RetrogeneDB ID: retro_mdom_1274

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 4:212533964..212535350(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HARS2
• Ensembl ID: ENSMODG00000011309
• Aliases: None
• Description: histidyl-tRNA synthetase 2, mitochondrial [Source:HGNC Symbol;Acc:4817]

Sequence

>retro_mdom_1274
AGGATGAAGACTCAGCTGGAATTAAATAAAGAGAAACCCAGTTTTGTTATCAAGACTCCCAAGGGTACCAGAGATCTTAG
CCCTCAAAAGATGGCTATTGGAGAGAAAATCCTTAATGCTGTCATCAATTGTTTCAAGTGCCATGGAGCTAAAGGAATAG
ACACTCTAGTGTTTAAACTAAAGGAAATATTAACAGAGAAGTATGGAGAAGAATACAGGCTCATCTCTGATATGAAGGAT
CAGGGTGGGGAGCTGCTAGCTCTTCAATATGACCTCACAGTTCCTTTTGCTCATTATCTGGCCATGAATAAGATAAAGAA
GATGAAATGCTATCACATTGGGAAGGTTTAGTGAAGGGAGAGTCCCTCCATAATTCAAGGTCGATATCAGGAGTTTTGCC
AAGGTGATTTTGACATTGCAGGGCAATTTAATCCCATGATCCCTGATGCAGAGTGATTAAAGATCATACATGAAATTCTC
AACACATTAAAATTGGGAGACTTCCTAATTAAGGTGAATGACAGGAGAGTTGTGGATGGTATGTTTGCTGTCTGTGGTGT
CCCTGATAACAAATTTCATTTTATTTGTGCTTCAGTTGATAAGCTTGGCAAGATGTCCTGGAAGGATGTGAGACAAGAGA
TGACAGGAAAGATGGGACTCACCCCTAATATAGCAAATCTAATTGGGGTGTGGTGTGGTGGAGTGTCCCTAGTAGAGCAG
CTACTACAGGATCCCAAACTCTCACAGAACAAACAGGCTCTGGAAGGATTAAAGGACCTGAAACTTCTGTTTGAGTATCT
GACCCTGTTTGGTATTGCAGAGAAGATTTCCTTCGACTTGAGCCTGGCTTGAGGCCTGAGCTATTACCCAGGAGTGATCT
ATGAAGCAGTGATTCTTCAGAGCCCAGCCCAATAGGGGGAGGAAGCACTTGGTGTGGGCAGTGTGGCTTCTGGAGGGTGC
TATGATGGACTTCTTGGCATATTTGACCCCAAGGGTCGCAAGGTGCCCTGTGTGTGGCTCAGCATTGGGTTTGAAAGGAT
CTTCTCCATTGTGGAACAAAGGATGGAGGCCACTAAGAAAATACAAACAACAGAGACAGAGGTCCTTGTGGCTACAGCAC
AAAAGAATTTTCTTAGGGAACTAATAAAACTGATTGTAGAGCTCTGGGATGCTGGGATCAGGGCTGAGATGTTATATAAG
AAGAATCCCAGTTTCCTGACTCAGCTACATTAATGTGAGGAGACAGGCATCCCATTGGTGGCTATCATTGGAGAACAAGA
GCTAAAGGATGGTGTCATTAAGCTTCCTTCTGTGGCTAGTAGGAAAGAGGTAGACATTAAACGGGAAGATATTGTAACCA
AAAGCCAGAGAAGAATGTCTGAATCC

Alignment

ORF - retro_mdom_1274 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.6 %
• Parental protein coverage: 91.9 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QMKTQLELNKEKSSFVIKTPKGTRDLSPQQMAIREKILNAVINCFKCHGAKGIDTPVFELKEILTEKYGE
          .MKTQLELNKEK.SFVIKTPKGTRDLSPQ.MAI.EKILNAVINCFKCHGAKGIDT.VF.LKEILTEKYGE
Retrocopy RMKTQLELNKEKPSFVIKTPKGTRDLSPQKMAIGEKILNAVINCFKCHGAKGIDTLVFKLKEILTEKYGE

Parental  ESRLIYELKDQGGELLALRYDLTVPFARYLAMNKIKKMKRYHVGKVWRRESPSIIQGRYREFCQCDFDIA
          E.RLI...KDQGGELLAL.YDLTVPFA.YLAMNKIKKMK.YH.GKV..RESPSIIQGRY.EFCQ.DFDIA
Retrocopy EYRLISDMKDQGGELLALQYDLTVPFAHYLAMNKIKKMKCYHIGKV**RESPSIIQGRYQEFCQGDFDIA

Parental  GQFDPMIPDAECLKIIHEILSTLQLGDFLIKVNDRRVVDGMFAVCGVPDNKFRFICASVDKLGKMSWKDV
          GQF.PMIPDAE.LKIIHEIL.TL.LGDFLIKVNDRRVVDGMFAVCGVPDNKF.FICASVDKLGKMSWKDV
Retrocopy GQFNPMIPDAE*LKIIHEILNTLKLGDFLIKVNDRRVVDGMFAVCGVPDNKFHFICASVDKLGKMSWKDV

Parental  RQEMTGKIGLTPDVADQIGDYIQQCGGVSLVEQLLQDPKLSQNKQALEGLKDLKLLFEYLTLFGIAEKIS
          RQEMTGK.GLTP..A..IG.....CGGVSLVEQLLQDPKLSQNKQALEGLKDLKLLFEYLTLFGIAEKIS
Retrocopy RQEMTGKMGLTPNIANLIGVW---CGGVSLVEQLLQDPKLSQNKQALEGLKDLKLLFEYLTLFGIAEKIS

Parental  FDLSLARGLDYYTGVIYEAVLLQSPTQQGEEALGVGSVAAGGRYDGLVGMFDPKGRKVPCVGLSIGVERI
          FDLSLA.GL.YY.GVIYEAV.LQSP.Q.GEEALGVGSVA.GG.YDGL.G.FDPKGRKVPCV.LSIG.ERI
Retrocopy FDLSLA*GLSYYPGVIYEAVILQSPAQ*GEEALGVGSVASGGCYDGLLGIFDPKGRKVPCVWLSIGFERI

Parental  FSIVEQRMEATKKIQTTETQVLVATAQKNFLRERMKLIAELWDAGIRAEMLYKKNPSFLTQLHYCEETGI
          FSIVEQRMEATKKIQTTET.VLVATAQKNFLRE..KLI.ELWDAGIRAEMLYKKNPSFLTQLH.CEETGI
Retrocopy FSIVEQRMEATKKIQTTETEVLVATAQKNFLRELIKLIVELWDAGIRAEMLYKKNPSFLTQLH*CEETGI

Parental  PLVAIIGEQELKDGVIKLRSVASRKEVDIKREDIVTEIQRRMSES
          PLVAIIGEQELKDGVIKL.SVASRKEVDIKREDIVT..QRRMSES
Retrocopy PLVAIIGEQELKDGVIKLPSVASRKEVDIKREDIVTKSQRRMSES

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	126.35 RPM
SRP007412_cerebellum	0.00 RPM	170.41 RPM
SRP007412_heart	0.00 RPM	106.85 RPM
SRP007412_kidney	0.00 RPM	169.87 RPM
SRP007412_liver	0.00 RPM	77.54 RPM
SRP007412_testis	0.00 RPM	88.20 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1274 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1274 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000011309	1 retrocopy	retro_mdom_1274 ,