RetrogeneDB ID: retro_mdom_897

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 2:362394390..362394977(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000015650
• Aliases: None
• Description: None

Sequence

>retro_mdom_897
TTGGAGCTGATCCAAGATGCCTCCTGGCCACTTCTGGTATCTGTGAAAGGTTTTCTATTCATCAAGTACTTTGCTGAAAC
TCTTGAACTGCTGAAGAATTTTCAGGCATGTCCAGATGATGTCCTCATCAGTACCTATCCCAAATCTGGAACAAAATGGG
TGAGTGAGATCCTAGGTCTGATTTATCAGAAGGATAACCAAAAGAAATGCCAAAGGGCCCCAGTCTTCATCTGAGTGCTA
TTTCTTGAATTCAAGGCTCCAGGGGTGCCCTCAGGCATGGAGTCTCTAAAGGGAATACCACCTCTACTCAAGACACATTT
GCCTCTGGCACTGGTCCCACAGACTTTGGTGCATCAGAAAGTTAAGATCATCCATGTGGCAAGAAATGCCAAAGATGTGG
CAGCCTCCTATTTCAATTTCAATAAGATGGCAAAGGTACACCCTGAGCCTGAGACCTGTGAGGAGTTCCTGGAGAAATTA
TGGCTGGGCAAGTATCATATGGCTCTTGGTTTCAGCACATATCAGAATGGTGGTAGTTGACCCAGTGGCATCCCATTCTC
TACCTCTTCTTTGAAGACATGAAAAAG

Alignment

ORF - retro_mdom_897 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.4 %
• Parental protein coverage: 63.67 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MELIQDTSRPPLVSVKGYPLIKYFAEALEQLKIFQARPDDVLISTYPKSGTTWVSEILDMIYQKGDQKKC
          .ELIQD.S.P.LVSVKG...IKYFAE.LE.LK.FQA.PDDVLISTYPKSGT.WVSEIL..IYQK..QKKC
Retrocopy LELIQDASWPLLVSVKGFLFIKYFAETLELLKNFQACPDDVLISTYPKSGTKWVSEILGLIYQKDNQKKC

Parental  QRAPIFIRVPFLEFKAPGIPSGMESLKETPAPRLLKTHLPLALLPQTLLDQKVKVIYVARNAKDVAASYF
          QRAP.FI.V.FLEFKAPG.PSGMESLK..P...LLKTHLPLAL.PQTL..QKVK.I.VARNAKDVAASYF
Retrocopy QRAPVFI*VLFLEFKAPGVPSGMESLKGIPP--LLKTHLPLALVPQTLVHQKVKIIHVARNAKDVAASYF

Parental  NFYKMAKVHPDPGTWEEFLEK-FMAGQVSYGSWYQHVSEWWELTKRHPILYLFFEDMKK
          NF.KMAKVHP.P.T.EEFLEK..MAGQVSYGSW.QH.SEWW.LT..HPILYLFFEDMKK
Retrocopy NFNKMAKVHPEPETCEEFLEK<IMAGQVSYGSWFQHISEWW*LTQWHPILYLFFEDMKK

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_897 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_897 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	ENSMODG00000015650	1 retrocopy	retro_mdom_897 ,