RetrogeneDB ID: retro_mdom_800

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 2:9226095..9226292(-)
• Located in intron of: ENSMODG00000002412

Retrocopy information

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

Parental gene information

• Parental gene symbol: LSM3
• Ensembl ID: ENSMODG00000007275
• Aliases: None
• Description: LSM3 homolog, U6 small nuclear RNA associated (S. cerevisiae) [Source:HGNC Symbol;Acc:17874]

Sequence

>retro_mdom_800
TATATATAAATGAGAAATGATTGAGAACTTCAAAAGAGAGTCAGTATTTAGGACTAGCATTTAAATATGATTTTGGGAGA
CGTAGATGAGAAGTGACCCCTATGGAAAGTAATGAATAAATTTGTGAAGAAATATGCAAATCAACCAAGCAGAATACTAT
AGTGCTGCATTTCTTAAATGAAGGCATTGTATTCATA

Alignment

ORF - retro_mdom_800 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.75 %
• Parental protein coverage: 64.71 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  YVKMRNDRELRGRLHAYDQHLNMILGDVEE-TVTTIEIDEETYEEIYKSTKRNIPMLFVRGDGVVLV
          Y..MRND.EL..R....D.HLNMILGDV.E..VT..E..E...EEI.KSTK.N...L.....G.V..
Retrocopy YI*MRND*ELQKRVSI*D*HLNMILGDVDE<EVTPMESNE*ICEEICKSTKQNTIVLHFLNEGIVFI

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_800 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_800 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 9 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016977	1 retrocopy	retro_cjac_54,
Gorilla gorilla	ENSGGOG00000010006	4 retrocopies	retro_ggor_104, retro_ggor_1699, retro_ggor_2068, retro_ggor_826,
Myotis lucifugus	ENSMLUG00000010677	4 retrocopies	retro_mluc_1148, retro_mluc_2306, retro_mluc_2337, retro_mluc_25,
Monodelphis domestica	ENSMODG00000007275	1 retrocopy	retro_mdom_800 ,
Oryctolagus cuniculus	ENSOCUG00000011088	1 retrocopy	retro_ocun_126,
Otolemur garnettii	ENSOGAG00000007659	6 retrocopies	retro_ogar_1031, retro_ogar_231, retro_ogar_242, retro_ogar_2490, retro_ogar_2818, retro_ogar_577,
Oreochromis niloticus	ENSONIG00000000370	1 retrocopy	retro_onil_12,
Sus scrofa	ENSSSCG00000011601	6 retrocopies	retro_sscr_1134, retro_sscr_1140, retro_sscr_395, retro_sscr_396, retro_sscr_457, retro_sscr_64,
Vicugna pacos	ENSVPAG00000010709	2 retrocopies	retro_vpac_121, retro_vpac_397,