RetrogeneDB ID: retro_mdom_1710

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 7:39927336..39927975(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAB25
• Ensembl ID: ENSMODG00000016955
• Aliases: None
• Description: RAB25, member RAS oncogene family [Source:HGNC Symbol;Acc:18238]

Sequence

>retro_mdom_1710
ATGGGAAACGGAACCAAAGAGGATTATAATTTTGTCTTCATGTTGGTGCTGATTGGGGAGTCCAGAGTGGGGAAGACCAA
CTTATAGTCAAGATTCACATGAAGTGAGTTTAGCCATAATAGTAGGACAACCATTGGGGTGGAATTCTCTACTCGAACTG
TGCTGCTAGGAAGAGCTGCTGTCAAAGCCCAGATCTGGGACACCGCTGGGCTGGAACGATACCATGCCATCACTTCAGCA
TATTATCAAGGGGTAATTGGGGCCCTGCTGGTATTTGACCTAAACAAGCATCAGACCTATGCTGTGGTAGAGCACTGGCT
GAAGGAGCTATATGCCATGCAGAGGCTACTGTTGCCATCATGCTGGTGGGCAACAAGAGAGATCTGAGCCAGACCAGAGG
AGTGCCCGCTGATGAGGCTCGAATGTTTGCTGAAAATAATGGACTCCTGTTTATTGAGACTTCTGATCTTGACTCCACTA
AATTTTGAACTGGCCTTTGAAACTGTCCTCAAAGAGATCTTCACTAAAATGTCCAACCAGCAACAGAACAATTCCCATGC
CAATGCAGTCACCCTAGGCAATGCCCAACCAGGGCAAGAGCTGGGGTCTGAGGAGAGGAAGGCTTGCTGTATCAGCCTC

Alignment

ORF - retro_mdom_1710 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.65 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MGNGTEEDYNFVFKVVLIGESGVGKTNLLSRFTRNEFSHDSRTTIGVEFSTRTVLLGTAAVKAQIWDTAG
          MGNGT.EDYNFVF..VLIGES.VGKTNL.SRFT..EFSH.SRTTIGVEFSTRTVLLG.AAVKAQIWDTAG
Retrocopy MGNGTKEDYNFVFMLVLIGESRVGKTNL*SRFT*SEFSHNSRTTIGVEFSTRTVLLGRAAVKAQIWDTAG

Parental  LERYRAITSAYYRGAVGALLVFDLTKHQTYAVVERWLKELYD-HAEATIVVMLVGNKSDLSQAREVPTDE
          LERY.AITSAYY.G..GALLVFDL.KHQTYAVVE.WLKELY..HAEAT...MLVGNK.DLSQ.R.VP.DE
Retrocopy LERYHAITSAYYQGVIGALLVFDLNKHQTYAVVEHWLKELYA<HAEATVAIMLVGNKRDLSQTRGVPADE

Parental  ARMFAENNGLLFIETSALDST-NVELAFETVLKEIFTKVSKQRQNNSRANAVTLSNAQPGQELGSVERKA
          ARMFAENNGLLFIETS.LDST.N.ELAFETVLKEIFTK.S.Q.QNNS.ANAVTL.NAQPGQELGS.ERKA
Retrocopy ARMFAENNGLLFIETSDLDST>NFELAFETVLKEIFTKMSNQQQNNSHANAVTLGNAQPGQELGSEERKA

Parental  CCISL
          CCISL
Retrocopy CCISL

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_1710 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1710 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 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007715	1 retrocopy	retro_cjac_1256,
Macropus eugenii	ENSMEUG00000016598	2 retrocopies	retro_meug_1684, retro_meug_770,
Monodelphis domestica	ENSMODG00000008556	2 retrocopies	retro_mdom_1999, retro_mdom_989,
Monodelphis domestica	ENSMODG00000016955	1 retrocopy	retro_mdom_1710 ,