RetrogeneDB ID: retro_mdom_1846

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 8:81015876..81017278(+)
• Located in intron of: ENSMODG00000003056

Retrocopy information

• Ensembl ID: ENSMODG00000003068
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CARM1
• Ensembl ID: ENSMODG00000006104
• Aliases: None
• Description: coactivator-associated arginine methyltransferase 1 [Source:HGNC Symbol;Acc:23393]

Sequence

>retro_mdom_1846
CCCTCTACAGCCATGAAGATGTTTGTGTGTTTAAGTGCTCCATGTCCAGAATGCAGCCGAGTTGGAAAGCAGTCCTTCAT
CATCATCCCGGGATGTAACAGCGTCCTTATACAATTTGCCACACCTAATGATTTCTGTTCATTATACAATATTCTGAAAA
CCTGTCGAGGTCACAACTTAGAGCACTCTGTCTTCAGTGAGCAGACAGAAGAATCCTCTGCTGTGCAGTACTTCCAGTTC
TATGGCTACCTGTCACAGCAACAGAATATGATGCAAGATTATGTACGAACAGGCACGTATCAAAGGGCAATCCTGCAGAA
CCATAGTGATTTTAAAGACAAGATTGTCTTAGATGTGAGTTGTGGCTTGGGGATCCTGTCTTTTTTTGCTGCTCAGGCAG
GAGCAAGAAAAGTCTATGCAGTGGAAGCAAGCATCATGGCTCAGCATGCTGAGGTTTTAGTAAAGAGTAACAACCTCACA
GACCGAATTGTGGTCATTCCTGGAAAGGTGGAGGAAATCTCACTTCCCGAGCAGGTGGACATAATTATTTCAGAGCCAAT
GGGCTACATGCTTTTCAATGAATGTATGTTGGAGAGCTACCTCCATGCCAAGAAGTACTTAAGCCTAGTGGGAATATGTT
TCCAACTATTGGGGATGTACATCTCGCACCATTTACAGATGAGCAGCTCTACACGGAACAGTTTACCAAGGCCAATTTTT
GGTATCAGTCATCTTTTCATGGAGTTGAGTCAACACTTAGAAGAGCAGCAGTAGACGAGTATTTCAGACAGCCTGTCGTG
GACACCTTTGATATCAGGATTTTAATGGCTAAGTCAGTAAAATATACGGTGAATTTTTAGAAGCCAAAGAAGGTGATTTG
CACAGGATAGAAATCCCATTCAAGTTCCACATGCTGCACTCAGGACTTGTCCATGGTTTGGCTTTCTGGTTTGATGTAGC
CTTCATTGGTTCAATAATGACAGTGTGGCTATCCACAGCACCCACAGAGCCTCGGACTCACTGGTACCAAGTTCGGTGTT
TGTTTCAGTCTCCACTTTTTGCAAAGGCTGGGGACACGCTCTCAGGGACATGTCTGCTCATTGCAAATAAGAGACAAAGC
TATGACATCAGTATTGTTGCCCAGGTGGATCAGACGGGTTCTAAATCCAGTAACCTCCTGGACCTGAAAAACCCTTTCTT
TAGATATACAGGTACGACGCCATCTCCTCCTCCTGGCTCCCACTATACGTCTCCCTCTGAAAACATGTGGAACACAGGCA
GTGCCTACAATCTGAGCAGTGGGATGGCTGTGGCTGGGATGCCAATGGCCTACGACCTGAGCAGTGTTATTGCTAGCGGG
ACCAGCGTCAGCCACAACAACCTTATCCCTTTAGGATCCTCC

Alignment

ORF - retro_mdom_1846 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.14 %
• Parental protein coverage: 81.99 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PDEDVCVFKCSVSRETECSRVGKQSFIITLGCNSVLIQFATPNDFCSFYNILKTCRGHNLERSVFSERTE
          P......F.C......ECSRVGKQSFII..GCNSVLIQFATPNDFCS.YNILKTCRGHNLE.SVFSE.TE
Retrocopy PSTAMKMFVCLSAPCPECSRVGKQSFIIIPGCNSVLIQFATPNDFCSLYNILKTCRGHNLEHSVFSEQTE

Parental  ESSAVQYFQFYGYLSQQQNMMQDYVRTGTYQRAILQNHSDFKDKIVLDVGCGSGILSFFAAQAGARKVYA
          ESSAVQYFQFYGYLSQQQNMMQDYVRTGTYQRAILQNHSDFKDKIVLDV.CG.GILSFFAAQAGARKVYA
Retrocopy ESSAVQYFQFYGYLSQQQNMMQDYVRTGTYQRAILQNHSDFKDKIVLDVSCGLGILSFFAAQAGARKVYA

Parental  VEASTMAQHAEVLVKSNNLTDRIVVIPGKVEEISLPEQVDIIISEPMGYMLFNERMLESYLHAKKY-LKP
          VEAS.MAQHAEVLVKSNNLTDRIVVIPGKVEEISLPEQVDIIISEPMGYMLFNE.MLESYLHAKKY.LKP
Retrocopy VEASIMAQHAEVLVKSNNLTDRIVVIPGKVEEISLPEQVDIIISEPMGYMLFNECMLESYLHAKKY<LKP

Parental  SGNMFPTIGDVHLAPFTDEQLYMEQFTKANFWYQPSFHGVDLSALRGAAVDEYFRQPVVDTFDIRILMAK
          SGNMFPTIGDVHLAPFTDEQLY.EQFTKANFWYQ.SFHGV..S.LR.AAVDEYFRQPVVDTFDIRILMAK
Retrocopy SGNMFPTIGDVHLAPFTDEQLYTEQFTKANFWYQSSFHGVE-STLRRAAVDEYFRQPVVDTFDIRILMAK

Parental  SVKYTVN-FLEAKEGDLHRIEIPFKFHMLHSGLVHGLAFWFDVAFIGSIMTVWLSTAPTEPLTHWYQVRC
          SVKYTVN.FLEAKEGDLHRIEIPFKFHMLHSGLVHGLAFWFDVAFIGSIMTVWLSTAPTEP.THWYQVRC
Retrocopy SVKYTVN<FLEAKEGDLHRIEIPFKFHMLHSGLVHGLAFWFDVAFIGSIMTVWLSTAPTEPRTHWYQVRC

Parental  LFQSPLFAKAGDTLSGTCLLIANKRQSYDISIVAQVDQTGSKSSNLLDLKNPFFRYTGTTPSPPPGSHYT
          LFQSPLFAKAGDTLSGTCLLIANKRQSYDISIVAQVDQTGSKSSNLLDLKNPFFRYTGTTPSPPPGSHYT
Retrocopy LFQSPLFAKAGDTLSGTCLLIANKRQSYDISIVAQVDQTGSKSSNLLDLKNPFFRYTGTTPSPPPGSHYT

Parental  SPSENMWNTGGAYNLSSGMAVAGMPTAYDLSSVIASGASVSHNNLIPLANT
          SPSENMWNTG.AYNLSSGMAVAGMP.AYDLSSVIASG.SVSHNNLIPL...
Retrocopy SPSENMWNTGSAYNLSSGMAVAGMPMAYDLSSVIASGTSVSHNNLIPLGSS

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_1846 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1846 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000006104	1 retrocopy	retro_mdom_1846 ,
Nomascus leucogenys	ENSNLEG00000012371	1 retrocopy	retro_nleu_75,