RetrogeneDB ID: retro_mmul_2139

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 7:28113718..28114838(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RLIM
• Ensembl ID: ENSMMUG00000009249
• Aliases: None
• Description: E3 ubiquitin-protein ligase RLIM [Source:RefSeq peptide;Acc:NP_001253768]

Sequence

>retro_mmul_2139
ATGGAAAACTCAGATTCTAACGACAAAGGAAGTGGTGATCAGTCTGCAGCACAGCGCAGAATTCAGATGGACCGATTGGA
TCGGGAAGAAGCTTTCTACCAATTTGTAAATAACCTGAGTGAAGAAGATTATAGGCTTAGGAGAGAGAACAGTTTGCTAG
GCACCCCAGGTGAAAGTACTGAGGAACAGTTGCTGAGAAGACTACAGCAAATTAAAGAAAGCCCGCCACCGCAAAACTCA
GGTGAAAATAGAGGAGGAGACTCTTCAGATGATGTGTCTAATGGTGACTCTACAACAGACTGGCTTAACTCTGTCAGACA
AACGGAAAATATAACAAGAAGTGGAAAAAGAGGAAACCAATCTTGGAGAGCAGTGAGCCGGACTAATCCAAACAGTGGTG
ACTGCAGATTCAGTTTAGAGATAAATGTTAACAGTAATAATGGGGGCCAAATTTCAGAGAATGAAAATGAGCCATCTGCA
AGACGTTCTAGTGGAGAAAATGTGGAAAACAACAGCCAAAGGCAAGTGGAAAACCCACGACCTGAATAGTATCTGCAAGG
CCATCTAGATCAGAACGAAATTCAGCTGAAGCATTAACAGAAGTTCCACTTACCAGAGGTCAGAGGAGGGCAGGAAGCAG
GAGGCTAGACTATCGGAGAACCAGAGCAAGAGCTGAGAGAAGGAGGTCACCTCTGCATCCAATGAGTGAAATTCCACGAA
GATCTCATCATCATATCTCATCTCAGATTTTTGAACATCTTTGGTAAATGAGACGGAGGGAAGTTCTAGAACCCGGCCCC
GTGTGACATTGAGAGAGCAAATATCTGGGCCTGAGTTGCTAAGTAGAGGTATTTTTGCAGCTTCTGGAACAAGAAATGCC
TCTCAAGGAGCAGGTTCTTCAGACACAGCTGCCAATGGTGAATCTACAGGATCAGGATAGAGACCAACCGTAGTCCTTGA
TCTTCAAGTAAGAAGAGTTCGTCCTGGAGAATATCAGCAGAGAGAGAGAATAGTCAGCGAAACGTGGTCTAGGTCTCAGA
CGCCAAACAATACTGTCACCTACGAAAGTGAACGAGGAGGTTTTAGGTGTACATTTTCACGTTCTGAGCAGGGAGGTGTG

Alignment

ORF - retro_mmul_2139 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.53 %
• Parental protein coverage: 60.1 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MENSDSNDKGSGDQSAAQRRSQMDRLDREEAFYQFVNNLSEEDYRLMRDNNLLGTPGESTEEELLRRLQQ
          MENSDSNDKGSGDQSAAQRR.QMDRLDREEAFYQFVNNLSEEDYRL.R.N.LLGTPGESTEE.LLRRLQQ
Retrocopy MENSDSNDKGSGDQSAAQRRIQMDRLDREEAFYQFVNNLSEEDYRLRRENSLLGTPGESTEEQLLRRLQQ

Parental  IKEGPPPQNSDENRGGDSSDDVSNGDSIIDWLNSVRQTGNTTRSGQRGNQSWRAVSRTNPNSGDFRFSLE
          IKE.PPPQNS.ENRGGDSSDDVSNGDS..DWLNSVRQT.N.TRSG.RGNQSWRAVSRTNPNSGD.RFSLE
Retrocopy IKESPPPQNSGENRGGDSSDDVSNGDSTTDWLNSVRQTENITRSGKRGNQSWRAVSRTNPNSGDCRFSLE

Parental  INVNRNNGSQNSENENEPSARRSSGENVENNSQRQVENPRSE-STSARPSRSERNSTEALTEVPPTRGQR
          INVN.NNG.Q.SENENEPSARRSSGENVENNSQRQVENPR.E...SARPSRSERNS.EALTEVP.TRGQR
Retrocopy INVNSNNGGQISENENEPSARRSSGENVENNSQRQVENPRPE<IVSARPSRSERNSAEALTEVPLTRGQR

Parental  RARSRSPDHRRTRARAERSRSPLHPMSEIPRRSHHSISSQTFEH-PLVNETEGSSRTRHHVTLRQQISGP
          RA.SR..D.RRTRARAER.RSPLHPMSEIPRRSHH.ISSQ.FEH..LVNETEGSSRTR..VTLR.QISGP
Retrocopy RAGSRRLDYRRTRARAERRRSPLHPMSEIPRRSHHHISSQIFEH<SLVNETEGSSRTRPRVTLREQISGP

Parental  ELLSRGLFAASGTRNASQGAGSSDTAANGESTGSGQRPPTIVLDLQVRRVRPGEYRQRDSIASRTRSRSQ
          ELLSRG.FAASGTRNASQGAGSSDTAANGESTGSG.R.PT.VLDLQVRRVRPGEY.QR..I.S.T.SRSQ
Retrocopy ELLSRGIFAASGTRNASQGAGSSDTAANGESTGSG*R-PTVVLDLQVRRVRPGEYQQRERIVSETWSRSQ

Parental  TPNNTVTYESERGGFRRTFSRSERAGV
          TPNNTVTYESERGGFR.TFSRSE..GV
Retrocopy TPNNTVTYESERGGFRCTFSRSEQGGV

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	0.78 RPM	31.60 RPM
SRP007412_brain_prefrontal_cortex	0.24 RPM	23.32 RPM
SRP007412_cerebellum	0.39 RPM	20.79 RPM
SRP007412_heart	0.06 RPM	6.30 RPM
SRP007412_kidney	0.23 RPM	7.04 RPM
SRP007412_liver	0.04 RPM	2.65 RPM
SRP007412_testis	3.54 RPM	10.03 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2139 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2139 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2139 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1495
Pan troglodytes	retro_ptro_1014
Pongo abelii	retro_pabe_1245

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000131263	1 retrocopy	retro_hsap_1495,
Macaca mulatta	ENSMMUG00000009249	1 retrocopy	retro_mmul_2139 ,
Pongo abelii	ENSPPYG00000020481	1 retrocopy	retro_pabe_1245,
Pan troglodytes	ENSPTRG00000022037	1 retrocopy	retro_ptro_1014,