RetrogeneDB ID: retro_ptro_2768

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 8:78632038..78632498(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: OCIAD2
• Ensembl ID: ENSPTRG00000016048
• Aliases: None
• Description: None

Sequence

>retro_ptro_2768
ATGCCCCCAATGTCTACTCATGGAAACCAAGAGAAAGGTCCCCATTTGCCACCACCAAGCAAGCAGAGACTGTTGTTTTA
TCCAAAATCAAACTGCACATCCACAGAGGAGAGATTTCAAACATTATAAGAGGATGTCAAGAAGAAAGTTTCTGGAAGAG
AGCTCTGCCTTTTTCTCCTGTAAGCATGCTCATCACCCAGGGACTAGTCTGCCAAGGTTATTTAGCAGCTAATCCAAGAT
TTGGATCATTGCCTAAAGTTACACTTGTTGGTATCTTGGGATTGGCCTTGGAAAGGTATCATACATAAGAGTATGCCAGA
GTAAATTCCATTTCTTTGAAGATCAGCTCCATGGGGCTGATCTTGGTCCACAGCAGAACAGGCACTGATTGCTTACCTGT
GAAGAATGCAAAATAAAGCATGGATTCAATGAGAAGAGAAGTTCACAGCCTTTGGCTTCC

Alignment

ORF - retro_ptro_2768 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.56 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MASASARGNQDKDPHFPPPSKQSLLFCPKS-KLHIHRAEISKIMRECQEESFWKRALPFSLVSMLITQGL
          M...S..GNQ.K.PH.PPPSKQ.LLF.PKS.KLHIHR.EIS.I.R.CQEESFWKRALPFS.VSMLITQGL
Retrocopy MPPMSTHGNQEKGPHLPPPSKQRLLFYPKS<KLHIHRGEISNIIRGCQEESFWKRALPFSPVSMLITQGL

Parental  VYQGYLAANSRFGSLPKVALAGL-LGFGLGKVSYIGVCQSKFHFFEDQLRGAGFGPQHNRHCLLTCEECK
          V.QGYLAAN.RFGSLPKV.L.G..LG.GLGKVSYI.VCQSKFHFFEDQL.GA..GPQ.NRH.LLTCEECK
Retrocopy VCQGYLAANPRFGSLPKVTLVGI<LGIGLGKVSYIRVCQSKFHFFEDQLHGADLGPQQNRH*LLTCEECK

Parental  IKHGLSEKGDSQASAS
          IKHG..EK..SQ..AS
Retrocopy IKHGFNEKRSSQPLAS

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	7.22 RPM
SRP007412_cerebellum	0.00 RPM	4.16 RPM
SRP007412_heart	0.03 RPM	4.63 RPM
SRP007412_kidney	0.03 RPM	68.70 RPM
SRP007412_liver	0.03 RPM	43.11 RPM
SRP007412_testis	0.00 RPM	0.63 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2768 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2768 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2768 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Callithrix jacchus	retro_cjac_1505
Pongo abelii	retro_pabe_3350

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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,