RetrogeneDB ID: retro_mdom_51

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 8:245722973..245723537(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000024118
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: NRAS
• Ensembl ID: ENSMODG00000004590
• Aliases: NRAS, N-ras
• Description: GTPase NRas [Source:UniProtKB/Swiss-Prot;Acc:Q95ME4]

Sequence

>retro_mdom_51
ATGACCGAGTACAAACTGGTGGTGGTCGGAGCTGGCGGTGTGGGGGAAAGCGCCTTGACCATCCAGCTCATCCAGAATCA
CTTTGTAGACGAGCATGATCCTACTACAAAGGACTCCTATCGAAAGCAAGTAGTTATTGATGGTGAAACCTGTTTGTGGG
CCATACTCGACACCTCTGGACGGGAAGAGTGCAGTGCTGTGAGAGACCAGTATATGAGGACAGGGGAAGGCTTTCTCTGT
GTCTTTGCCATCAACAATAGCAAGTCATTTGCAGATATGAACCTCTACAAGCAACCTCTAAAGGAGCGAAAGACTGATGA
TGTGCCCAGGGTGCTGATGGGAAATAAGTGTGATTTGCCAACCAGGACAGCTGACACAAAACAGGCTCAGGAACTAGCCA
AGAGCTATGGAATTCCCTTCATTGAAACTTCAGCCAAGACTAGGCAGGGTGTTGATGCTTTTTACACACTGGTAAGAGAA
ATACGGCAATACTGCATGAAAAAACTCAACAGTAGCAATAATGGGACTCAAGGTTGTCCAGGTTTCTCGTGGGCAGTCAT
GTAA

Alignment

ORF - retro_mdom_51 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.13 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQ
          MTEYKLVVVGAGGVG.SALTIQLIQNHFVDE.DPT..DSYRKQVVIDGETCL..ILDT.G.EE.SA.RDQ
Retrocopy MTEYKLVVVGAGGVGESALTIQLIQNHFVDEHDPTTKDSYRKQVVIDGETCLWAILDTSGREECSAVRDQ

Parental  YMRTGEGFLCVFAINNSKSFADINLYREQIKRVKDSDDVPMVLVGNKCDLPTRTVDTKQAHELAKSYGIP
          YMRTGEGFLCVFAINNSKSFAD.NLY....K..K..DDVP.VL.GNKCDLPTRT.DTKQA.ELAKSYGIP
Retrocopy YMRTGEGFLCVFAINNSKSFADMNLYKQPLKERK-TDDVPRVLMGNKCDLPTRTADTKQAQELAKSYGIP

Parental  FIETSAKTRQGVEDAFYTLVREIRQYRMKKLNSSDDGTQGCLGLSCAVM
          FIETSAKTRQGV.DAFYTLVREIRQY.MKKLNSS..GTQGC.G.S.AVM
Retrocopy FIETSAKTRQGV-DAFYTLVREIRQYCMKKLNSSNNGTQGCPGFSWAVM

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_51 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_51 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 13 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017134	1 retrocopy	retro_amel_885,
Callithrix jacchus	ENSCJAG00000036517	1 retrocopy	retro_cjac_2400,
Felis catus	ENSFCAG00000019026	1 retrocopy	retro_fcat_1191,
Loxodonta africana	ENSLAFG00000020706	1 retrocopy	retro_lafr_492,
Macropus eugenii	ENSMEUG00000002675	1 retrocopy	retro_meug_2136,
Myotis lucifugus	ENSMLUG00000022354	1 retrocopy	retro_mluc_741,
Monodelphis domestica	ENSMODG00000001323	3 retrocopies	retro_mdom_1327, retro_mdom_139, retro_mdom_1777,
Monodelphis domestica	ENSMODG00000004590	1 retrocopy	retro_mdom_51 ,
Monodelphis domestica	ENSMODG00000007323	5 retrocopies	retro_mdom_11, retro_mdom_1570, retro_mdom_1756, retro_mdom_1897, retro_mdom_429,
Monodelphis domestica	ENSMODG00000017458	1 retrocopy	retro_mdom_153,
Oryctolagus cuniculus	ENSOCUG00000022455	1 retrocopy	retro_ocun_850,
Rattus norvegicus	ENSRNOG00000023079	2 retrocopies	retro_rnor_2867, retro_rnor_619,
Sus scrofa	ENSSSCG00000006753	1 retrocopy	retro_sscr_520,