RetrogeneDB ID: retro_mdom_560

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:305733608..305734000(-)
• Located in intron of: ENSMODG00000027692

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000025514
• Aliases: None
• Description: None

Sequence

>retro_mdom_560
CTCGAGTCCTTTTATGAAAAACCTCCTCCTGGACTTATTAAGGAAGATGAGACTAAGCCAGAAGACTGTATCCCAGATGT
ATCAGGCAATGAACATGCCAGAGAATTTCTGGCTCATGCTCCAACTAAAGGTCTCTGGATGCCCCTGGGGAAAGAAGTCA
AGGTTATGCAATGCTGGCGCTGTAAATGGTATGGACATAGAACAGGTGACAAAAATGCCCATTCTTTATCAAAGGCAATC
AGAAATTAGAACAATTCAGAGTAGCACACGAAGATCCCATATATGACATCATAAGAGAGAATAAGCAGCATGAAAAGGAT
GTGAGGATACAACAGTCAAAGAAGCTACTAGAAGATTCTACCTCAGATGAAGATGGCACTAGTTCCAGCTCC

Alignment

ORF - retro_mdom_560 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.7 %
• Parental protein coverage: 62.38 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LESFYEKPPPGLIKEDETKPEDCIPDVPGNEHAREFLAHAPTKGLWMPLGKEVKVMQCWRCKRYGHRTGD
          LESFYEKPPPGLIKEDETKPEDCIPDV.GNEHAREFLAHAPTKGLWMPLGKEVKVMQCWRCK.YGHRTGD
Retrocopy LESFYEKPPPGLIKEDETKPEDCIPDVSGNEHAREFLAHAPTKGLWMPLGKEVKVMQCWRCKWYGHRTGD

Parental  K-ECPFFIKGNQKLEQFRVAHEDPMYDIIRENKRHEKDVRIQQLKKLLEDSTSDEDGTSSSS
          K..CPFFIKGNQKLEQFRVAHEDP.YDIIRENK.HEKDVRIQQ.KKLLEDSTSDEDGTSSSS
Retrocopy K<KCPFFIKGNQKLEQFRVAHEDPIYDIIRENKQHEKDVRIQQSKKLLEDSTSDEDGTSSSS

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	0.20 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.39 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_560 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_560 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 4 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000025514	17 retrocopies	retro_mdom_1205, retro_mdom_1515, retro_mdom_1553, retro_mdom_1622, retro_mdom_1759, retro_mdom_1840, retro_mdom_1905, retro_mdom_1912, retro_mdom_265, retro_mdom_317, retro_mdom_386, retro_mdom_560 , retro_mdom_623, retro_mdom_687, retro_mdom_761, retro_mdom_818, retro_mdom_896,
Oryctolagus cuniculus	ENSOCUG00000029333	1 retrocopy	retro_ocun_1635,
Sarcophilus harrisii	ENSSHAG00000001730	2 retrocopies	retro_shar_440, retro_shar_650,
Tupaia belangeri	ENSTBEG00000009535	1 retrocopy	retro_tbel_280,