RetrogeneDB ID: retro_ptro_159

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 1:70554324..70554618(+)
• Located in intron of: ENSPTRG00000000848

Retrocopy information

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

Parental gene information

• Parental gene symbol: PIN1
• Ensembl ID: ENSPTRG00000010452
• Aliases: None
• Description: None

Sequence

>retro_ptro_159
AGCCAGTCAAGGCGGCCCTCGACCTGGCGGCAGGAAATCACCCGGACCAAGGAGGAGGCCCTGGAGCTGATCAGCGGCTA
CATCCAGAAGATCAAGGCAGGAGAGAAGGACTTTGAGTCTCCGGCCTCACAATTCAGCGACTGCAGCTTGGCCAAGGCCA
GGGGAGACCTGGGTGCCTTCAGCAAAGGTCAGATGCAGAAGCCATTTGAAGACCCCTGGTTTGCGCGGTGGACGGGGGAG
ATGAGCGGGACAGTGTTCACGGATTCCGGCATCCACGTCATTGTCAGCACGGAG

Alignment

ORF - retro_ptro_159 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.84 %
• Parental protein coverage: 60.74 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SQSRRPSSWRQEKITRTKEEALELINGYIQKIKSGEEDFESLASQFSDCSSAKARGDLGAFSRGQMQKPF
          SQSRRPS.WRQE.ITRTKEEALELI.GYIQKIK.GE.DFES.ASQFSDCS.AKARGDLGAFS.GQMQKPF
Retrocopy SQSRRPSTWRQE-ITRTKEEALELISGYIQKIKAGEKDFESPASQFSDCSLAKARGDLGAFSKGQMQKPF

Parental  EDASFALRTGEMSGPVFTDSGIHIILRTE
          ED..FA..TGEMSG.VFTDSGIH.I..TE
Retrocopy EDPWFARWTGEMSGTVFTDSGIHVIVSTE

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	138.12 RPM
SRP007412_cerebellum	0.00 RPM	53.24 RPM
SRP007412_heart	0.00 RPM	13.12 RPM
SRP007412_kidney	0.00 RPM	34.73 RPM
SRP007412_liver	0.00 RPM	24.16 RPM
SRP007412_testis	0.00 RPM	36.99 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_159 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_159 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_159 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_168
Gorilla gorilla	retro_ggor_252
Pongo abelii	retro_pabe_462
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,