RetrogeneDB ID: retro_pabe_2087

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 2b:115787316..115787987(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DKFZP468J1719
• Ensembl ID: ENSPPYG00000008387
• Aliases: None
• Description: max-like protein X [Source:RefSeq peptide;Acc:NP_001127572]

Sequence

>retro_pabe_2087
ATGATGGAGCTAGGTGCCTGTCCCAAAGACCCCTGGGTAAAAGTGGAGTACGTCTATAGCTACAAAAGCTCAGACCTCAA
GTATTTTATAGAAAGCACCCACAATGGGACGGTAGTGTCTAGAGCTAATAGCATCGGTTCCACCAGTGCCTCTTCCATCC
CCAACACAGATGAGAAGGACAGTGATTACCACCAAGAGTCCTACAAGGACCAGTAGCGGTGAGCACACACTGAGGCTGAG
CAGAAGAGGAAGGATGTCATCAAGAGAGGCTGTGATGACCTTCAGACCATCATCCCCACATGCCAGCAGCAGGACTCCTG
TATTGGCTCCCGAAAGCTCAGCAAAGCCATCATTCTACAAAAGATCATTGACTACACTCAGTTTTTGCACAAGGAGAAGA
AAATGCAGGAGGAGGAGGTGTCCACACTATGGAAGGACCTCACAGCCCTAAAGATCATGAGAGGGAACTATGAGCAGACT
GTGAAGGCACACCAGGAAAACCCCCATGAGGGGAGGACCAGGCCTCTGACCAAGTCAAGGTCAGTGTGTTTCGAGGTATC
ATGGACTCGCTGTTCCAGTCCTTCAATGCCTTCATCTCTGTGACCAACTTCCAGGAGCTGTCAGCCTGTGTCTTCAGCTA
GATTGAGGAGCACTGCAAGCCACAAGCCATG

Alignment

ORF - retro_pabe_2087 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.42 %
• Parental protein coverage: 93.44 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MTEPGASPEDPWVKVEYAYSDNSLDPGLFVESTRKGSVVSRANSIGSTSASSVPNTDDEDSDYHQEAYKE
          M.E.GA.P.DPWVKVEY.YS..S.D...F.EST..G.VVSRANSIGSTSASS.PNTD..DSDYHQ....E
Retrocopy MMELGACPKDPWVKVEYVYSYKSSDLKYFIESTHNGTVVSRANSIGSTSASSIPNTDEKDSDYHQ----E

Parental  SYKDRRRRAHTQAEQKRRDAIKRGYDDLQTIVPTCQQQDFSIGSQKLSKAIVLQKTIDYIQFLHKEKKKQ
          SYKD..R.AHT.AEQKR.D.IKRG.DDLQTI.PTCQQQD..IGS.KLSKAI.LQK.IDY.QFLHKEKK.Q
Retrocopy SYKDQ*R*AHTEAEQKRKDVIKRGCDDLQTIIPTCQQQDSCIGSRKLSKAIILQKIIDYTQFLHKEKKMQ

Parental  EEEVSTLRKDVTALKIMKVNYEQIVKAHQDNPHE-GEDQVSDQVKFNVFQGIMDSLFQSFNASISVASFQ
          EEEVSTL.KD.TALKIM..NYEQ.VKAHQ.NPHE.GEDQ.SDQVK..VF.GIMDSLFQSFNA.ISV..FQ
Retrocopy EEEVSTLWKDLTALKIMRGNYEQTVKAHQENPHE<GEDQASDQVKVSVFRGIMDSLFQSFNAFISVTNFQ

Parental  ELSACVFSWIEEHCKPQTL
          ELSACVFS.IEEHCKPQ..
Retrocopy ELSACVFS*IEEHCKPQAM

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	0.11 RPM	27.70 RPM
SRP007412_cerebellum	0.00 RPM	38.67 RPM
SRP007412_heart	0.00 RPM	35.52 RPM
SRP007412_kidney	0.27 RPM	38.52 RPM
SRP007412_liver	0.15 RPM	54.69 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2087 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2087 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2087 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2216
Pan troglodytes	retro_ptro_1681
Gorilla gorilla	retro_ggor_1748

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000005011	1 retrocopy	retro_cjac_2774,
Homo sapiens	ENSG00000108788	1 retrocopy	retro_hsap_2216,
Gorilla gorilla	ENSGGOG00000010869	1 retrocopy	retro_ggor_1748,
Microcebus murinus	ENSMICG00000010258	1 retrocopy	retro_mmur_1373,
Monodelphis domestica	ENSMODG00000014918	2 retrocopies	retro_mdom_501, retro_mdom_539,
Nomascus leucogenys	ENSNLEG00000011638	1 retrocopy	retro_nleu_2338,
Pongo abelii	ENSPPYG00000008387	1 retrocopy	retro_pabe_2087 ,
Pan troglodytes	ENSPTRG00000009208	1 retrocopy	retro_ptro_1681,