RetrogeneDB ID: retro_pabe_1517

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 17:57899373..57900258(-)
• Located in intron of: ENSPPYG00000008570

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPPYG00000008498
• Aliases: None
• Description: None

Sequence

>retro_pabe_1517
GAGCCTAGTGCAGAGGTGGAAACTTCTCCAGTCCACCAGGAGGCTACAGCTCAGACTCCAGATCCCCCTAAGGAGGCAGA
ACCTTCTCCAGTCCAGCAAGAGTTCCCAGCTGGGCCACCAGAGCCCCCTAAGGAGGCTGAACCATCTGCAACCCAGCAGG
AAGCCTCAGGTCATCCTCAGAAGTCCACTGAAGAGGTCAGTCCTCCACCACAGTGGGAGATACCAGCTCAGCCATCAGAG
CCATCTGAGAAGGTCGAACCATCTCCAGTCCTACAGCAGGCCCCAACTCGGCTTTTAGAGCCACCTAAACAGGTAGAATC
CTCTCCAGTCCAGCAGGCAGTCCCTGCTCAGTCTTCAGACCCTGCTCTGGTGATAGAACCCTCTCTGACCCAGCAGATGG
CCCCATCTTTGCCTCCAGAGTTCCCTCAGGAGGTAGAACCATCTGTAACTCAGCAGGAGGTTCCAGCTCAGATTCCAGAG
CCCCCTGTGGAGGCAGAACCTTCTGTGACCCAGCAGGAGGCCACAGTTCAGGCTCCAGAGGCCCCTAAGGAGGTAGAACC
TTCAAGGCAGCATATGGTCCCAGTTCAGCTTCCAGAGCCACCTAAGGAAGTTGCAGCTCAACCTCCAGCTCATTATGAGG
TGACAGTCCCAACACCAGGCCAGGATCCAGCTCAGCATTCAACATTGCCCAGTGTCACTGTTCAACCTTTGGACCTGGGA
CTTACCATCATTCCAGAATCCACAACAGAGGTTGAATTTTCTCCAACCATGCAGGAGACCCCAACTCAGCCTCCTAAGAA
AGTTGTACCCCATCTTGCATATCAAGAGGTAACAATTCCAACACCAGGTCAGGATCAAGCTCAGCATCCAATGTCACCCA
GCATT

Alignment

ORF - retro_pabe_1517 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.18 %
• Parental protein coverage: 54.6 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ETLEDIQSSSLQEEAPEQLPQLPEEAEPS-TPQEAPAQPPESSTESAAQTPPNHEVTVHPPGEDQAHYNL
          E.......S....EA..Q.P..P.EAEPS...QE.PA.PPE...E.A.......E...HP..........
Retrocopy EPSAEVETSPVHQEATAQTPDPPKEAEPSPVQQEFPAGPPEPPKE-AEPSATQQEASGHPQKSTEEVSPP

Parental  PNVTVKPVDVEVTITSEPTKETESSEAQQEAPVQPPEVEPSVSQEEAPTEPSGPPVEPERSPSEQEQPAQ
          P.........E.....EP.............P..P..VE.S..Q...P...S.P....E.S...Q..P..
Retrocopy PQWEIPAQPSEPSEKVEPSPVLQQAPTRLLEP--PKQVESSPVQQAVPAQSSDPALVIEPSLTQQMAPSL

Parental  PSISSGKAESSPAQQEAPAQPPEHH-EAEPSPIQQEATVQTPEPPMEVEPSSQQLVPAQHPEPPKEVAAQ
          P.......E.S..QQE.PAQ.PE...EAEPS..QQEATVQ.PE.P.EVEPS.Q..VP.Q.PEPPKEVAAQ
Retrocopy PPEFPQEVEPSVTQQEVPAQIPEPPVEAEPSVTQQEATVQAPEAPKEVEPSRQHMVPVQLPEPPKEVAAQ

Parental  PPAHYEVTIPTPGQDQAQHSILPSVTVQPLGLGLTITPESTTEFELSPTMQETPNQPPKEVVPQPPVYQE
          PPAHYEVT.PTPGQD.AQHS.LPSVTVQPL.LGLTI.PESTTE.E.SPTMQETP.QPPK.VVP....YQE
Retrocopy PPAHYEVTVPTPGQDPAQHSTLPSVTVQPLDLGLTIIPESTTEVEFSPTMQETPTQPPKKVVPH-LAYQE

Parental  VTVPTPGQDKAQHPMSPSV
          VT.PTPGQD.AQHPMSPS.
Retrocopy VTIPTPGQDQAQHPMSPSI

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	1.66 RPM	0.61 RPM
SRP007412_cerebellum	6.81 RPM	0.00 RPM
SRP007412_heart	0.63 RPM	0.06 RPM
SRP007412_kidney	2.45 RPM	0.00 RPM
SRP007412_liver	1.71 RPM	0.00 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1517 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1517 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1517 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Loxodonta africana	ENSLAFG00000028514	1 retrocopy	retro_lafr_708,
Pongo abelii	ENSPPYG00000008498	1 retrocopy	retro_pabe_1517 ,