RetrogeneDB ID: retro_mmul_143

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 1:89413754..89414444(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000031997
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: MMU.8841
• Ensembl ID: ENSMMUG00000019376
• Aliases: None
• Description: None

Sequence

>retro_mmul_143
ATGATCATCAAGCCCACCGGCCCTTGCCTTCTCCCAGACCCACTGCAGGAGCCGTACTACCAGCCACCCTACACGCTCGT
TTTGGAGCTCACCGGCGTCCTCTTGCATCCTGAGTGGTCGCTGGCCACTGGCTGGAGGTTTAAGAAGCGCCCAGGCATCG
AGACCTTGTTCCAGCAGCTCACCCCTTTATATGAAATTGTCATCTTTACGTCAGAGACTGGCATGACTACGTTTCCACTC
ATTGATAGCGTGGACCCCCACGGCTTCATCTCCTACCGCCTATTCCGGGAAGCCACAAGATACATGAATGGACACCATGT
TAAGGACATTTCATGTCTGAATCGGGACCCAGCTCGAGTAGTAGTTGTGAACTGCAAGAAGGAAGCCTTCCGCCTGCAGC
CCTATAATGGCGTCGCCCTGCAGCCCTGGGACGGCAACCCTGATGACCGGGTCTTGTTGGACCTGTCTGCCTTCCTCAAG
ACTATTGCACTGAACGGTGTGGAGGACGTGCGAAACATACTGGAGCACTACGCCCTGGAGGATGATCCGCTGGCAGCTTT
CAAACAGCAGCAAAGCCGGCTAGAGCAGGAGGAGCAGCGGCGCCTGGCCGAGCTCTCCAAGTCCAAGAAGCAGAACCTCT
TCCTCGGCTCCCTCATCAGCCGCTTGTGGTCTCGCTCCAAACAGCCCTGA

Alignment

ORF - retro_mmul_143 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.58 %
• Parental protein coverage: 50.55 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MIIEPTSPCLLPDPLQEPYYQPPYTLVLELTGVLLHPEWSLATGWRFKKRPGIETLFQQLAPLYEIVIFT
          MII.PT.PCLLPDPLQEPYYQPPYTLVLELTGVLLHPEWSLATGWRFKKRPGIETLFQQL.PLYEIVIFT
Retrocopy MIIKPTGPCLLPDPLQEPYYQPPYTLVLELTGVLLHPEWSLATGWRFKKRPGIETLFQQLTPLYEIVIFT

Parental  SETGMTAFPLIDSVDPHGFISYRLFRDATRYMDGHHVKDISCLNRDPARVVVVDCKKEAFRLQPYNGVAL
          SETGMT.FPLIDSVDPHGFISYRLFR.ATRYM.GHHVKDISCLNRDPARVVVV.CKKEAFRLQPYNGVAL
Retrocopy SETGMTTFPLIDSVDPHGFISYRLFREATRYMNGHHVKDISCLNRDPARVVVVNCKKEAFRLQPYNGVAL

Parental  RPWDGNSDDRVLLDLSAFLKTIALNGVEDVRTVLEHYALEDDPLAAFKQRQSRLEQEEQQRLAELSKSNK
          .PWDGN.DDRVLLDLSAFLKTIALNGVEDVR..LEHYALEDDPLAAFKQ.QSRLEQEEQ.RLAELSKS.K
Retrocopy QPWDGNPDDRVLLDLSAFLKTIALNGVEDVRNILEHYALEDDPLAAFKQQQSRLEQEEQRRLAELSKSKK

Parental  QNLFLGSLTSRLWPRSRQP
          QNLFLGSL.SRLW.RS.QP
Retrocopy QNLFLGSLISRLWSRSKQP

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	0.34 RPM	21.63 RPM
SRP007412_brain_prefrontal_cortex	1.43 RPM	33.40 RPM
SRP007412_cerebellum	0.19 RPM	14.34 RPM
SRP007412_heart	0.24 RPM	20.55 RPM
SRP007412_kidney	0.23 RPM	19.84 RPM
SRP007412_liver	0.20 RPM	39.94 RPM
SRP007412_testis	0.83 RPM	58.58 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_143 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_143 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_143 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Macaca mulatta	ENSMMUG00000019376	1 retrocopy	retro_mmul_143 ,
Oryctolagus cuniculus	ENSOCUG00000002166	1 retrocopy	retro_ocun_1046,
Drosophila melanogaster	FBgn0250874	2 retrocopies	retro_dmel_72, retro_dmel_8,