RetrogeneDB ID: retro_ptro_619

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 11:73670888..73671230(-)
• Located in intron of: ENSPTRG00000004088

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPP1R1A
• Ensembl ID: ENSPTRG00000005044
• Aliases: None
• Description: protein phosphatase 1, regulatory (inhibitor) subunit 1A [Source:HGNC Symbol;Acc:9286]

Sequence

>retro_ptro_619
AACACGGATCCTCGACCCACTTTGGTAATGTCTCCACAGCGACAGAAGATGACAAGGATCACACCCACAACGAGAGAGCT
CCAGATGATGGCTGAACATCACCTGGGGCAACAGCACCAAGGAGAGGCGCCTGAGAAAGCTTCTGAGAGCACAGGGACCC
AGGAAACGTGCCCACCCAGGATCACAGACACGGAAGTGGAGTCAAGGCTGGGCACCTTTGGGCTAGCACAAGAGCCTGCA
GAATCTATCCCCACAACTCAGGAGAGAGGCAGTAAAAAATGCAGCACAAAGGAACCCTCGATCCATGTACCACCACTGGA
TTCCCAGGAAGCCAGCTCGGTT

Alignment

ORF - retro_ptro_619 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.3 %
• Parental protein coverage: 79.86 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NPHLKSTLAMSPRQRKKMTRITPTMKELQMMVEHHLGQQQQGEEPEGAAESTGTQESRPPGIPDTEVESR
          N.....TL.MSP.QR.KMTRITPT..ELQMM.EHHLGQQ.QGE.PE.A.ESTGTQE..PP.I.DTEVESR
Retrocopy NTDPRPTLVMSP-QRQKMTRITPTTRELQMMAEHHLGQQHQGEAPEKASESTGTQETCPPRITDTEVESR

Parental  LGTSGTAKKPAECIPKTHERGSKEPSTKEPSTHIPPLDSKGANSV
          LGT.G.A..PAE.IP.T.ERGSK..STKEPS.H.PPLDS..A.SV
Retrocopy LGTFGLAQEPAESIPTTQERGSKKCSTKEPSIHVPPLDSQEASSV

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	21.34 RPM
SRP007412_cerebellum	0.00 RPM	17.75 RPM
SRP007412_heart	0.00 RPM	23.52 RPM
SRP007412_kidney	0.05 RPM	38.18 RPM
SRP007412_liver	0.00 RPM	78.17 RPM
SRP007412_testis	0.00 RPM	0.11 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_619 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_619 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_619 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_896
Pongo abelii	retro_pabe_774

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000010159	1 retrocopy	retro_fcat_1131,
Homo sapiens	ENSG00000135447	2 retrocopies	retro_hsap_1633, retro_hsap_896,
Gorilla gorilla	ENSGGOG00000008380	1 retrocopy	retro_ggor_1231,
Pongo abelii	ENSPPYG00000004608	1 retrocopy	retro_pabe_774,
Pan troglodytes	ENSPTRG00000005044	2 retrocopies	retro_ptro_1138, retro_ptro_619 ,
Tupaia belangeri	ENSTBEG00000001193	20 retrocopies	retro_tbel_1191, retro_tbel_1233, retro_tbel_1251, retro_tbel_1264, retro_tbel_138, retro_tbel_1881, retro_tbel_2036, retro_tbel_2437, retro_tbel_2574, retro_tbel_2720, retro_tbel_3243, retro_tbel_3316, retro_tbel_3377, retro_tbel_3380, retro_tbel_3414, retro_tbel_3426, retro_tbel_4551, retro_tbel_537, retro_tbel_669, retro_tbel_899,