RetrogeneDB ID: retro_mdom_1586

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 6:52578360..52578834(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000025686
• Aliases: None
• Description: None

Sequence

>retro_mdom_1586
AATGTGATAGAGAATAGAAAAATAGGAAACACATGTGGTGAAAATCTCTTTATGTCAACTATTCCCATAGAATGGCCAAA
GGTTATCCAAGATTGGTATGATGAAGTTTCAAATTTTGATTACGAAAAAGGACGAACTAACCCAAAAGGACAAATTGAAC
ATTATTCACAGATAGTGTGGTATTCATCTTTCAAAGTTATATGTGCAATGGCCCATTGCCCTGATGTGTCTTTCTGGTAC
TATTATGTTTACCAATACTGCCCAGGTGGAAATTACAGGCCTGATTACTTTTATGAAATAAGAGCATCTTGTGACAAGTG
CCCAGATTCCTGTAGTAACAACCTGTGCACCCATCCCTGTCTATACACCAATAAATTTGCAAACTGTGAAGACCTGAAAA
ATCAAGTTTCCTGCCAACATGAATTTTTCAAGAACAACTATAAGGTTACCTGTCAGTGACCCAATCAAATCTAT

Alignment

ORF - retro_mdom_1586 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.86 %
• Parental protein coverage: 65.83 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SLVKNRTIGSPCGENLFMSTVPMHWSKAIQAWHDEVSNFEYGKGPIDPNQPVGHYTQVVWHSSFKVGCGV
          ....NR.IG..CGENLFMST.P..W.K.IQ.W.DEVSNF.Y.KG...P.....HY.Q.VW.SSFKV.C..
Retrocopy NVIENRKIGNTCGENLFMSTIPIEWPKVIQDWYDEVSNFDYEKGRTNPKGQIEHYSQIVWYSSFKVICAM

Parental  AYCPDATYPYFFVCQYCPSGNYGTKYPYEKGASCDKCPHSCTNNLCNNPCLYTNKFGNCEEMKNKVSCRN
          A.CPD....Y..V.QYCP.GNY...Y.YE..ASCDKCP.SC.NNLC..PCLYTNKF.NCE..KN.VSC..
Retrocopy AHCPDVSFWYYYVYQYCPGGNYRPDYFYEIRASCDKCPDSCSNNLCTHPCLYTNKFANCEDLKNQVSCQH

Parental  KYVKSNCKATCLCVNEIY
          ...K.N.K.TC...N.IY
Retrocopy EFFKNNYKVTCQ*PNQIY

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_1586 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1586 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Myotis lucifugus	ENSMLUG00000010302	1 retrocopy	retro_mluc_2168,
Monodelphis domestica	ENSMODG00000025686	1 retrocopy	retro_mdom_1586 ,
Vicugna pacos	ENSVPAG00000009962	1 retrocopy	retro_vpac_172,