RetrogeneDB ID: retro_mdom_240

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 2:45892083..45893769(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000000609
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: HNRNPR
• Ensembl ID: ENSMODG00000016144
• Aliases: None
• Description: heterogeneous nuclear ribonucleoprotein R [Source:HGNC Symbol;Acc:5047]

Sequence

>retro_mdom_240
ATGGCTACTGAACATGTTAATGGGAATGGTACTGAAGAGCCCATGGATACTTCTTCTGCAGTTACCCATTCTGAGCATTT
CCAGACATTGCTTGATGCTGGTTTACCACAGAAAGTTGCTGAAAAACTAGATGAAATTTACGTTGCAGGTTTAGTTGCAC
ACAGTGATCTAGATGAAAGAGCAATTGAAGCTTTAAAAGAATTTAATGAAGACGGTGCATTGGCAGTACTTCAACAGTTT
AAAGACAGTGATCTCTCACATGTTCAGAACAAAAGTGCCTTTTTATGTGGAGTCATGAAGACATATAGGCAGAGAGAAAA
ACAGGGGACCAAAGTGGCCGATTCTAGCAAAGGACCAGATGAGGCAAAAATTAAGGCACTCTTGGAAAGAACAAGCTACA
CACTTGATGTGACCACTGGACAGAGGAAGTATGGAGGACCTCCTCCAGATTCAGTATATTCAGGACAACAGCCTTCTGTT
GGTACAGAGATATTTGTGGGAAAGATTCCAAGAGATCTATTTGAAGATGAACTTGTTCCATTATTTGAAAAAGCTGGACC
GATTTGGGATCTGCGCTTAATGATGGATCCTCTGACTGGTCTGAATAGAGGATATGCTTTTGTAACTTTCTGTACAAAAG
AAGCAGCTCAGGAGGCTGTTAAATTGTATAATAATCATGAAATTCGCTCTGGAAAACACATTGGTGTTTGCATCTCAGTT
GCAAATAATAGACTTTTTGTTGGGTCTATTCCCAAGAGTAAAACAAAGGAGCAGATTCTTGAAGAATTTAGCAAAGTAAC
AGAGGGCCTTACAGATGTCATTTTGTACCACCAACCGGATGATAAGAAAAAGAACAGAGGTTTTTGTTTCCTTGAGTATG
AAGATCACAAAACTGCTGCTCAGGCCAGGCGTAGGTTAATGAGTGGCAAAGTGAAAGTCTGGGGAAATGTGGGCACAGTT
GAATGGGCTGACCCTATAGAAGATCCAGATCCTGAAGTCATGGCAAAGGTCAAAGTGCTATTTGTACGTAACCTTGCCAA
TACTGTAACAGAAGAGATTTTAGAAAAAGCATTTAGTCAGTTTGGGAAACTGGAACGAGTGAAGAAACTAAAGGATTATG
CATTCATTCATTTTGATGAGAGAGATGGTGCTGTAAAGGCAATGGAAGAAATGAATGGCAAAGACTTAGAAGGAGAAAAT
ATTGAAATTGTTTTTGCTAAGCCACCAGATCAAAAAAGGAAAGAACGTAAAGCTCAGAGGCAAGCGGCTAAAAATCAAAT
GTATGATGATTACTACTATTATGGTCCACCTCACATGCCCCCTCCAACGAGAGGTCGAGGCCGTGGAGGTAGAGGTGGTT
ATGGATATCCTCCAGATTATTATGGATATGAAGATTATTATGATTATTATGGATATGATTACCATAACTATCGTGGTGGA
TATGAAGATCCATACTATGGTTATGAAGATTTTCAAGTTGGAGCTAGAGGAAGGGGTGGTAGAGGAGCAAGGGGTGCTGC
TCCATCCAGAGTTCGCAGGGCTGCTCCTCCCCGTGGCAGAGCCGGTTATTCACAGAGAGGTGGTCCTGGATCAGCAAGAG
GCGTTCGTGGTGCGAGAGGAGGTGCCCAACAACAAAGAGGCCGCGGGGGAAAAGGGGTCGAGGCCGGTCCTGACCTGTTA
CAATGA

Alignment

ORF - retro_mdom_240 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.64 %
• Parental protein coverage: 82.04 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EEPMDTSS-VTHTEHYKTLIEAGLPQKVAERLDEIFQTGLVAYVDLDERAIDALREFNEEGALSVLQQFK
          EEPMDTSS.VTH.EH..TL..AGLPQKVAE.LDEI...GLVA..DLDERAI.AL.EFNE.GAL.VLQQFK
Retrocopy EEPMDTSSAVTHSEHFQTLLDAGLPQKVAEKLDEIYVAGLVAHSDLDERAIEALKEFNEDGALAVLQQFK

Parental  ESDLSHVQNKSAFLCGVMKTYRQREKQGSKVQESTKGPDEAKIKALLERTGYTLDVTTGQRKYGGPPPDS
          .SDLSHVQNKSAFLCGVMKTYRQREKQG.KV..S.KGPDEAKIKALLERT.YTLDVTTGQRKYGGPPPDS
Retrocopy DSDLSHVQNKSAFLCGVMKTYRQREKQGTKVADSSKGPDEAKIKALLERTSYTLDVTTGQRKYGGPPPDS

Parental  VYSGVQPGIGTEVFVGKIPRDLYEDELVPLFEKAGPIWDLRLMMDPLSGQNRGYAFITFCGKDAAQEAVK
          VYSG.QP..GTE.FVGKIPRDL.EDELVPLFEKAGPIWDLRLMMDPL.G.NRGYAF.TFC.K.AAQEAVK
Retrocopy VYSGQQPSVGTEIFVGKIPRDLFEDELVPLFEKAGPIWDLRLMMDPLTGLNRGYAFVTFCTKEAAQEAVK

Parental  LCDSYEIRPGKHLGVCISVANNRLFVGSIPKNKTKENILEEFSKVTGLTEGLVDVILYHQPDDKKKNRGF
          L....EIR.GKH.GVCISVANNRLFVGSIPK.KTKE.ILEEFSKVT...EGL.DVILYHQPDDKKKNRGF
Retrocopy LYNNHEIRSGKHIGVCISVANNRLFVGSIPKSKTKEQILEEFSKVT---EGLTDVILYHQPDDKKKNRGF

Parental  CFLEYEDHKSAAQARRRLMSGKVKVWGNVVTVEWADPVEEPDPEVMAKVKVLFVRNLATTVTEEILEKSF
          CFLEYEDHK.AAQARRRLMSGKVKVWGNV.TVEWADP.E.PDPEVMAKVKVLFVRNLA.TVTEEILEK.F
Retrocopy CFLEYEDHKTAAQARRRLMSGKVKVWGNVGTVEWADPIEDPDPEVMAKVKVLFVRNLANTVTEEILEKAF

Parental  SEFGKLERVKKLKDYAFVHFEDRGAAVKAMDEMNGKEIEGEEIEIVLAKPPDKKRKERQAARQASRSTAY
          S.FGKLERVKKLKDYAF.HF..R..AVKAM.EMNGK..EGE.IEIV.AKPPD.KRKER.A.RQA.....Y
Retrocopy SQFGKLERVKKLKDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFAKPPDQKRKERKAQRQAAKNQMY

Parental  EDYYYHPPPRMPPPLRGRGRGGGRGGYGYPPDYYGYEDYYDDYYGYDYHDYRGGYEDPYYGYDDGYAVRG
          .DYYY..PP.MPPP.RGRGR.GGRGGYGYPPDYYGYEDYY.DYYGYDYH.YRGGYEDPYYGY.D...V..
Retrocopy DDYYYYGPPHMPPPTRGRGR-GGRGGYGYPPDYYGYEDYY-DYYGYDYHNYRGGYEDPYYGYED-FQVGA

Parental  RG-GGRGGRGAPPPPRGRGAPPPRGRAGYSQRGAPLGPPRGARGGRGGPAQPQRGRGSRG
          RG.GGRG.RGA..P.R.R.A.PPRGRAGYSQRG.P.G..RG.RG.RGG.AQ.QRGRG..G
Retrocopy RGRGGRGARGA-APSRVRRAAPPRGRAGYSQRGGP-GSARGVRGARGG-AQQQRGRGGKG

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	0.00 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.00 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_240 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_240 was not experimentally validated.

Homology

Retrocopy orthology:

Monodelphis domestica does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000125944	1 retrocopy	retro_hsap_651,
Gorilla gorilla	ENSGGOG00000013250	1 retrocopy	retro_ggor_568,
Macaca mulatta	ENSMMUG00000010970	1 retrocopy	retro_mmul_2433,
Monodelphis domestica	ENSMODG00000007003	1 retrocopy	retro_mdom_39,
Monodelphis domestica	ENSMODG00000016144	1 retrocopy	retro_mdom_240 ,
Mus musculus	ENSMUSG00000066037	1 retrocopy	retro_mmus_458,
Otolemur garnettii	ENSOGAG00000009179	1 retrocopy	retro_ogar_3144,
Procavia capensis	ENSPCAG00000010462	1 retrocopy	retro_pcap_88,
Pan troglodytes	ENSPTRG00000000324	1 retrocopy	retro_ptro_474,
Tupaia belangeri	ENSTBEG00000002251	1 retrocopy	retro_tbel_4256,