RetrogeneDB ID: retro_pabe_462

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1:159440171..159440465(-)
• Located in intron of: ENSPPYG00000001247

Retrocopy information

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

Parental gene information

• Parental gene symbol: PIN1
• Ensembl ID: ENSPPYG00000009537
• Aliases: None
• Description: peptidylprolyl cis/trans isomerase, NIMA-interacting 1 [Source:HGNC Symbol;Acc:8988]

Sequence

>retro_pabe_462
AGCCAGTCAAGGCGGCTCTCGACCTGGCTTCAGGAAATCACCGGGACCAAGGAGGAGGCCCTGGAGCTGATCAGCGGCTA
CATCCAGAAGATCAAGGCAGGAGAAAAAGACTTGGAGTCTCTGGCCTCACAATTCAATGACTGCAGCTCGGCCAAGGCCA
GGGGAGACCTGGGTGCCTTCAGCAAAGGTCAGATGCAGAAGCCATTTGAAGACCCCTGCTTTGCGCGGTGGACGCGGGAG
ATGAGCGGGACAGTGTTCACGGATTCCGGCATCCACGTCATTGTCCGCACGGAG

Alignment

ORF - retro_pabe_462 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.81 %
• Parental protein coverage: 60.74 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SQSRRPSSWRQEKITRTKEEALELINGYIQKIKSGEEDFESLASQFSDCSSAKARGDLGAFSRGQMQKPF
          SQSRR.S.W.QE.IT.TKEEALELI.GYIQKIK.GE.D.ESLASQF.DCSSAKARGDLGAFS.GQMQKPF
Retrocopy SQSRRLSTWLQE-ITGTKEEALELISGYIQKIKAGEKDLESLASQFNDCSSAKARGDLGAFSKGQMQKPF

Parental  EDASFALRTGEMSGPVFTDSGIHIILRTE
          ED..FA..T.EMSG.VFTDSGIH.I.RTE
Retrocopy EDPCFARWTREMSGTVFTDSGIHVIVRTE

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	103.39 RPM
SRP007412_cerebellum	0.00 RPM	20.92 RPM
SRP007412_heart	0.00 RPM	12.73 RPM
SRP007412_kidney	0.00 RPM	26.48 RPM
SRP007412_liver	0.00 RPM	12.33 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_462 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_462 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_462 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_168
Pan troglodytes	retro_ptro_159
Gorilla gorilla	retro_ggor_252
Callithrix jacchus	retro_cjac_2925

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006079	1 retrocopy	retro_cjac_2925,
Homo sapiens	ENSG00000127445	1 retrocopy	retro_hsap_168,
Gorilla gorilla	ENSGGOG00000006008	1 retrocopy	retro_ggor_252,
Microcebus murinus	ENSMICG00000001996	1 retrocopy	retro_mmur_1157,
Mus musculus	ENSMUSG00000032171	1 retrocopy	retro_mmus_2072,
Nomascus leucogenys	ENSNLEG00000011999	1 retrocopy	retro_nleu_980,
Pongo abelii	ENSPPYG00000009537	1 retrocopy	retro_pabe_462 ,
Pan troglodytes	ENSPTRG00000010452	1 retrocopy	retro_ptro_159,
Rattus norvegicus	ENSRNOG00000020474	1 retrocopy	retro_rnor_1220,
Tupaia belangeri	ENSTBEG00000003793	1 retrocopy	retro_tbel_1546,