RetrogeneDB ID: retro_mdom_1477

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 5:223359284..223360053(+)
• 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_1477
GAAAAAGAGACACATGAACTAAAAGAAGAAAATAGTGTCTTGAAAGCTAGAATTGACCAGCTTGAAAACAAGGCAAAGAT
GATGAAAGATGACTTACAAAGAAAATCAGACCAGAAGAAGGATGACCAAAAATTCAGGAATGAAATTCTGTCTTTAAAAA
TTAGGATCCAACAACTAGAAGCAAATGACTTCACAAAGCAGCAAGGATCTATAAAACAAAATCAAAAGAATGAAAAAATT
GAGGAAAATATGAAATATCTCATTGACAAAAATGTCAGACCATGAAAACAGATTCAGAAGAGAGAATTTAAAAATTATTG
GACTACTGGAAGATCATGATAAAAGAAAAAACCTGGATATCATTCTACAGGAAATTATCCAAGAAAACTGCCCTGACATT
CTAGAGCAAGAGGGAAAAGTGGAGATTGAAGGAATCCACATATCACCTTCTATACTTAATGTTATAGCCAAATTCAAGAA
CTATCAGACCAAGGGAAAAATATTACAAGCTTCTAAGAAGAAGTCATTCAGATACCATGGAACCGCAGTTAGGATAACAC
AGGCTGCATCTACACTGAAGGACTGAAAGGCATGGAATACGATTTTCCAGAAAACAATGGAATTGGGTCTACAACCAAGA
ATCAACTACCCAGCAAAACTGACTATATTCTTACAGGGGAAAGTATGGTCATTTAATAAATCAGAATACTTCCAAGCATT
CATAGAGAAAATACAAGACTTAAACAGAAAATTTGATGCCCAGAACCAA

Alignment

ORF - retro_mdom_1477 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.15 %
• Parental protein coverage: 75.88 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EKQKQSLKTRIKQLEDKQEKHEKVNTKHRETEKRISDQKEKDDEKARDEIQSFKTRIQQLEASDFTRHQH
          EK....LK.....L.......E...........R.SDQK.KDD.K.R.EI.S.K.RIQQLEA.DFT..Q.
Retrocopy EKETHELKEENSVLKARIDQLENKAKMMKDDLQRKSDQK-KDDQKFRNEILSLKIRIQQLEANDFTKQQG

Parental  TIKQNQKNKIIEENMKHLIHKT-EDLENRSRRDNLRIIGLLEDYDKRKSLDIILQEIIQENCPDITEQEG
          .................LI.K...D.ENR.RR.NL.IIGLLED.DKRK.LDIILQEIIQENCPDI.EQEG
Retrocopy SXXXXXXXXXXXXXXXXLIDKN>SDHENRFRRENLKIIGLLEDHDKRKNLDIILQEIIQENCPDILEQEG

Parental  KVEIERIHRS-THRNVLAKFKKSQTKEKILQVDKKKSFRKHGTIVRITQDLTASTLKDLQAWNMIFWKAR
          KVEIE.IH.S....NV.AKFK..QTK.KILQ..KKKSFR.HGT.VRITQ...ASTLKD..AWN.IF.K..
Retrocopy KVEIEGIHISPSILNVIAKFKNYQTKGKILQASKKKSFRYHGTAVRITQ--AASTLKD*KAWNTIFQKTM

Parental  ELGLQPRIIYTAKLTIFLQGKVWSFNKIEDFQAFVKKRPDMNRKFDAEAQ
          ELGLQPRI.Y.AKLTIFLQGKVWSFNK.E.FQAF..K..D.NRKFDA..Q
Retrocopy ELGLQPRINYPAKLTIFLQGKVWSFNKSEYFQAFIEKIQDLNRKFDAQNQ

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_1477 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1477 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,