RetrogeneDB ID: retro_mdom_1642

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 6:23745123..23745661(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000025406
• Aliases: None
• Description: None

Sequence

>retro_mdom_1642
GACCTTGAAAACAGATGCAGAAGAGACAATTTAAGAATTATTAGATTACCAGAAGATCAAGACAAAAGAAAAAGCCTGGA
CATCATCATACAGGAAAGTATCCAAGAAAACTTCCCCAACATTCTTGAAAAAGAGGGAAAAGTGGAGATCATTCCAGCTT
TTAATTCCCAACTGACCATTCCCAGGAATGTTATAGCCAAATTCAAGAACTACCAGAAAAAGGGAAAAAATATTACAAGC
TGCTAAGAAGTCATTCAGATACCATGGAAGTACAGTGAGGATAACGCAGGACCTTACTGCATCTACACTGAAGGACCAGA
AGGCATGGAATATGATATTCCAGAAAGTAAGGGAACTGAGTCTACAACCAAAATCAACTACACAGCAAAACTGACTATAT
TCTTGCTGAGGAAAGTATGGCCATTTAACAAAAATAGAAGACTCCCAAGCATCCATAAAGAAAAGACCATACTTAAACAG
AAAATTTGATGCCCAAACACAGAACTCAAGAGAATAACCAAAAGGTCATTAAGAAAGA

Alignment

ORF - retro_mdom_1642 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.48 %
• Parental protein coverage: 57.46 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  DLENRSRRDNLRIIGLPEDHDKRKSLDIMLQEIIKENFPNILEQEGINTRSHPVLNPQLTTARNVIAKFK
          DLENR.RRDNLRII.LPED.DKRKSLDI..QE.I.ENFPNILE.EG......P..N.QLT..RNVIAKFK
Retrocopy DLENRCRRDNLRIIRLPEDQDKRKSLDIIIQESIQENFPNILEKEG-KVEIIPAFNSQLTIPRNVIAKFK

Parental  NYQTK-EKILQAAKKKSFRYHGTTVRITQDLAASTLKHRKARKNIIHTQRKNCLQP-RINYPAKLTIFLQ
          NYQ.K.EKILQAA.KKSFRYHG.TVRITQDL.ASTLK..KA...I....R...LQP..INY.AKLTIFL.
Retrocopy NYQKK>EKILQAA-KKSFRYHGSTVRITQDLTASTLKDQKAWNMIFQKVRELSLQP<KINYTAKLTIFLL

Parental  GKVWSFN-KIEEFQEFVKKRPHLIRKFDVQAQNSRESSKDNLKR
          .KVW.FN.KIE..Q...KKRP.L.RKFD.Q.QNSRE..K....R
Retrocopy RKVWPFN>KIEDSQASIKKRPYLNRKFDAQTQNSRE*PKGH*ER

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_1642 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1642 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 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000025406	12 retrocopies	retro_mdom_1000, retro_mdom_1578, retro_mdom_1642 , retro_mdom_1712, retro_mdom_1767, retro_mdom_1795, retro_mdom_2008, retro_mdom_502, retro_mdom_770, retro_mdom_842, retro_mdom_900, retro_mdom_972,