RetrogeneDB ID: retro_mmul_1540

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 2:160152046..160152916(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000005642
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PPA1
• Ensembl ID: ENSMMUG00000006397
• Aliases: None
• Description: None

Sequence

>retro_mmul_1540
GTGAGCGGTCTCAGCACCGAGGTGCACACCGTGCCCTTCTCCCTGGAGTACCGAGTCTTCTTCAAAAATGAGAAAGGACA
ATATGTATTTCCATTTCATGATATTCCAATTTATGCAGATAAGGATGTGTTCCACATGGTAGTTGGAAGTACCACGCTGG
TCTAATGCAAAAATGGAGATTGCTACAAAGCACCCTTTACACATCATTAAACAAGATGTAAAAAAAGAAAAACTTCGTTA
TTTTGTGAATCTGTTCCCATATAAAGGATATATCTGGAACTATGGTGCCATCCCTCAGACTTGGGAAGACCCAGGACACA
ATGATAAACATACTGGCTGTTGTGGTGACAATGACCCAACTGATGTGTGTGAAATTGGAAGCAAAGTATGTGCAAGAGGT
GAAATAATTGACACAAAAGCCCTAGGCATATTGGCTATGATTGACAAAAGGGAAACCGACTGGAAAGTCATTGCCACATT
AACTGTGGATGATCCTTATGCAGCCAATTATAGTGATATCAATGATGTCAAATGGCTGAAACCTGGCTACTTAGAAGCTA
CCTTGGACTGGGTTAGAAGGTATAAGGTTCCTGATGGAAAACCAGAAATGAGTTTGCTTTTAAGGCAGCATTTAAAGATA
AGGACTTTACAACTGATATTATTAAAAGTACTCATGATCATTGGAAAGCATTAGTGACTAAGAAAATTAATGGAAAAGGA
ATCAGTTGCATGAATACAACTGTGTCCGAGAGCCCCTTCAAGTGTGATCCTGATGCTGCCAGAGCCATTGTGGATGCTTT
ACCACCATCCTGTGAATCTGCCTGCACAGTACCAACAGATGTGGATAAGTGGTTCCGTCACCAGAAAAAC

Alignment

ORF - retro_mmul_1540 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.62 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSGFSTEERAAPFSLEYRVFLKNEKGQYISPFHDIPIYADKDVFHMVV-EVPRWSNAKMEIATKDPLNPI
          .SG.STE....PFSLEYRVF.KNEKGQY..PFHDIPIYADKDVFHMVV.EVPRWSNAKMEIATK.PL..I
Retrocopy VSGLSTEVHTVPFSLEYRVFFKNEKGQYVFPFHDIPIYADKDVFHMVV>EVPRWSNAKMEIATKHPLHII

Parental  KQDVKKGKLRYVANLFPYKGYIWNYGAIPQTWEDPGHNDKHTGCCGDNDPIDVCEIGSKVCARGEIIGVK
          KQD.....LRY..NLFPYKGYIWNYGAIPQTWEDPGHNDKHTGCCGDNDP.DVCEIGSKVCARGEII..K
Retrocopy KQDXXXXXLRYFVNLFPYKGYIWNYGAIPQTWEDPGHNDKHTGCCGDNDPTDVCEIGSKVCARGEIIDTK

Parental  VLGILAMIDEGETDWKVIA-INVDDPDAANYNDINDVKRLKPGYLEATVDWFRRYKVPDGKPE-NEFAFN
          .LGILAMID..ETDWKVIA...VDDP.AANY.DINDVK.LKPGYLEAT.DW.RRYKVPDGKPE.NEFAF.
Retrocopy ALGILAMIDKRETDWKVIATLTVDDPYAANYSDINDVKWLKPGYLEATLDWVRRYKVPDGKPE<NEFAFK

Parental  AEFKDKDFAIDIIKSTHDHWKALVTKKTNGKGISCMNTTVSESPFKCDPDAARAIVDALPPPCESACTVP
          A.FKDKDF..DIIKSTHDHWKALVTKK.NGKGISCMNTTVSESPFKCDPDAARAIVDALPP.CESACTVP
Retrocopy AAFKDKDFTTDIIKSTHDHWKALVTKKINGKGISCMNTTVSESPFKCDPDAARAIVDALPPSCESACTVP

Parental  TDVDKWFHHQKN
          TDVDKWF.HQKN
Retrocopy TDVDKWFRHQKN

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	100.51 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	63.15 RPM
SRP007412_cerebellum	0.00 RPM	95.12 RPM
SRP007412_heart	0.00 RPM	31.15 RPM
SRP007412_kidney	0.00 RPM	31.45 RPM
SRP007412_liver	0.08 RPM	92.43 RPM
SRP007412_testis	0.00 RPM	29.51 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1540 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1540 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1540 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2756
Pan troglodytes	retro_ptro_1864

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000014023	1 retrocopy	retro_cpor_615,
Homo sapiens	ENSG00000180817	2 retrocopies	retro_hsap_2756, retro_hsap_3267,
Loxodonta africana	ENSLAFG00000004048	1 retrocopy	retro_lafr_990,
Myotis lucifugus	ENSMLUG00000017790	1 retrocopy	retro_mluc_2469,
Macaca mulatta	ENSMMUG00000006397	1 retrocopy	retro_mmul_1540 ,
Macaca mulatta	ENSMMUG00000017004	1 retrocopy	retro_mmul_1278,
Nomascus leucogenys	ENSNLEG00000016098	1 retrocopy	retro_nleu_7,
Oryctolagus cuniculus	ENSOCUG00000016001	2 retrocopies	retro_ocun_1373, retro_ocun_883,
Procavia capensis	ENSPCAG00000006788	1 retrocopy	retro_pcap_247,
Pan troglodytes	ENSPTRG00000002585	2 retrocopies	retro_ptro_1864, retro_ptro_2210,
Tupaia belangeri	ENSTBEG00000008947	3 retrocopies	retro_tbel_3560, retro_tbel_3561, retro_tbel_848,
Tarsius syrichta	ENSTSYG00000005511	1 retrocopy	retro_tsyr_1856,