RetrogeneDB ID: retro_mmul_2013

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 6:72085095..72086121(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.18525
• Ensembl ID: ENSMMUG00000023163
• Aliases: None
• Description: None

Sequence

>retro_mmul_2013
ATGAGCAAGCTGAACCACAATCTCTAGGAGGTGATGAGCAAACTGGAGAAGCAACATTCCAATAAAGTGTTTGTGGTAAA
GGGACTATCAAGCAGCAGCAGGCGCTCTTTAGTCATTTCTCCCCCGGTTCAAACATCTGTGGTCTCCAGTCCTCTTGCCT
CACCTACTAGTCCCTCTACACTTTCCTTGAAGAGTGAGAGTGAATCTGTCTCAACAACTGAAGATCTGGCACCTGATGCA
GCCCAGGGGGAAGATAATTGTGAGATCAAGGAGCCCTTAGAAGATGAAGAAATAGAAAAGGAAGAATCTGAAGCAAGCTT
CTCTGAGGAAGAAGAGCCTCTACCAGCCTGCAATAGCCCCACCCAGGCCCAGCCCTCGCCTACCATTGAGAGTGGCAAGT
CCCAGGAGGAAGTTCTCCCTAGCTCCCCAGCTCCATCACCAGGCAGAGCCCTGCGTCCTTCAAGGCAGCCTGCATTATCT
GCCACAGAAGTAGTCCTCCGAACTCGCACCACAAGTGAAGGATTTGAACAACCAAAGAAGAGAGCCTCTCTCCAGAGGAC
CTCAGCACCCCCTAGTAGGCCTCCTCCACCCAGAGACACTCCAAGCCCCAGGCCCTCCTCAGGGAACATACCCTCCAGCC
CTCCAGCCTCTTGAGGGGATTCACCCACCAGCCCTAGGGTCTCCTTGGGGACTGAGACTCCAAGTCCTAGGACCTCCCTA
GAGGTCTCTCCTAATCCAGAACCACCAGAGAAACCAGTAAGAACTCCTGAGGCCAAAGAAAATGAAAACATCCACGATCA
GAACCCCGAAGAACTTTGCACTTTTCCCACCTTAATGACATCTCAGATTGCTTCAGAACCTGGAGAGGCAAAGAAGATGG
AAGATAAGGAAGAGGATAATAAGCTTGTCTTAGCTGACTCCTCAGAGGGCCAAGACCAGTTTAAAGTCTCCATGGTACCA
GACCAGAGCAACTTCGCAGCACCTGAACCTCAAGAAGAGGTACCTACCAGTGAAAATGCACAACTC

Alignment

ORF - retro_mmul_2013 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.38 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSKLNHNLYEVMSKLEKQHSNKVFVVKGLSSS-RRSLVISPPVQTTMVSSPLTSPTSPSTLSLKSESESV
          MSKLNHNL.EVMSKLEKQHSNKVFVVKGLSSS.RRSLVISPPVQT..VSSPL.SPTSPSTLSLKSESESV
Retrocopy MSKLNHNL*EVMSKLEKQHSNKVFVVKGLSSSSRRSLVISPPVQTSVVSSPLASPTSPSTLSLKSESESV

Parental  SATEDLAPDAAQGDDNSEIKELLEDEEIEKEGSEASSSEEEEPLPACNGPAQAQPSLTIESVKSQEEVLP
          S.TEDLAPDAAQG.DN.EIKE.LEDEEIEKE.SEAS.SEEEEPLPACN.P.QAQPS.TIES.KSQEEVLP
Retrocopy STTEDLAPDAAQGEDNCEIKEPLEDEEIEKEESEASFSEEEEPLPACNSPTQAQPSPTIESGKSQEEVLP

Parental  SSPAPSPGEAPSPSGQPSSSAAEVVLRTRTASEGSEQPKKTASLQRTSAPPSRPPPPRATASPRPSSGNI
          SSPAPSPG.A..PS.QP..SA.EVVLRTRT.SEG.EQPKK.ASLQRTSAPPSRPPPPR.T.SPRPSSGNI
Retrocopy SSPAPSPGRALRPSRQPALSATEVVLRTRTTSEGFEQPKKRASLQRTSAPPSRPPPPRDTPSPRPSSGNI

Parental  PSSPPASGGGSPTSPRASLGTGTPSPRTSLEVSPNPETPEKPVRTPEAKENENMNNQNPEELCTSPTLMT
          PSSPPAS.G.SPTSPR.SLGT.TPSPRTSLEVSPNPE.PEKPVRTPEAKENEN...QNPEELCT.PTLMT
Retrocopy PSSPPAS*GDSPTSPRVSLGTETPSPRTSLEVSPNPEPPEKPVRTPEAKENENIHDQNPEELCTFPTLMT

Parental  SQIASEPGEAKKMEDKEEDDKLISVDSSEGQDQLQVSAVPENNNLTAPEPQEEVSTSENPQL
          SQIASEPGEAKKMEDKEED.KL...DSSEGQDQ..VS.VP...N..APEPQEEV.TSEN.QL
Retrocopy SQIASEPGEAKKMEDKEEDNKLVLADSSEGQDQFKVSMVPDQSNFAAPEPQEEVPTSENAQL

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	3.36 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	2.30 RPM
SRP007412_cerebellum	0.00 RPM	2.58 RPM
SRP007412_heart	0.00 RPM	3.06 RPM
SRP007412_kidney	0.00 RPM	15.14 RPM
SRP007412_liver	0.00 RPM	8.23 RPM
SRP007412_testis	0.00 RPM	63.48 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2013 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2013 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2013 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3192
Pan troglodytes	retro_ptro_2251
Gorilla gorilla	retro_ggor_1336
Pongo abelii	retro_pabe_2648

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Macaca mulatta	ENSMMUG00000023163	1 retrocopy	retro_mmul_2013 ,