RetrogeneDB ID: retro_mdom_1251

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 4:104778379..104779277(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBLCP1
• Ensembl ID: ENSMODG00000008063
• Aliases: None
• Description: ubiquitin-like domain containing CTD phosphatase 1 [Source:HGNC Symbol;Acc:28110]

Sequence

>retro_mdom_1251
CTCTCTCTCTCACACATAATATAATGGGGTGGACAGGAATATTTAATAACCACACTTTCCAAAGAAGATACGGTGCTAGA
CCTCAAGCAGTCCCTCAAGACACTTACAGGAGTGCTCCCAGAATGCCAAAAGTTGCTTGGTCTAAAGGTTAAAGGCAAAC
CTGCAGAAAATGACGTTAAGCTTGGAGCTCTCAAACTGAAACCAAATACTAAAATCATGATGATGGGAACTGGAGAGGAG
AGCTTGGAAGATGTCTTGGGCCCACCACCTGACAATGATGATGTTGTCAATGATTTTGATATTGAAGAGGAAGTAGTTGA
AGTAGAGAATAGGGAAGAAAGCCTGCCAAAAATTTATAGAAGAGTTAAAGATTACAAAGTGGAAATTTTGAATCCTCCTA
GGGAAGGAAAAAAACTTTTGGTACTAGATGTTGATTATACATTGTTTGATGATAGGTCCTGTGCAGAAACTGGGGTAGAA
TTAATGCGGCCATATCTTCATGAATTCTTAACATCTGCATATGAAGATTATGACATTGTTATTTGGTCTGCTACAAATAT
GAAGTGGATTGAAGCTGAAATGAAGGAACTGGGAGTAAGTACAAATGCAAACTAGAAGATCACCTTCATGTTGGACAGTG
CTGCTATGATAACAGTGCATACCCCAAGAAGAGGCCTAATAGATGTAAAACCTCTTGGTGTTATATGGGGGAAATTTTCA
GAGTTTTACAGCCAAAAAAAAAAATACCATTATGTTTGATGATATCAGAAGAAATTTTCTTATGAACCCACAGAATGGAT
TAAAGATAAGGCCTTTTATGAAAGCTCATCTAAATAGAGATAAAGATAAAGAACTTTTAAAGTTAACCCAATACCTCAAG
GAAATAGCATAATTAGAT

Alignment

ORF - retro_mdom_1251 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.33 %
• Parental protein coverage: 93.71 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSLSLIIKWGGQEYLITTLSEEDTVLDLKQSLKTLTGVLPERQKLLGLKVKGKPAENDVKLGALKLKPNT
          .SLS.II.WGGQEYLITTLS.EDTVLDLKQSLKTLTGVLPE.QKLLGLKVKGKPAENDVKLGALKLKPNT
Retrocopy LSLSHII*WGGQEYLITTLSKEDTVLDLKQSLKTLTGVLPECQKLLGLKVKGKPAENDVKLGALKLKPNT

Parental  KIMMMGTREESLEDVLGPPPDNDDVVNDFDIEEEVVEVENREENLLKISRRVKDYKVEILNPPREGKKLL
          KIMMMGT.EESLEDVLGPPPDNDDVVNDFDIEEEVVEVENREE.L.KI.RRVKDYKVEILNPPREGKKLL
Retrocopy KIMMMGTGEESLEDVLGPPPDNDDVVNDFDIEEEVVEVENREESLPKIYRRVKDYKVEILNPPREGKKLL

Parental  VLDVDYTLFDHRSCAETGVELMRPYLHEFLTSAYEDYDIVIWSATNMKWIEAKMKELGVSTNANYKITFM
          VLDVDYTLFD.RSCAETGVELMRPYLHEFLTSAYEDYDIVIWSATNMKWIEA.MKELGVSTNAN.KITFM
Retrocopy VLDVDYTLFDDRSCAETGVELMRPYLHEFLTSAYEDYDIVIWSATNMKWIEAEMKELGVSTNAN*KITFM

Parental  LDSAAMITVHTPRRGLIDVKPLGVIWGK-FSEFYSKKN-TIMFDDIGRNFLMNPQNGLKIRPFMKAHLNR
          LDSAAMITVHTPRRGLIDVKPLGVIWGK.F..F......TIMFDDI.RNFLMNPQNGLKIRPFMKAHLNR
Retrocopy LDSAAMITVHTPRRGLIDVKPLGVIWGK>FQSFTAXXXXTIMFDDIRRNFLMNPQNGLKIRPFMKAHLNR

Parental  DKDKELLKLTQYLKEIAKLD
          DKDKELLKLTQYLKEIA.LD
Retrocopy DKDKELLKLTQYLKEIA*LD

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	49.71 RPM
SRP007412_cerebellum	0.00 RPM	31.34 RPM
SRP007412_heart	0.00 RPM	35.48 RPM
SRP007412_kidney	0.00 RPM	31.60 RPM
SRP007412_liver	0.00 RPM	19.64 RPM
SRP007412_testis	0.00 RPM	76.81 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1251 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1251 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 10 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007691	1 retrocopy	retro_chof_51,
Echinops telfairi	ENSETEG00000000170	1 retrocopy	retro_etel_1142,
Microcebus murinus	ENSMICG00000010060	2 retrocopies	retro_mmur_1083, retro_mmur_1319,
Myotis lucifugus	ENSMLUG00000006359	1 retrocopy	retro_mluc_1367,
Monodelphis domestica	ENSMODG00000008063	2 retrocopies	retro_mdom_1251 , retro_mdom_1351,
Mustela putorius furo	ENSMPUG00000013396	1 retrocopy	retro_mputfur_1098,
Mus musculus	ENSMUSG00000041231	1 retrocopy	retro_mmus_762,
Oryctolagus cuniculus	ENSOCUG00000002224	1 retrocopy	retro_ocun_1036,
Tupaia belangeri	ENSTBEG00000008983	1 retrocopy	retro_tbel_41,
Tursiops truncatus	ENSTTRG00000005876	1 retrocopy	retro_ttru_761,