RetrogeneDB ID: retro_mdom_994

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:151183266..151183641(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000006162
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RAB31
• Ensembl ID: ENSMODG00000021443
• Aliases: None
• Description: RAB31, member RAS oncogene family [Source:HGNC Symbol;Acc:9771]

Sequence

>retro_mdom_994
TTCCATTCATTGGCACCCATGTACTATCGAGCATCTGCAGCAGCTGTTATAGTGTATGATATCACTAAACAGGATTCTTT
TAATACCTTGAGGAAATGGGTGAAAGAATTAAAAGAACATGGTCCAGAAAATATTGTAATGGCCATCCCTGGAAACAAAT
GTGATCTCTTAGATATTAGGGAGGTTCCTATGAAGGATAAAAAGGAATATGCTGAACCCATAGGAGTAGTTGTAGTCGAA
ACAAATGCAAAATGTGCTATTAATATTGAGGAACTCTTTCAAGGAATCAGTCATCAGATCCCAACCTTGGACCCTCATGA
AAATGGAGCAATCAAGTTTGGGAAGCAGCCACCACAAACTGGCAGGCAATGTTGC

Alignment

ORF - retro_mdom_994 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.5 %
• Parental protein coverage: 65.64 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FHSLAPMYYRGSAAAVIVYDITKQDSFNTLKKWVKELKEHGPENIVMAIAGNKCDLSDIREVPMKDAKEY
          FHSLAPMYYR.SAAAVIVYDITKQDSFNTL.KWVKELKEHGPENIVMAI.GNKCDL.DIREVPMKD.KEY
Retrocopy FHSLAPMYYRASAAAVIVYDITKQDSFNTLRKWVKELKEHGPENIVMAIPGNKCDLLDIREVPMKDKKEY

Parental  AESIGAVVVETSAKCAINIEELFQGISRQIPPLDPHENGNNGAIKLGKQPPQTSRRCC
          AE.IG.VVVET.AKCAINIEELFQGIS.QIP.LDPHENG...AIK.GKQPPQT.R.CC
Retrocopy AEPIGVVVVETNAKCAINIEELFQGISHQIPTLDPHENG---AIKFGKQPPQTGRQCC

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_994 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_994 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 7 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000004529	2 retrocopies	retro_cjac_1178, retro_cjac_1179,
Microcebus murinus	ENSMICG00000002882	1 retrocopy	retro_mmur_1453,
Macaca mulatta	ENSMMUG00000005692	1 retrocopy	retro_mmul_1557,
Monodelphis domestica	ENSMODG00000014792	1 retrocopy	retro_mdom_1399,
Monodelphis domestica	ENSMODG00000014793	2 retrocopies	retro_mdom_1219, retro_mdom_1993,
Monodelphis domestica	ENSMODG00000021443	3 retrocopies	retro_mdom_1491, retro_mdom_1766, retro_mdom_994 ,
Pteropus vampyrus	ENSPVAG00000016514	1 retrocopy	retro_pvam_874,