RetrogeneDB ID: retro_mmur_1319

Retrocopy location

• Organism: Mouse Lemur (Microcebus murinus)
• Coordinates: scaffold_44428:1011..1691(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBLCP1
• Ensembl ID: ENSMICG00000010060
• Aliases: None
• Description: ubiquitin-like domain containing CTD phosphatase 1 [Source:HGNC Symbol;Acc:28110]

Sequence

>retro_mmur_1319
ATGGCTCTCCCTATCATCGTAAAGTGGGGTGGACAGGAATATTCAATGACCACACTTTCAGAAGATGATACTGTGCTAGA
TCTCAATTTCTTAAGACCCTTACGGGAGTGCTGCCAGAACGCCAGAAGTTACTTGGACTCAAAGTTCAAGGCAAACCTGC
AGAAAATGATGTTAAGCTTGGAGCTGTCAAATTGAAACCAAATACTAAAATCATAATGATGGGAACTCATGAGGAGAGCT
TGGAAGATGTCTTAGGTCCACCCCCTGACAATGATGATGTTGTTAACGACTTTGATATTGAAGACGAAGTAGTTGAAGTA
GAAAATAGGGAAGAGAACCTACTGAAAATTTCTCGCAGAGTAAAAGAGTACAAAGTGGACATTTTGAATCCTCCCAGGGA
AGGGAAAAAGCCTTTGGTACTAGATGTTGATTATACATTATTTGACCACAGGTCTTGTGCAGAGACTGGGGTAGAATTAA
TGCAGCCATATCTTCATGAATTCCTAGCATCTGCATAGGAAGATTATGACATTGTTATTTGGTCTGCAACAAATATGAAG
TGGATTGAAGCTAAAATGAAAGAGCTGGGAGTGAGCACAAATGCAAATTATAAGATTACCTTCATGTTGGACAGTGCTGC
TATGATAACAGTGCATACCCCAAGGAGAGGATTAATAGAT

Alignment

ORF - retro_mmur_1319 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.32 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MALPIIVKWGGQEYSVTTLSEDDTVLDLKQFL-KTLTGVLPERQKLLGLKVKGKPAENDVKLGALKLKPN
          MALPIIVKWGGQEYS.TTLSEDDTVLDL..FL.KTLTGVLPERQKLLGLKV.GKPAENDVKLGA.KLKPN
Retrocopy MALPIIVKWGGQEYSMTTLSEDDTVLDL-NFL<KTLTGVLPERQKLLGLKVQGKPAENDVKLGAVKLKPN

Parental  TKIMMMGTREESLEDVLGPPPDNDDVVNDFDIEDEVVEVENREENLLKISRRVKEYKVEILNPPREGKKL
          TKI.MMGT.EESLEDVLGPPPDNDDVVNDFDIEDEVVEVENREENLLKISRRVKEYKV.ILNPPREGKK.
Retrocopy TKIIMMGTHEESLEDVLGPPPDNDDVVNDFDIEDEVVEVENREENLLKISRRVKEYKVDILNPPREGKKP

Parental  LVLDVDYTLFDHRSCAETGVELMRPYLHEFLTSAYEDYDIVIWSATNMKWIEAKMKELGVSTNANYKITF
          LVLDVDYTLFDHRSCAETGVELM.PYLHEFL.SA.EDYDIVIWSATNMKWIEAKMKELGVSTNANYKITF
Retrocopy LVLDVDYTLFDHRSCAETGVELMQPYLHEFLASA*EDYDIVIWSATNMKWIEAKMKELGVSTNANYKITF

Parental  MLDSAAMITVHTPRRGLID
          MLDSAAMITVHTPRRGLID
Retrocopy MLDSAAMITVHTPRRGLID

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Microcebus murinus was not studied using RNA-Seq expression data.

ChIP-Seq

Microcebus murinus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmur_1319 retrocopy.

TSS

Microcebus murinus was not studied using FANTOM5 data.

Lab

retro_mmur_1319 was not experimentally validated.

Homology

Retrocopy orthology:

Microcebus murinus 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,