RetrogeneDB ID: retro_pabe_382

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1:46028138..46028506(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C12orf45
• Ensembl ID: ENSPPYG00000004897
• Aliases: None
• Description: chromosome 12 open reading frame 45 [Source:HGNC Symbol;Acc:28628]

Sequence

>retro_pabe_382
CCCAGGACTGCTACAGAGGGAGTCTTGGTGCCTAAGGAGTGGCTGACGGTAGGGAACAACAGCCAAGAGGTGTATCAGAC
AGGTTGCTCATCAACTCCCAGCCTGATTCTAGAAAGAACTCCACTCTCCAAACAGTCCAGATACAGAGGAGTCCCTTAGT
GGACCAAGGACAGACCTTTCTCCCACAGATGGCCCAGGCACATGAAAAGCTAAGAAAATAAATGGCGGGTTCACCACCTG
GTTGTTTCAATATTGAAAATATTGATGGTTCTCTTAGAAAAGTTATACAAATGGATGTGGTCTTGTTTGAGATGAACCAG
TCAGATTCAAAAGTGGACAGCTCAGAATCTGAGGATGAAGATGACAGC

Alignment

ORF - retro_pabe_382 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68. %
• Parental protein coverage: 67.03 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PTRDSSGVPVSKELLTAGSDGRG-GIWDRLLINSQPKSRKTSTLQTVRIERSPLLDQVQTFLPQMARANE
          P.....GV.V.KE.LT.G......G..DRLLINSQP.SRK.STLQTV.I.RSPL.DQ.QTFLPQMA.A.E
Retrocopy PRTATEGVLVPKEWLTVGNNSQE<GVSDRLLINSQPDSRKNSTLQTVQIQRSPLVDQGQTFLPQMAQAHE

Parental  KLRKEMAAAPPGRFNIENIDGPHGKVIQMDVALFEMNQSDSKEADSSEESSQDSS
          KLRK.MA..PPG.FNIENIDG...KVIQMDV.LFEMNQSDSK..DSSE....D.S
Retrocopy KLRK*MAGSPPGCFNIENIDGSLRKVIQMDVVLFEMNQSDSK-VDSSESEDEDDS

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	4.59 RPM
SRP007412_cerebellum	0.00 RPM	3.53 RPM
SRP007412_heart	0.00 RPM	1.63 RPM
SRP007412_kidney	0.10 RPM	3.94 RPM
SRP007412_liver	0.09 RPM	6.64 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_382 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_382 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_382 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_292
Pan troglodytes	retro_ptro_240
Gorilla gorilla	retro_ggor_331
Macaca mulatta	retro_mmul_551

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000014728	1 retrocopy	retro_cjac_333,
Dasypus novemcinctus	ENSDNOG00000017235	1 retrocopy	retro_dnov_2327,
Homo sapiens	ENSG00000151131	1 retrocopy	retro_hsap_292,
Gallus gallus	ENSGALG00000012694	1 retrocopy	retro_ggal_15,
Gorilla gorilla	ENSGGOG00000027272	1 retrocopy	retro_ggor_331,
Macaca mulatta	ENSMMUG00000017133	1 retrocopy	retro_mmul_551,
Nomascus leucogenys	ENSNLEG00000006584	1 retrocopy	retro_nleu_2414,
Pongo abelii	ENSPPYG00000004897	1 retrocopy	retro_pabe_382 ,
Pan troglodytes	ENSPTRG00000005381	1 retrocopy	retro_ptro_240,
Sus scrofa	ENSSSCG00000027792	2 retrocopies	retro_sscr_105, retro_sscr_153,
Tursiops truncatus	ENSTTRG00000005714	1 retrocopy	retro_ttru_1381,