RetrogeneDB ID: retro_pabe_774

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 11:71366905..71367420(-)
• Located in intron of: ENSPPYG00000003695

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPP1R1A
• Ensembl ID: ENSPPYG00000004608
• Aliases: None
• Description: protein phosphatase 1, regulatory (inhibitor) subunit 1A [Source:HGNC Symbol;Acc:9286]

Sequence

>retro_pabe_774
GCCCAGCCCCGAGTCCCGCGGCCTTCCCTCCGACCACAGTGCCAGCCCAGCAGGTGCCACCCCAACCATGGAGCAAGACA
ACAGCCCCCAGACCCCGAGGGGGCAGAGCAGATTTGGACATGTCGCCCAATGCTGCCACCCTTGTGCTGACCAGTCATCC
CCAGAGAGAGATGAACACGGATCCTCGACCCACTTTGGTAATGTCTCCACAGCGACAGAAGATGACAAGGATCACACCCA
CAACGAGAGAGCTCCAGATGATGGCTGAACATCACCTGGGGCAACAGCAGCAAGGAGAGGCGCCTGAGAAAGCTGCTGAG
AGCACAGGGACCCAGGAAACCTGCCCACCCGGGATCACAGACACGGAAGTGGAGTCAAGGCTGGGCACCTTTGGGCCAGC
ACAAGAGCCTGCAGAATCTATCCCCACAACTCAGGAGAGAGGCAGTAAAAAATGCAGCACAAAGGAACCCTCGATCCATG
TACCACCACTGGATTCCCAGGAAGCCAGCTCGGTT

Alignment

ORF - retro_pabe_774 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60. %
• Parental protein coverage: 78.51 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AGPAAAAPAMEQDSSPRKIQFTVPLLEPHLDPEAAEQIRRRRP-TPATLVLTSDQSSPEVDEDRIPNPHL
          A.P....P.......P..............DPE.AEQI...RP...ATLVLT...S.P.......P.P..
Retrocopy AQPRVPRPSLRPQCQPSRCHPNHGARQQPPDPEGAEQIWTCRP<NAATLVLT---SHPQREMNTDPRP--

Parental  STLAMSPRQRKKMTRITPTMKELQMMVEHHLGQQQQGEEPEGAAESTGTQESRPPGIPDTEVESRLGTSG
          .TL.MSP.QR.KMTRITPT..ELQMM.EHHLGQQQQGE.PE.AAESTGTQE..PPGI.DTEVESRLGT.G
Retrocopy -TLVMSP-QRQKMTRITPTTRELQMMAEHHLGQQQQGEAPEKAAESTGTQETCPPGITDTEVESRLGTFG

Parental  TAKKPAESIPKTQERGSKEPSTKAPSTHIPPLDSKGANSV
          .A..PAESIP.TQERGSK..STK.PS.H.PPLDS..A.SV
Retrocopy PAQEPAESIPTTQERGSKKCSTKEPSIHVPPLDSQEASSV

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	15.70 RPM
SRP007412_cerebellum	0.00 RPM	15.69 RPM
SRP007412_heart	0.03 RPM	7.65 RPM
SRP007412_kidney	0.03 RPM	90.13 RPM
SRP007412_liver	0.00 RPM	221.16 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_774 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_774 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_774 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_896
Pan troglodytes	retro_ptro_619

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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,