RetrogeneDB ID: retro_mdom_1993

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: X:22407890..22408281(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000002960
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RAB5A
• Ensembl ID: ENSMODG00000014793
• Aliases: None
• Description: RAB5A, member RAS oncogene family [Source:HGNC Symbol;Acc:9783]

Sequence

>retro_mdom_1993
GAATCCGCCATTGGAAAAGCAAGTCTTGTGCTTTGATTTGTGAAGGGCCAATTTCAGGAATTTCAAGCGAGAACCATTGG
GGCGGCTTTTCTAACCCAGATTATGTGTTTTGATGACACAGCGGTGAAATTTGAAATATGGGATACAGCTGTACAAGAAC
GATATCATAGCTTAGCACCGATGTACGCCAGAGTTGCACAAGCAGCAATAGTTGTATATGATATCACAAATGAGGAGTCC
TTTGCAAGAGCAAAAAACTGGGTCAAAGAAGCAGAGGCAAGCAAGTCCTAACATTGTAATAGCTTTAGCAGGGAACAAGG
CTGATCTAGCAAGGAAAAGAACTGTAGATTTCCAGGAAGCACAGTCTTATGCAGATGACAAGTTTATTATT

Alignment

ORF - retro_mdom_1993 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.45 %
• Parental protein coverage: 60.93 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ESAVGKSSLVLRFVKGQFHEFQESTIGAAFLTQTVCLDDTTVKFEIWDTAGQERYHSLAPMYYRGAQAAI
          ESA.GK.SLVL.FVKGQF.EFQ..TIGAAFLTQ..C.DDT.VKFEIWDTA.QERYHSLAPMY.R.AQ.A.
Retrocopy ESAIGKASLVL*FVKGQFQEFQARTIGAAFLTQIMCFDDTAVKFEIWDTAVQERYHSLAPMYARVAQ-AA

Parental  VV-YDITNEESFARAKNWVKELQRQASPNIVIALAGNKADLASKRAVDFQEAQSYADDNSLL
          .V.Y.I....S...........QRQASPNIVIALAGNKADLA.KR.VDFQEAQSYADD....
Retrocopy IV>YMISQMRSPLQEQKTGSKKQRQASPNIVIALAGNKADLARKRTVDFQEAQSYADDKFII

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_1993 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1993 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 21 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000954	1 retrocopy	retro_amel_958,
Bos taurus	ENSBTAG00000046385	1 retrocopy	retro_btau_300,
Callithrix jacchus	ENSCJAG00000003731	1 retrocopy	retro_cjac_3268,
Cavia porcellus	ENSCPOG00000005322	2 retrocopies	retro_cpor_1213, retro_cpor_219,
Dipodomys ordii	ENSDORG00000012429	1 retrocopy	retro_dord_288,
Felis catus	ENSFCAG00000004455	2 retrocopies	retro_fcat_1349, retro_fcat_984,
Homo sapiens	ENSG00000144566	1 retrocopy	retro_hsap_1074,
Gorilla gorilla	ENSGGOG00000015981	1 retrocopy	retro_ggor_848,
Loxodonta africana	ENSLAFG00000008321	1 retrocopy	retro_lafr_267,
Macaca mulatta	ENSMMUG00000006992	2 retrocopies	retro_mmul_227, retro_mmul_839,
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,
Mus musculus	ENSMUSG00000017831	1 retrocopy	retro_mmus_1645,
Nomascus leucogenys	ENSNLEG00000003434	1 retrocopy	retro_nleu_2466,
Oryctolagus cuniculus	ENSOCUG00000012200	1 retrocopy	retro_ocun_1034,
Pongo abelii	ENSPPYG00000014074	2 retrocopies	retro_pabe_3094, retro_pabe_894,
Pan troglodytes	ENSPTRG00000014682	1 retrocopy	retro_ptro_731,
Ictidomys tridecemlineatus	ENSSTOG00000026229	1 retrocopy	retro_itri_398,
Tarsius syrichta	ENSTSYG00000007642	3 retrocopies	retro_tsyr_1544, retro_tsyr_315, retro_tsyr_946,
Tursiops truncatus	ENSTTRG00000001374	1 retrocopy	retro_ttru_949,