RetrogeneDB ID: retro_mdom_70

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 5:285687585..285688572(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000024403
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000010450
• Aliases: None
• Description: None

Sequence

>retro_mdom_70
AATTGCGCGCTGCACAATAACAGAAGTTCACCAGCCGGCACCAGGACTGGCCCAGAGTATTCCGGCATGAGGGTTCCCTC
CGGCATTCTCTGGAACGAGGCTGGGGCTGCCTGGCGGAGCGGCTTCTCCTTTGCAGGCCAGGATGTAAGAAGCTGGTTCC
CAGGACACATGGCCAAAGGTCTCAAGAAGATGCAGAGCAGCCTGAAGCTGGTGGACTGTATCATTGAGGTGCATGATGCT
CGGATTCCATTATCTGGTCGTAATCCCTTGTTCCAGGAAACCCTTGGAATTAAGCCTCACCTGTTTGTACTTATCAAAAT
GGATTTGGCAGATCTTAAAGAGAAACAGAAAATCGTGGGGTGCCTGAACAAAGAGAGCATGAAAAATGTCATTTTTACCA
AATGTATAAAGGATGAAAACATAAAACAGATTGTTCCACTGGTTACCGAACTGATAGAGAGTGGCTACCACTATCATCGA
GGAGAGAACCTGGAATATTGTATCATGGTGATTGGGGTGCTGAATGTGGGCAAGTCCTCACTCATCAACTCCCTCAGGAG
ACAGCACCTCAAAAAAGAAAAAGCCTCTCCAGTAGGTGGCCATCCTGGGGTCACCAAAGCAGTTATGTCCAGAATTCAGG
TATGTGAGCGGCCTTTGATGTTCCTGCTGGATACTCCTGGTGTGCTGACTCCATGGATCCAGGATGTAGAGACTGGGCTG
AAACTTGCCACGTGTGGAACTATATTGGATCATTTGGTAGGGGAAGACATCATTGCTGATTATCTTCTTTTTACACTTAA
TAAGCAACAACAGTTCTGGTATGTGGAGCATTATGACCTCGGGGAAGCTTGTGATGACATGGGAAGGGTGCTGAAAAAAA
TTGCTATAAAACTCAAGAAGATAAATAAAGTAAAAGTGCTCACTGGAACAGGAGATGTTAATGTAATTCAGCCCGACTAT
ACTTTAGCAGCCTATGACTTCATCTGA

Alignment

ORF - retro_mdom_70 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.52 %
• Parental protein coverage: 92.46 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NCALHNNGSAPAGTGTGPGHSGMRIPAGVLWSAAGAAWRNGFSFAGQDVARWFPGHMAKGLKKMQSSLKL
          NCALHNN.S.PAGT.TGP..SGMR.P.G.LW..AGAAWR.GFSFAGQDV..WFPGHMAKGLKKMQSSLKL
Retrocopy NCALHNNRSSPAGTRTGPEYSGMRVPSGILWNEAGAAWRSGFSFAGQDVRSWFPGHMAKGLKKMQSSLKL

Parental  VDCIIEMQNVSLNNIPLSGRNPLFQETLGIKPHLLVLNKMDLADLKEKQKIVGCLNKKGVKNVIFTNCIK
          VDCIIE........IPLSGRNPLFQETLGIKPHL.VL.KMDLADLKEKQKIVGCLNK...KNVIFT.CIK
Retrocopy VDCIIEVHDA---RIPLSGRNPLFQETLGIKPHLFVLIKMDLADLKEKQKIVGCLNKESMKNVIFTKCIK

Parental  DENIKQIVPMVTKLIESGYRYHRGENLEYCIMVIGVPNVGKSSLINSLRRQHLKKGKASPVGGHPGVTKA
          DENIKQIVP.VT.LIESGY.YHRGENLEYCIMVIGV.NVGKSSLINSLRRQHLKK.KASPVGGHPGVTKA
Retrocopy DENIKQIVPLVTELIESGYHYHRGENLEYCIMVIGVLNVGKSSLINSLRRQHLKKEKASPVGGHPGVTKA

Parental  VMSRVQVCERPLMFLLDTPGVLTPRIQDVETGLKLATCGTILDHLVGEDIIADYLLFTLNKQQQFRYVEH
          VMSR.QVCERPLMFLLDTPGVLTP.IQDVETGLKLATCGTILDHLVGEDIIADYLLFTLNKQQQF.YVEH
Retrocopy VMSRIQVCERPLMFLLDTPGVLTPWIQDVETGLKLATCGTILDHLVGEDIIADYLLFTLNKQQQFWYVEH

Parental  YDLGEACDDIGSVLKKIAIKLKKINKVKVLTGTGDVNVIQPDYTAAAYDFI
          YDLGEACDD.G.VLKKIAIKLKKINKVKVLTGTGDVNVIQPDYT.AAYDFI
Retrocopy YDLGEACDDMGRVLKKIAIKLKKINKVKVLTGTGDVNVIQPDYTLAAYDFI

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	38.26 RPM
SRP007412_cerebellum	0.00 RPM	53.87 RPM
SRP007412_heart	0.00 RPM	70.77 RPM
SRP007412_kidney	0.00 RPM	53.99 RPM
SRP007412_liver	0.00 RPM	76.53 RPM
SRP007412_testis	0.00 RPM	20.04 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_70 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_70 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	ENSMODG00000010450	1 retrocopy	retro_mdom_70 ,