RetrogeneDB ID: retro_mdom_1723

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 7:89417271..89418021(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000002633
• Aliases: None
• Description: None

Sequence

>retro_mdom_1723
CAAGATAAGTCTTCTGGAAAAGAAAACAGTGTCTTGAAAGCCAAAATTAATAAGCTTGAAAATGAGACAAAGGAAATGAA
AGAGGAAGCAAAGAAGTTGAAAGATGACCTCTAAAGAAAATCAGACCAGAAGGAGAAGGATGAACAAAAAGCCAGGGATA
AAAATCAGTCTTTAAGAACCAGAAAACCACAATTAGAAGCAAGTGACTTCACAAGGAAGGAGGACACTATAAAACAAAAT
CAAAAGAATGAAAAAATTGAGGAAAATATGAAGCATCTCATTCACAAAACAGAAGATTTAGGAAATTTTTCCAGGAGAGA
CAACGTAAGAATCATTGGTCTAACAGATGACAATGACAAAAGAAAAAGCCTGGACATCATACAACATGAAATTATCCAAG
AAAACTGCCCTGTTATTCTAGAACAAGAGGGAAAAATGGAGATTGAAATAATCCACAGAGACAACACCCAGGATTGTTAT
AGCCAAATTCAAGAACTATCAGACCAAGGAAAAACTATTACAAGCTACTACAAAGAATTCATTCAGATACCATGGAAACA
TAGTGAAGATAACACAGGATCTGGCTGCATCCACACTGAAGCATTAAAAGGAATCAATTATCATATCCTGGAAAGCAAGG
GAACTAGGTCTACAACCAAGAATCAACTACCTAGCAAAACTAACTATATTCTTACAAAGGAAAGTGTGGTCATTTAACAA
ATAGAATAATTCCAAGCATTTATAAAGAAG

Alignment

ORF - retro_mdom_1723 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.11 %
• Parental protein coverage: 73.53 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  REDQTEKQKQSLKTRIKQLEDKQEKHEKVNTKHRETEKRISDQKEKDDEKARDEIQSFKTRIQQLEASDF
          ......K....LK..I..LE...........K......R.SDQKEKD..KARD..QS..TR..QLEASDF
Retrocopy QDKSSGKENSVLKAKINKLENETKEMKEEAKKLKDDL*RKSDQKEKDEQKARDKNQSLRTRKPQLEASDF

Parental  TRHQHTIKQNQKNKIIEENMKHLIHKTEDLENRSRRDNLRIIGLLEDYDKRKSLDIILQEIIQENCPDIT
          TR...T.............MKHLIHKTEDL.N.SRRDN.RIIGL..D.DKRKSLDII..EIIQENCP.I.
Retrocopy TRKEDTXXXXXXXXXXXXXMKHLIHKTEDLGNFSRRDNVRIIGLTDDNDKRKSLDIIQHEIIQENCPVIL

Parental  EQEGKVEIERIHR-STHRNVLAKFKKSQTKEKILQVDKKKSFRKHGTIVRITQDLTASTLKDLQAWNMIF
          EQEGK.EIE.IHR..T.R.V.AKFK..QTKEK.LQ...K.SFR.HG.IV.ITQDL.ASTLK.......I.
Retrocopy EQEGKMEIEIIHR>TTPRIVIAKFKNYQTKEKLLQATTKNSFRYHGNIVKITQDLAASTLKH*KESIIIS

Parental  WKARELGLQPRIIYTAKLTIFLQGKVWSFNK-IEDFQAFVKK
          WKARELGLQPRI.Y.AKLTIFLQ.KVWSFNK.IE.FQAF.KK
Retrocopy WKARELGLQPRINYLAKLTIFLQRKVWSFNK<IE*FQAFIKK

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_1723 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1723 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 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000002633	6 retrocopies	retro_mdom_1009, retro_mdom_1362, retro_mdom_1477, retro_mdom_1723 , retro_mdom_1764, retro_mdom_329,