RetrogeneDB ID: retro_mdom_1491

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 5:1916664..1917249(-)
• Located in intron of: None

Retrocopy information

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

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_1491
ATGATGGCAATACGAGAGCTGAAAGTGTGTCTTCTCGGGGATACTGGAGTTGGAAAGTCAAGCATTGTTTGCCAATTTGT
ACAGGATCACTTTGACCACAACATCAGCCCTACAATTGGTGCTTCTTTCATGACTAAAACTGTGCCTTGTGGAAATGAAC
TTCATAAGTTTCTCATCTGGGATACGGCTGGTCAGGAACGTTTCCATTCATTGGCACCCATGTACTATTGAGGATCTGCA
GCAGCTGTTATAGTATATGATATCACTAAACAGGATTCTTTTAATACCTTGAAGAAATGGGTGAAAGAATTAAAAGAACA
TGGTCCAGAAAATATTGTAATGGCCATCGCTGGAAACAAATGTGATCTCTCAGATATTAGGGAGGCTCCCATGAAGGATG
CCAAGGAATATGCTGAATCCATAGGAGCAGTTGTAGTCGAAACAAGTGCAAAATGTGCTATTAATATTGAGGAACTCTTT
CAAGGAATCAGTCGTCAGATCCCACCCTTGGACCCTCATGAAGATGGGAACAACGGAGCAATCAAGCTTGGAAAGCAGCC
ACCACAAACTAGCAGGCGATGTTGC

Alignment

ORF - retro_mdom_1491 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.95 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MMAIRELKVCLLGDTGVGKSSIVCRFVQDHFDHNISPTIGASFMTKTVPCGNELHKFLIWDTAGQERFHS
          MMAIRELKVCLLGDTGVGKSSIVC.FVQDHFDHNISPTIGASFMTKTVPCGNELHKFLIWDTAGQERFHS
Retrocopy MMAIRELKVCLLGDTGVGKSSIVCQFVQDHFDHNISPTIGASFMTKTVPCGNELHKFLIWDTAGQERFHS

Parental  LAPMYYRGSAAAVIVYDITKQDSFNTLKKWVKELKEHGPENIVMAIAGNKCDLSDIREVPMKDAKEYAES
          LAPMYY.GSAAAVIVYDITKQDSFNTLKKWVKELKEHGPENIVMAIAGNKCDLSDIRE.PMKDAKEYAES
Retrocopy LAPMYY*GSAAAVIVYDITKQDSFNTLKKWVKELKEHGPENIVMAIAGNKCDLSDIREAPMKDAKEYAES

Parental  IGAVVVETSAKCAINIEELFQGISRQIPPLDPHENGNNGAIKLGKQPPQTSRRCC
          IGAVVVETSAKCAINIEELFQGISRQIPPLDPHE.GNNGAIKLGKQPPQTSRRCC
Retrocopy IGAVVVETSAKCAINIEELFQGISRQIPPLDPHEDGNNGAIKLGKQPPQTSRRCC

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_1491 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1491 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,