RetrogeneDB ID: retro_pabe_3025

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 6_cox_hap1:1406560..1407037(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPP1R2
• Ensembl ID: ENSPPYG00000014429
• Aliases: None
• Description: protein phosphatase 1, regulatory (inhibitor) subunit 2 [Source:HGNC Symbol;Acc:9288]

Sequence

>retro_pabe_3025
ATGGCGGCCTCCACGGCCTCCCAACGGCCCATCACGGGGATCCTGAAGGACAAGACCTCTACGACTTCCTCTATGGTGGC
GTCTGCCCAACAGCCCCGTGGGAGTGTCCACGAGGAGCTGAGCAAAAAATCCCAGAAGTGGGATGAAATGAACATCCTGG
AGACATATCGTCCAGCAGACAAAGACTATGGTTTAATGAAAATAGATGAACCAAACACTCCTTACCATAATATGATGGGT
GATGATGAAGATGCATGTAGTGATACAGAAACCACTGAAGCCATGGCACCAGATATCTTGGCTAAGAAATTAGCTGCTGC
TGAACGCTGGGAGCCAAAGTGTCAGGTTCAGGGACAAGAAAGCAGTGGAGAGGAGGATAGTGACATCTCACCTGAAGAAT
GAGAAAAAAAGCGACAATTTGAAATGAAAAGGATGCTTCACTACAATGAAGGACTCAATATCAAACTAGCTAGACAA

Alignment

ORF - retro_pabe_3025 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.05 %
• Parental protein coverage: 77.56 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAASTASHRPIKGILKNKTSTTSSMVASAEQPRGNVDEELSKKSQKWDEMNILATYHPADKDYGLMKIDE
          MAASTAS.RPI.GILK.KTSTTSSMVASA.QPRG.V.EELSKKSQKWDEMNIL.TY.PADKDYGLMKIDE
Retrocopy MAASTASQRPITGILKDKTSTTSSMVASAQQPRGSVHEELSKKSQKWDEMNILETYRPADKDYGLMKIDE

Parental  PSTPYHSMMGDDEDACSDTETTEAMAPDILAKKLAAAEGLEPKYRIQEQESSGEEDSDLSPEEREKKRQF
          P.TPYH.MMGDDEDACSDTETTEAMAPDILAKKLAAAE..EPK...Q.QESSGEEDSD.SPEE.EKKRQF
Retrocopy PNTPYHNMMGDDEDACSDTETTEAMAPDILAKKLAAAERWEPKCQVQGQESSGEEDSDISPEE*EKKRQF

Parental  EMKRKLHYNEGLNIKLARQ
          EMKR.LHYNEGLNIKLARQ
Retrocopy EMKRMLHYNEGLNIKLARQ

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	1.16 RPM	25.99 RPM
SRP007412_cerebellum	1.09 RPM	19.94 RPM
SRP007412_heart	0.24 RPM	12.79 RPM
SRP007412_kidney	0.17 RPM	19.89 RPM
SRP007412_liver	0.09 RPM	9.15 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3025 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3025 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3025 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3576
Gorilla gorilla	retro_ggor_2412
Callithrix jacchus	retro_cjac_2429

---

Parental genes homology:

Parental genes homology involve 23 parental genes, and 58 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009410	2 retrocopies	retro_amel_1164, retro_amel_53,
Canis familiaris	ENSCAFG00000032648	1 retrocopy	retro_cfam_44,
Choloepus hoffmanni	ENSCHOG00000013210	2 retrocopies	retro_chof_1353, retro_chof_2148,
Callithrix jacchus	ENSCJAG00000013876	2 retrocopies	retro_cjac_1252, retro_cjac_2429,
Cavia porcellus	ENSCPOG00000022006	2 retrocopies	retro_cpor_1144, retro_cpor_82,
Dasypus novemcinctus	ENSDNOG00000023619	1 retrocopy	retro_dnov_1698,
Equus caballus	ENSECAG00000018050	1 retrocopy	retro_ecab_3,
Felis catus	ENSFCAG00000024749	1 retrocopy	retro_fcat_55,
Homo sapiens	ENSG00000184203	7 retrocopies	retro_hsap_1262, retro_hsap_1271, retro_hsap_2303, retro_hsap_2505, retro_hsap_3258, retro_hsap_3576, retro_hsap_3800,
Gorilla gorilla	ENSGGOG00000025908	5 retrocopies	retro_ggor_1563, retro_ggor_1705, retro_ggor_2412, retro_ggor_2554, retro_ggor_992,
Loxodonta africana	ENSLAFG00000012010	1 retrocopy	retro_lafr_85,
Macaca mulatta	ENSMMUG00000019396	2 retrocopies	retro_mmul_1314, retro_mmul_1666,
Mustela putorius furo	ENSMPUG00000003753	2 retrocopies	retro_mputfur_1269, retro_mputfur_172,
Mus musculus	ENSMUSG00000047714	8 retrocopies	retro_mmus_1540, retro_mmus_1610, retro_mmus_1611, retro_mmus_1868, retro_mmus_2760, retro_mmus_3350, retro_mmus_3428, retro_mmus_3580,
Nomascus leucogenys	ENSNLEG00000008371	6 retrocopies	retro_nleu_123, retro_nleu_1435, retro_nleu_1943, retro_nleu_2147, retro_nleu_2315, retro_nleu_2740,
Oryctolagus cuniculus	ENSOCUG00000014123	2 retrocopies	retro_ocun_188, retro_ocun_942,
Otolemur garnettii	ENSOGAG00000002597	1 retrocopy	retro_ogar_10,
Procavia capensis	ENSPCAG00000013614	1 retrocopy	retro_pcap_397,
Pongo abelii	ENSPPYG00000014429	6 retrocopies	retro_pabe_105, retro_pabe_1056, retro_pabe_1979, retro_pabe_3025 , retro_pabe_3105, retro_pabe_96,
Pteropus vampyrus	ENSPVAG00000011638	1 retrocopy	retro_pvam_18,
Rattus norvegicus	ENSRNOG00000001733	2 retrocopies	retro_rnor_245, retro_rnor_2860,
Sus scrofa	ENSSSCG00000011830	1 retrocopy	retro_sscr_1191,
Sus scrofa	ENSSSCG00000030455	1 retrocopy	retro_sscr_1161,