RetrogeneDB ID: retro_mmul_1001

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 13:100451426..100451758(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARPP19
• Ensembl ID: ENSMMUG00000008344
• Aliases: None
• Description: cAMP-regulated phosphoprotein 19 [Source:RefSeq peptide;Acc:NP_001253378]

Sequence

>retro_mmul_1001
ATGTCTGTGGAAGTCTCCGGGGCAGCCTCTGTGGAGAAGCAGAAGGAAATGGAAGATACAGTGAATAGTCCAGAGAAAAC
TGAAGAAGCAAAATTAAAAGCAAGATATCCTCATCTGGGACAAATGCCTGCAGGTTCAGATTTCTTAAGGAAACGATTGC
AGAAAGGGCAAAAATATTTTGATTCTGGGATTACAACATGGCTAAAGCAAAGATGAAGAACAAGCAACTTCCTACTGCAG
CTCTGGAGAAGACAGAGGTCACTGGTGACCACATTCCCACTCCAAAGGACCTTGCTCAATGGAAACCATCCCTTGTTGCT
AGCAAGCTGGCT

Alignment

ORF - retro_mmul_1001 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.82 %
• Parental protein coverage: 99.11 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSAEVPEAASAEEQKEMEDKVTSPEKAEEAKLKARYPHLGQKPGGSDFLRKRLQKGQKYFDSG-DYNMAK
          MS.EV..AAS.E.QKEMED.V.SPEK.EEAKLKARYPHLGQ.P.GSDFLRKRLQKGQKYFDSG.DYNMAK
Retrocopy MSVEVSGAASVEKQKEMEDTVNSPEKTEEAKLKARYPHLGQMPAGSDFLRKRLQKGQKYFDSG<DYNMAK

Parental  AKMKNKQLPAAAPDKTEVTGDHIPTPQDLPQRKPSLVASKLA
          AKMKNKQLP.AA..KTEVTGDHIPTP.DL.Q.KPSLVASKLA
Retrocopy AKMKNKQLPTAALEKTEVTGDHIPTPKDLAQWKPSLVASKLA

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	83.14 RPM
SRP007412_brain_prefrontal_cortex	0.08 RPM	100.35 RPM
SRP007412_cerebellum	0.06 RPM	20.92 RPM
SRP007412_heart	0.00 RPM	15.37 RPM
SRP007412_kidney	0.00 RPM	21.13 RPM
SRP007412_liver	0.00 RPM	3.76 RPM
SRP007412_testis	0.00 RPM	111.50 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1001 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1001 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1001 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000011321	2 retrocopies	retro_dord_194, retro_dord_33,
Gorilla gorilla	ENSGGOG00000025250	1 retrocopy	retro_ggor_198,
Macaca mulatta	ENSMMUG00000008344	1 retrocopy	retro_mmul_1001 ,
Otolemur garnettii	ENSOGAG00000013865	1 retrocopy	retro_ogar_591,
Pongo abelii	ENSPPYG00000006487	2 retrocopies	retro_pabe_120, retro_pabe_1923,
Pteropus vampyrus	ENSPVAG00000004012	1 retrocopy	retro_pvam_205,