RetrogeneDB ID: retro_mdom_1577

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 6:35192471..35192807(+)
• Located in intron of: ENSMODG00000003634

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAB10
• Ensembl ID: ENSMODG00000015821
• Aliases: None
• Description: RAB10, member RAS oncogene family [Source:HGNC Symbol;Acc:9759]

Sequence

>retro_mdom_1577
TATGACATCACCAATGGGAAACACTTTGAAAACATCAGCAAATAGTTTAGAAACATAGATGAGCATGCCAATGAAGATGT
GGAAAGGATGCTGCTAGGAAACAAGCGTGACATGGAAGATAAGAGAGTTGTACCTAAACAAAAAGGAGAACAGATTGCAA
GGGAGCATGGTATTAGGTTTTTTGAAACTAGTGCAAAAGCAAATATAAACATTGAGAAGGCTTTACCCCCATTAGCGGAA
GACATACTTTGAAAGACCCCTGTAAAAGAGCCCAACAGTGAAAATGTACATATCAGCAGTGGAGGAAGAGTAACAGGCTG
AAAGAATAAATGTTGT

Alignment

ORF - retro_mdom_1577 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.39 %
• Parental protein coverage: 65.12 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  YDITNGKSFENISKWLRNIDEHANEDVERMLLGNKCDMEDKRVVPKGKGEQIAREHGIRFFETSAKANIN
          YDITNGK.FENISK..RNIDEHANEDVERMLLGNK.DMEDKRVVPK.KGEQIAREHGIRFFETSAKANIN
Retrocopy YDITNGKHFENISK*FRNIDEHANEDVERMLLGNKRDMEDKRVVPKQKGEQIAREHGIRFFETSAKANIN

Parental  IEKAFLTLAEDILRKTPVKEPNSENVDISSGGGVTGWKSKCC
          IEKA...LAEDIL.KTPVKEPNSENV.ISSGG.VTG.K.KCC
Retrocopy IEKALPPLAEDIL*KTPVKEPNSENVHISSGGRVTG*KNKCC

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	562.85 RPM
SRP007412_cerebellum	0.00 RPM	444.96 RPM
SRP007412_heart	0.00 RPM	378.97 RPM
SRP007412_kidney	0.00 RPM	395.05 RPM
SRP007412_liver	0.00 RPM	351.94 RPM
SRP007412_testis	0.00 RPM	216.47 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1577 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1577 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Ciona intestinalis	ENSCING00000003959	1 retrocopy	retro_cint_21,
Echinops telfairi	ENSETEG00000010795	1 retrocopy	retro_etel_661,
Myotis lucifugus	ENSMLUG00000009937	1 retrocopy	retro_mluc_2453,
Monodelphis domestica	ENSMODG00000008371	1 retrocopy	retro_mdom_196,
Monodelphis domestica	ENSMODG00000015821	1 retrocopy	retro_mdom_1577 ,
Tupaia belangeri	ENSTBEG00000016698	1 retrocopy	retro_tbel_4738,