RetrogeneDB ID: retro_mdom_1967

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: Un:68775864..68776568(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000014106
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RRAGC
• Ensembl ID: ENSMODG00000017710
• Aliases: None
• Description: Ras-related GTP binding C [Source:HGNC Symbol;Acc:19902]

Sequence

>retro_mdom_1967
TCAGGGGCATTAATAGATGTCATTGATGCACAGGATGACCACATGGAGGTTTTAACAAGACTTCATATTACGGTTTCTAA
AGCCTACAAAGTTCATTCGGAGGTTTTTATTCATAAAGTTGATGGCTTGTCTGACGATCATAAAATAGAAACTCAGAGGG
GCATCCATCAGAGGGCCAATGATGACCGTGCAGATGCAGTACTAGGAAAGCTCCATCGTAGCTTTGATTTGACCAATATC
TGTGGCCATTCAATATTTGAAGCCTTTAGTAAGGCAGTGCAGAAACGCATTCCACAGCTGCTGACTTTGGAAAACCTATT
AAATATCTTTAGATCTAAACAGGTATCGAAAAAGCTTTCCTCTTTGATGTTGTCAGCAAAATCTACTTTGCAACAGACGC
TCCCCCCGTGGATGTGCTGTCATATGAACTGTGCTGTGACATGACGGATGTTGTAATTGATGTGTCTTGTCTATATGGGT
TAAAGGAAGATGGCCGTGGAACAGCATATCATAAAGAATTGATGGCAATGATCAAACTAAATAATACAATAAAGGAAGTG
ACAACATTTGGGGCACTGGTCTGCATTCTTAGGGAAGAAAGCGTTGAATGTAAAGGTTTGACAGACTACAACTTCCACTG
TTTCCCCAAAGCTATTCATGAAGTTTTTGAGGTGGGTTTGACCTCTCACAGAGCCTGCAGCCAT

Alignment

ORF - retro_mdom_1967 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.51 %
• Parental protein coverage: 61.52 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TGALIYVIDAQDDYMEALTRLHITVSKAYKVNPEMNFEVFIHKVDGLSDDHKIETQRDIHQRANDDLADA
          .GALI.VIDAQDD.ME.LTRLHITVSKAYKV......EVFIHKVDGLSDDHKIETQR.IHQRANDD.ADA
Retrocopy SGALIDVIDAQDDHMEVLTRLHITVSKAYKVHS----EVFIHKVDGLSDDHKIETQRGIHQRANDDRADA

Parental  GLEKLHLSFYLTSIYDHSIFEAFSKVVQKLIPQLPTLENLLNIFISN-SGIEKAFLFDVVSKIYIATDSS
          .L.KLH.SF.LT.I..HSIFEAFSK.VQK.IPQL.TLENLLNIF.S...GIEKAFLFDVVSKIY.ATD..
Retrocopy VLGKLHRSFDLTNICGHSIFEAFSKAVQKRIPQLLTLENLLNIFRSK<TGIEKAFLFDVVSKIYFATDAP

Parental  PVDMQSYELCCDMIDVVIDVSCIYGLKEDGSGSAYDKESMAIIKLNNTTVLYLKEVTKFLALVCILREES
          PVD..SYELCCDM.DVVIDVSC.YGLKEDG.G.AY.KE.MA.IKLNNT.....KEVT.F.ALVCILREES
Retrocopy PVDVLSYELCCDMTDVVIDVSCLYGLKEDGRGTAYHKELMAMIKLNNT----IKEVTTFGALVCILREES

Parental  FERKGLIDYNFHCFRKAIHEVFEVGVTSHRACSH
          .E.KGL.DYNFHCF.KAIHEVFEVG.TSHRACSH
Retrocopy VECKGLTDYNFHCFPKAIHEVFEVGLTSHRACSH

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_1967 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1967 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 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009368	2 retrocopies	retro_btau_1023, retro_btau_851,
Microcebus murinus	ENSMICG00000006241	1 retrocopy	retro_mmur_1581,
Monodelphis domestica	ENSMODG00000017710	1 retrocopy	retro_mdom_1967 ,