RetrogeneDB ID: retro_mmul_1314

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 17:43452304..43452907(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPP1R2
• Ensembl ID: ENSMMUG00000019396
• Aliases: None
• Description: protein phosphatase inhibitor 2 [Source:RefSeq peptide;Acc:NP_001247610]

Sequence

>retro_mmul_1314
ATGGCGGCCTGGACTGCCTCGCACTGGCCCATCAAAGGGATCCTGAAGAACAAGACCTCTACAGCTTCCCCTATGGTGGC
GTCGGCTGAACAGCCCAGCGGTAGTGTCGACGAGGAGCGGAGCAAAAAATTCCAGAAGTGGAAAGAAATGAACATCCTGG
CGACATATCATCCAGCAGACAAAGACGATGGTTTAATGAAAATAGATGAACCAAGCACTCCTTACTGTCGTTAAGATGGG
GATGGTGAAGATGCATGTAGTGATACAGAAACCACTGAAGCCATGGCAGCAGATACCTTAGCTAACAAATTAGCTGCTGC
TGAAGGCTTGGATCCAAAGTATAGGGTTCAAGAACAAGAAAACAGTGGACAGGAGGCTAGTGACCTCTCACCTGAGGAAG
GAGAAAAAAGGCGACAATTTGAAATGAAAAGGAAGCTTCACTACAACGAATGACTTAATATCAAATTAGCTAGAGAATTA
ATGTCAAAAGATCTATATGATGATGGCAAAGATGAAGAAATGTTAAAGACTGCAGATGGAGAAAGCATGAAGACAGAAGA
ATCAAATCAAGGCTCTACTACAGGTGACCAACGGCAAAACAAA

Alignment

ORF - retro_mmul_1314 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.59 %
• Parental protein coverage: 98.05 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAASTASHRPIKGILKNKTSTTSSMVASAEQPRGSVDEELSKKSQKWDEMNILATYHPADKDYGLMKIDE
          MAA.TASH.PIKGILKNKTST.S.MVASAEQP.GSVDEE.SKK.QKW.EMNILATYHPADKD.GLMKIDE
Retrocopy MAAWTASHWPIKGILKNKTSTASPMVASAEQPSGSVDEERSKKFQKWKEMNILATYHPADKDDGLMKIDE

Parental  PSTPYHSMMGDDEDACSDTETTEAMAPDILAKKLAAAEGLEPKYRIQEQESSGEEDSDLSPEEREKKRQF
          PSTPY....GD.EDACSDTETTEAMA.D.LA.KLAAAEGL.PKYR.QEQE.SG.E.SDLSPEE.EK.RQF
Retrocopy PSTPYCR*DGDGEDACSDTETTEAMAADTLANKLAAAEGLDPKYRVQEQENSGQEASDLSPEEGEKRRQF

Parental  EMKRKLHYNEGLNIKLARQLISKDLHDDDEDEEMLETADGESMNTEESNQGSTPSDQQQNK
          EMKRKLHYNE.LNIKLAR.L.SKDL.DD..DEEML.TADGESM.TEESNQGST..DQ.QNK
Retrocopy EMKRKLHYNE*LNIKLARELMSKDLYDDGKDEEMLKTADGESMKTEESNQGSTTGDQRQNK

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	0.00 RPM	27.56 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	15.79 RPM
SRP007412_cerebellum	0.06 RPM	20.47 RPM
SRP007412_heart	0.00 RPM	13.13 RPM
SRP007412_kidney	0.00 RPM	14.55 RPM
SRP007412_liver	0.00 RPM	3.72 RPM
SRP007412_testis	1.21 RPM	211.23 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1314 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1314 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1314 has 0 orthologous retrocopies within eutheria group .

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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,