RetrogeneDB ID: retro_mdom_351

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:259801145..259801939(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C11orf57
• Ensembl ID: ENSMODG00000014393
• Aliases: None
• Description: chromosome 11 open reading frame 57 [Source:HGNC Symbol;Acc:25569]

Sequence

>retro_mdom_351
AAGGAGACAGATATATGGAAGATAAGAAGGGTGGAGAAATAGTTGGGAGATGCTTACTGGAGAACAGAAAAGAGAAGATT
GACCAGGAACTTGAACCAAATGTGAAGTGATAATTTCAATGAAGAAAGTCTCTGAATCTACTGGAGGACAAAGCAAGAAA
TTCCTAAGACAATGGAAGAAGATCTGCTTAGGGCTTGATCCTGGAATAGTCCATATGATTATGAGGCCAACCTGCCAGAT
AGATGGGGTCATAATGGATTATAGGAACCATATCCTACAGAATTTGACACAAAGAGTGATCAGGAAGATGCTGCTAGTGG
AAGAAAAACACTTCCCAAGAAAAGTAATCTCTTCATAAGTCCCATAAACTTAAGTGGTTAAAGAAATCCCACAGAAAAGC
AGAAAAAATGGTCACACACACAGAGAGAAAAAAGGATAAAGGAAGACATAGAGAGCTGCAGATTCCTCATGTGAATATCT
GGGAGAAAGTCAAGTTTCCAGTGCTAGGAAGGTGAAACAATCACATAAAGGAAGAATAAAATTAAGGAAGAAGGATATTA
AGAAATTTATTTCTTTCTCAGTCATAAAACGATTCTTCTCACGCTGATGATTTCAGCATTCAACAGTTCTGAGGAAAGTG
AAGAAAAAGATTCCAAGGACACCAAAAGGAAAAAGAATCAGAAAGATCATATCACCCCAAAGAAGAGGAAGCATGAGGTA
TGAGAGGAAGTCAGCAAATGGAAGAAGTGAAAGTGGTCACAGACAAAAAGATGGACATGAATTGCAAGGATGAT

Alignment

ORF - retro_mdom_351 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.57 %
• Parental protein coverage: 91.47 %
• Number of stop codons detected: 10
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  EETDMWKIRELEKQMEDAYRGTQRRILPRSSSRMRSDGFDEESHRVYWRTKQEIPGTFEDDLLRTRSWNK
          .ETD.WKIR..EK...DAY..T..R.L.R....M.SD.F.EES...YWRTKQEIP.T.E.DLLR..SWN.
Retrocopy KETDIWKIRRVEK*LGDAYWRTEKRRLTRNLNQM*SDNFNEESL*IYWRTKQEIPKTMEEDLLRA*SWNS

Parental  RLYNYEANMPDRWGHSGYKELYPEEFDTDSDQQDAINGRKTPP-QEKSSTHESHKRKRSKKSHKKKQKKR
          ..Y.YEAN.PDRWGH.G..E.YP.EFDT.SDQ.DA..GRKT.P.QEK.S.H.SHK.K..KKSH.K..K..
Retrocopy P-YDYEANLPDRWGHNGL*EPYPTEFDTKSDQEDAASGRKTLP<QEK*SLHKSHKLKWLKKSHRKAEKMV

Parental  SHK-KQKKSKKEATDRAADSSSECSGETQVSSDRKGKQSHK-RKKKSRK-KAPKKPVSFSESESDSSHPD
          .H....KK.....T.RAADSS.E..GE.QVSS.RK.KQSHK.RK.K.............S.S..DSSH.D
Retrocopy THT<REKKG*RK-T*RAADSSCEYLGESQVSSARKVKQSHK<RKNKIKE<RRILRNLFLSQS*NDSSHAD

Parental  N-SPSSSSEESEEKEAKKTRRKKDQKGHITPTKRKSEVQERTSKRK-NWKVATDEKTDESSEED
          ..S...SSEESEEK..K.T.RKK.QK.HITP.KRK.EV.E..SK.K...KV.TD.K.D.....D
Retrocopy D>SAFNSSEESEEKDSKDTKRKKNQKDHITPKKRKHEV*EEVSKWK<EVKVVTDKKMDMNCKDD

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_351 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_351 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001999	1 retrocopy	retro_btau_1726,
Cavia porcellus	ENSCPOG00000011060	1 retrocopy	retro_cpor_1008,
Monodelphis domestica	ENSMODG00000014393	1 retrocopy	retro_mdom_351 ,
Tursiops truncatus	ENSTTRG00000010518	1 retrocopy	retro_ttru_73,