFHLTRAFED-DDITHVEGS
          RFDFLCQ..KPASKIP.FLNVVDIAGLVKGAHNGQGLGNAFLSH.SACDGIFHLTRAF...DDITHVE.S
Retrocopy RFDFLCQHYKPASKIPTFLNVVDIAGLVKGAHNGQGLGNAFLSHFSACDGIFHLTRAFQE<DDITHVEES

Parental  VDPIRDIEIIHEELQLKDEEMIGPIIDKLEKVAVRGGDKKLKPEYDIMCKVKSWVIDQKKPVRFYHDWND
          VDP.RDIEIIHEELQLKDEEMI..IIDKLEKVAVRGGDKKLKP.YDIMCKVKSWVIDQKKPV.FYHDWND
Retrocopy VDPVRDIEIIHEELQLKDEEMIRSIIDKLEKVAVRGGDKKLKPKYDIMCKVKSWVIDQKKPVHFYHDWND

Parental  KEIEVLNKHLFLTSKPMVYLVNLSEKD
          KEIEVLNKHLFLTSKPMVYLVNLSEK.
Retrocopy KEIEVLNKHLFLTSKPMVYLVNLSEKE

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	0.00 RPM	44.12 RPM
SRP007412_cerebellum	0.12 RPM	42.80 RPM
SRP007412_heart	0.03 RPM	20.32 RPM
SRP007412_kidney	0.00 RPM	32.52 RPM
SRP007412_liver	0.00 RPM	20.69 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1912 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1912 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1912 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2593
Pan troglodytes	retro_ptro_1517
Gorilla gorilla	retro_ggor_1623

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006970	1 retrocopy	retro_btau_1737,
Choloepus hoffmanni	ENSCHOG00000005044	1 retrocopy	retro_chof_1295,
Callithrix jacchus	ENSCJAG00000007877	1 retrocopy	retro_cjac_2875,
Dipodomys ordii	ENSDORG00000008681	1 retrocopy	retro_dord_556,
Homo sapiens	ENSG00000138430	1 retrocopy	retro_hsap_2593,
Gorilla gorilla	ENSGGOG00000022215	1 retrocopy	retro_ggor_1623,
Myotis lucifugus	ENSMLUG00000025196	1 retrocopy	retro_mluc_626,
Monodelphis domestica	ENSMODG00000009296	1 retrocopy	retro_mdom_1428,
Nomascus leucogenys	ENSNLEG00000005817	1 retrocopy	retro_nleu_1526,
Otolemur garnettii	ENSOGAG00000016557	1 retrocopy	retro_ogar_1697,
Pongo abelii	ENSPPYG00000012943	2 retrocopies	retro_pabe_1912 , retro_pabe_928,
Pan troglodytes	ENSPTRG00000012650	1 retrocopy	retro_ptro_1517,
Sorex araneus	ENSSARG00000010743	1 retrocopy	retro_sara_545,
Tarsius syrichta	ENSTSYG00000005517	2 retrocopies	retro_tsyr_1845, retro_tsyr_394,
Vicugna pacos	ENSVPAG00000009660	2 retrocopies	retro_vpac_52, retro_vpac_613,