RetrogeneDB ID: retro_mdom_1399

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 4:280135202..280135835(-)
• Located in intron of: ENSMODG00000004979

Retrocopy information

• Ensembl ID: ENSMODG00000024204
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RAB5C
• Ensembl ID: ENSMODG00000014792
• Aliases: None
• Description: RAB5C, member RAS oncogene family [Source:HGNC Symbol;Acc:9785]

Sequence

>retro_mdom_1399
GGCACAGCTCGGTCCAATAGCCATCTCCAGACCAGCAATATCTGTCAATTCAAACTTGTCCTGCTGGGGGAGTCTACAGT
AGGCAAGTCTAGCTTAGTGCTATGCTTTGTCAAGGGGCAATTCCATTAATATCAGGAGAGCACATTTGGAGCCACCTTCC
TCACACAGTCTGTCTATCTTGATGACACAACAGTCAAGTTTGAAATCTGGGACTCAGCAGGACAGGAACAATATCACAGC
TAGGTGCCTATGTACTACCGGGGTGCCCAGGCTGCTATTGTGGTCTATGATATCACCAACCAGGAAACCTTTGCCTGAGC
AAAGACATGGGTGAAGGAACTACAGTGACAGGCCAGTCCCAGCATTGTCATTGCCCTGGCAGGAAACAAGGCTGATTTGG
CCAACAAGCACATGGTGGAATATGAAGAGGTCCAGGCATATGCAGATGACAACAGCTTATTGTTTATTGAGACATCGGTC
AAGACAGCCATGAATGTTAATGACTTCTTCTTGGCAATAGCTAAGAAATTGCCCAAGAGTGAACCTCAGAGCATGGGGGG
TACAGCAGGCTGAAGCCGGGGAGTGGATCTTCATGAGCAGTCGCAGCAGAACAAGAGCCAGTGTTGTAGCAAC

Alignment

ORF - retro_mdom_1399 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.41 %
• Parental protein coverage: 81.47 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GAARPNGPAAGNKICQFKLVLLGESAVGKSSLVLRFVKGQFHEYQESTIGAAFLTQTVCLDDTTVKFEIW
          G.AR.N.......ICQFKLVLLGES.VGKSSLVL.FVKGQFH.YQEST.GA.FLTQ.V.LDDTTVKFEIW
Retrocopy GTARSNSHLQTSNICQFKLVLLGESTVGKSSLVLCFVKGQFH*YQESTFGATFLTQSVYLDDTTVKFEIW

Parental  DTAGQERYHSLAPMYYRGAQAAIVVYDITNTDTFARAKNWVKELQRQASPNIVIALAGNKADLGSKRAVD
          D.AGQE.YHS..PMYYRGAQAAIVVYDITN..TFA.AK.WVKELQ.QASP.IVIALAGNKADL..K..V.
Retrocopy DSAGQEQYHS*VPMYYRGAQAAIVVYDITNQETFA*AKTWVKELQ*QASPSIVIALAGNKADLANKHMVE

Parental  FQEAQAYAEDNSLLFMETSAKTAMNVNEIFMAIAKKLPKNEPQNAPGAPGRNRGVDLQENSPTSRSQCCS
          ..E.QAYA.DNSLLF.ETS.KTAMNVN..F.AIAKKLPK.EPQ...G..G..RGVDL.E.S....SQCCS
Retrocopy YEEVQAYADDNSLLFIETSVKTAMNVNDFFLAIAKKLPKSEPQSMGGTAG*SRGVDLHEQSQQNKSQCCS

Parental  N
          N
Retrocopy N

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_1399 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1399 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 15 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006003	1 retrocopy	retro_amel_543,
Callithrix jacchus	ENSCJAG00000000472	2 retrocopies	retro_cjac_189, retro_cjac_1948,
Cavia porcellus	ENSCPOG00000011190	2 retrocopies	retro_cpor_333, retro_cpor_473,
Dipodomys ordii	ENSDORG00000006819	1 retrocopy	retro_dord_428,
Gorilla gorilla	ENSGGOG00000005472	1 retrocopy	retro_ggor_2182,
Macropus eugenii	ENSMEUG00000005614	1 retrocopy	retro_meug_2118,
Macaca mulatta	ENSMMUG00000014761	1 retrocopy	retro_mmul_2022,
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,
Otolemur garnettii	ENSOGAG00000009456	2 retrocopies	retro_ogar_2175, retro_ogar_985,
Pongo abelii	ENSPPYG00000008398	1 retrocopy	retro_pabe_2664,
Pan troglodytes	ENSPTRG00000009194	1 retrocopy	retro_ptro_2237,
Rattus norvegicus	ENSRNOG00000018568	2 retrocopies	retro_rnor_393, retro_rnor_73,
Tupaia belangeri	ENSTBEG00000007092	1 retrocopy	retro_tbel_4668,