RetrogeneDB ID: retro_pabe_3350

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 8:83436837..83437289(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: OCIAD2
• Ensembl ID: ENSPPYG00000014722
• Aliases: None
• Description: OCIA domain containing 2 [Source:HGNC Symbol;Acc:28685]

Sequence

>retro_pabe_3350
GTGGCCCCAGTGTCTACTCATGGAAACCAAGAGAAAGGTCCCCATTTGCCACTACCAAGCAAGCAGAGCCTGCACAAAAT
CAAACTGCACATCCACAGAGGAGAGATTTCAAACATTATAAGAGGATGTCAAGAAGAAAGTTTCTGGAAGAGAGCTCTGC
CTTTTTCTCCTGTAAGCATGCTCGTCACCCAGGGACTAGTCTGCCAAGGTTATTTAGCAGCTAATCCAAGATTTGGATCA
TTGCCTAAAGTTACACTTGTTGGTATCTTGGGATTGGCCTTGGAAAGGTATCATACATAAGAGTATGCCAGAGTAAATTC
CATTTCTTTGAAGATCAACTCCATGGGGCTGATTTTGGTCCACAGCAGAACAGGCATTGATTGCTTACCTGTGAAGAATG
CAAAATAAAGCATGGATTCAATGAGAAGGGAAGTTCACAGCCTTTGGCTTCC

Alignment

ORF - retro_pabe_3350 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.06 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MASASAHGNQDKDPHFPPPSKQSLLFCPKSKLHIHRAEISKIMQECQEESFWKRALPFSLVSMLVTQGLV
          .A..S.HGNQ.K.PH.P.PSKQSL....K.KLHIHR.EIS.I...CQEESFWKRALPFS.VSMLVTQGLV
Retrocopy VAPVSTHGNQEKGPHLPLPSKQSL---HKIKLHIHRGEISNIIRGCQEESFWKRALPFSPVSMLVTQGLV

Parental  YQGYLAANPRFGSLPKVALAGL-LGFGLGKVSYIGVCQSKFHFFEDQLRGAGFGPQHNRHCLLTCEECKI
          .QGYLAANPRFGSLPKV.L.G..LG.GLGKVSYI.VCQSKFHFFEDQL.GA.FGPQ.NRH.LLTCEECKI
Retrocopy CQGYLAANPRFGSLPKVTLVGI<LGIGLGKVSYIRVCQSKFHFFEDQLHGADFGPQQNRH*LLTCEECKI

Parental  KHGLSEKGDSQPSAS
          KHG..EKG.SQP.AS
Retrocopy KHGFNEKGSSQPLAS

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	16.37 RPM
SRP007412_cerebellum	0.00 RPM	1.95 RPM
SRP007412_heart	0.00 RPM	1.26 RPM
SRP007412_kidney	0.00 RPM	121.48 RPM
SRP007412_liver	0.00 RPM	25.71 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3350 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3350 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3350 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Callithrix jacchus	retro_cjac_1505
Pan troglodytes	retro_ptro_2768

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018637	1 retrocopy	retro_cjac_1505,
Erinaceus europaeus	ENSEEUG00000006759	1 retrocopy	retro_eeur_504,
Homo sapiens	ENSG00000145247	1 retrocopy	retro_hsap_4082,
Gorilla gorilla	ENSGGOG00000013778	1 retrocopy	retro_ggor_2738,
Microcebus murinus	ENSMICG00000006147	1 retrocopy	retro_mmur_1402,
Macaca mulatta	ENSMMUG00000014869	1 retrocopy	retro_mmul_2353,
Monodelphis domestica	ENSMODG00000025531	1 retrocopy	retro_mdom_1006,
Nomascus leucogenys	ENSNLEG00000017430	1 retrocopy	retro_nleu_2048,
Oryctolagus cuniculus	ENSOCUG00000007907	2 retrocopies	retro_ocun_1734, retro_ocun_1780,
Otolemur garnettii	ENSOGAG00000011039	1 retrocopy	retro_ogar_561,
Pongo abelii	ENSPPYG00000014722	1 retrocopy	retro_pabe_3350 ,
Pan troglodytes	ENSPTRG00000016048	1 retrocopy	retro_ptro_2768,
Vicugna pacos	ENSVPAG00000011765	1 retrocopy	retro_vpac_331,