RetrogeneDB ID: retro_mdom_1027

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:287335415..287335637(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LSM6
• Ensembl ID: ENSMODG00000000526
• Aliases: None
• Description: LSM6 homolog, U6 small nuclear RNA associated (S. cerevisiae) [Source:HGNC Symbol;Acc:17017]

Sequence

>retro_mdom_1027
AAGCAAACTCCAAGTGAATTCCTAAAGCAGATTATAGGAAGATCAGTATTAAAGTTAAATTCTGGAAAGGATTATCAAGG
TGTCCTGGCTTGCTTGTATGGCATGAATATAACTCTGAATCAAACAAAATAATATGTAAATAGACAACTAAAGAATAAAT
ATGGGGATACATTTATTTGAGGAAACAATGTATTATATATAAGCACCCAGAAGAGAAGACTT

Alignment

ORF - retro_mdom_1027 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.95 %
• Parental protein coverage: 95. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KQTPSDFLKQIIGRPVVVKLNSGVDYRGVLACLDGYMNIALEQTEEYVNGQLKNKYGDAFIRGNNVLYIS
          KQTPS.FLKQIIGR.V..KLNSG.DY.GVLACL.G.MNI.L.QT..YVN.QLKNKYGD.FI.GNNVLYIS
Retrocopy KQTPSEFLKQIIGRSVL-KLNSGKDYQGVLACLYG-MNITLNQTK*YVNRQLKNKYGDTFI*GNNVLYIS

Parental  TQKRRM
          TQKRR.
Retrocopy TQKRRL

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_1027 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1027 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 12 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014060	1 retrocopy	retro_btau_861,
Cavia porcellus	ENSCPOG00000015389	1 retrocopy	retro_cpor_368,
Dasypus novemcinctus	ENSDNOG00000009322	5 retrocopies	retro_dnov_1118, retro_dnov_176, retro_dnov_2092, retro_dnov_301, retro_dnov_664,
Homo sapiens	ENSG00000164167	2 retrocopies	retro_hsap_1948, retro_hsap_2107,
Gorilla gorilla	ENSGGOG00000001310	2 retrocopies	retro_ggor_1417, retro_ggor_1638,
Myotis lucifugus	ENSMLUG00000026355	1 retrocopy	retro_mluc_1859,
Monodelphis domestica	ENSMODG00000000526	4 retrocopies	retro_mdom_1027 , retro_mdom_1383, retro_mdom_1983, retro_mdom_621,
Monodelphis domestica	ENSMODG00000008091	3 retrocopies	retro_mdom_550, retro_mdom_780, retro_mdom_811,
Nomascus leucogenys	ENSNLEG00000005584	2 retrocopies	retro_nleu_1275, retro_nleu_1479,
Otolemur garnettii	ENSOGAG00000026665	1 retrocopy	retro_ogar_233,
Sus scrofa	ENSSSCG00000009036	2 retrocopies	retro_sscr_474, retro_sscr_475,
Tarsius syrichta	ENSTSYG00000012759	4 retrocopies	retro_tsyr_1332, retro_tsyr_1727, retro_tsyr_340, retro_tsyr_653,