RetrogeneDB ID: retro_pabe_1485

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 17:20721144..20721638(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PDLIM1
• Ensembl ID: ENSPPYG00000002507
• Aliases: None
• Description: PDZ and LIM domain 1 [Source:HGNC Symbol;Acc:2067]

Sequence

>retro_pabe_1485
ATGACCACCCAGTAGACAGTCCCTCAGGGTCCAGGACCATGGGGCTTCTGCGTCATGGGCAGCAAGGACTTCAAGCATCC
TCTCCATTTCCAGGTCACCCCCGGAAGCAAGGCTGCTGTAGCTAATTTGTGTATCGGAGATGTAATCACAGCCATGGGCT
GGGGAAACACCAGCCATAGGGCACAGTGGGAAGCTCAGAACAAAATCAAAAACAGCGCAGATGACATGACTCTCATGGGA
GCCAGATCTGAACATAAAATCTGGTCTCTGGTGACAGAGGAAGAGGAACATCATCCATACAAAATGAACTTATCCTCTGC
ACCCCAGGAGGTCCTGCATGTAGGAAGGGCCCATGTCCAAAGCGCCATGCCCTTCACCACCTCACCAGCCTCCAGCACTG
CCACCAGGGTTATCACGAATCAGTGCGACCACCCGGCTGGCCTCTGCTCCATCGAAAAATCTCCAGCTTTATCCGTGCCT
TGCAGTCAAAGACA

Alignment

ORF - retro_pabe_1485 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.07 %
• Parental protein coverage: 50.76 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MTTQQIVLQGPGPWGFRLVGGKDFEQPLAISRVTPGSKAALANLCIGDVITAIDGENTSNMTHLEAQNRI
          MTTQ..V.QGPGPWGF...G.KDF..PL....VTPGSKAA.ANLCIGDVITA....NTS.....EAQN.I
Retrocopy MTTQ*TVPQGPGPWGFCVMGSKDFKHPLHF-QVTPGSKAAVANLCIGDVITAMGWGNTSHRAQWEAQNKI

Parental  KGCTDNLTLTVARSEHKVWSPLVTEEGKRHPYRMNLASEPQEVLHIGSAHNRSAMPFTASPASSTTARVI
          K...D..TL..ARSEHK.WS.LVTEE...HPY.MNL.S.PQEVLH.G.AH..SAMPFT.SPASST..RVI
Retrocopy KNSADDMTLMGARSEHKIWS-LVTEEEEHHPYKMNLSSAPQEVLHVGRAHVQSAMPFTTSPASSTATRVI

Parental  TNQYNNPAGLYSSE-NISNFNNALESKT
          TNQ...PAGL.S.E..IS.F..AL.SKT
Retrocopy TNQCDHPAGLCSIE<KISSFIRALQSKT

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	10.62 RPM
SRP007412_cerebellum	0.00 RPM	2.31 RPM
SRP007412_heart	0.00 RPM	136.40 RPM
SRP007412_kidney	0.00 RPM	25.36 RPM
SRP007412_liver	0.00 RPM	84.00 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1485 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1485 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1485 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000011182	1 retrocopy	retro_btau_690,
Canis familiaris	ENSCAFG00000028553	1 retrocopy	retro_cfam_2080,
Dasypus novemcinctus	ENSDNOG00000012381	1 retrocopy	retro_dnov_1119,
Homo sapiens	ENSG00000107438	2 retrocopies	retro_hsap_1815, retro_hsap_2681,
Macaca mulatta	ENSMMUG00000000454	2 retrocopies	retro_mmul_1250, retro_mmul_1419,
Mus musculus	ENSMUSG00000055044	2 retrocopies	retro_mmus_2558, retro_mmus_779,
Nomascus leucogenys	ENSNLEG00000013055	3 retrocopies	retro_nleu_1819, retro_nleu_2767, retro_nleu_2970,
Oryctolagus cuniculus	ENSOCUG00000013643	1 retrocopy	retro_ocun_417,
Pongo abelii	ENSPPYG00000002507	2 retrocopies	retro_pabe_1109, retro_pabe_1485 ,
Pan troglodytes	ENSPTRG00000002783	1 retrocopy	retro_ptro_912,
Tarsius syrichta	ENSTSYG00000000834	2 retrocopies	retro_tsyr_1056, retro_tsyr_1224,
Tursiops truncatus	ENSTTRG00000012118	2 retrocopies	retro_ttru_1777, retro_ttru_976,