RetrogeneDB ID: retro_ocun_1036

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 2:40169593..40170547(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBLCP1
• Ensembl ID: ENSOCUG00000002224
• Aliases: None
• Description: ubiquitin-like domain containing CTD phosphatase 1 [Source:HGNC Symbol;Acc:28110]

Sequence

>retro_ocun_1036
ATGGCTCTTCCTATCATTGTAAAATGGGGTGGACAGGAATATTCCACGACTACCCTTTCAGAAGATGATACTGTGCTGGA
CCTCAAGCAGTTTCTCAAGACCCTTTCAGGGGTGCTGCCAGAACGCCAGAAGTTGCTGGGACTCAAAGTTAAAGGCAAAC
CTGCAGAAAATGGTGTTAAGCTTGGAGCTCTCAAACTGAAACCAAATACTAAAATCATGGTGATGGGAACTCATGAGGAG
AGCTTGGAAGATGTCTTGGGTCTACCCCCTGACAATGATGATGTTGTCAATGATTTTGATATTGAAGATGAAGTTGTTGA
AGTAGAAAATAGGGAAGAAAACCTACTAAAAATTTCTCACAGAGTGAAAGAGTACAAAGTGGAAATTCTGAATGCTCCTA
GGGAAGGGAAAAAGCTTTTGGTACTAGATGTTAATTATACATTATTTGACCATAGGTCTTGTGCTGAGACTGGGGTAGAA
TTAATGAGGCCATATCTTCATGAATTCTTCACATCTGCATATGAAGATTATGACATTGTTATTTGGTCTGCAACAAATAT
GAAGTGGATTGAAGCTAAAATGAAATAGCTAGGAGTGAGCACAAACGCAAATTGTAAAATTACCTTCATGTTGGACAGTG
CTGCTATGATAACAGTGCATACTCCCAGGAGAGGATTAATAGATGTAAAACCTCTTGGTGTTATGTGGGGAAAGTTTTTG
GAATTTTACAGCAAGAAAAATACCATTATGTTTTATGACATATGACGGAATTTTCTGATGAACCCACAGAATAGACTAAA
GATAAGGCCCTTTATGAAAGCACACCTAAATCGAGAGAAAGACAAGGAACTTTTAAAATTAACTCAGTACTTCAAGGAAA
TAGCAAAATTAGGTGACTTTTTGGAGTTAAATCACAAATATTGGGAAAGGTATCTCTCAAAGAAGAAAGGACAA

Alignment

ORF - retro_ocun_1036 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.4 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MALPIIVKWGGQEYSVTTLSEDDTVLDLKQFLKTLTGVLPERQKLLGLKVKGKPAENDVKLGALKLKPNT
          MALPIIVKWGGQEYS.TTLSEDDTVLDLKQFLKTL.GVLPERQKLLGLKVKGKPAEN.VKLGALKLKPNT
Retrocopy MALPIIVKWGGQEYSTTTLSEDDTVLDLKQFLKTLSGVLPERQKLLGLKVKGKPAENGVKLGALKLKPNT

Parental  KIMMMGTREESLEDVLGPPPDNDDVVNDFDIEDEVVEVENREENLLKISRRVKEYKVEILNPPREGKKLL
          KIM.MGT.EESLEDVLG.PPDNDDVVNDFDIEDEVVEVENREENLLKIS.RVKEYKVEILN.PREGKKLL
Retrocopy KIMVMGTHEESLEDVLGLPPDNDDVVNDFDIEDEVVEVENREENLLKISHRVKEYKVEILNAPREGKKLL

Parental  VLDVDYTLFDHRSCAETGVELMRPYLHEFLTSAYEDYDIVIWSATNMKWIEAKMKELGVSTNANYKITFM
          VLDV.YTLFDHRSCAETGVELMRPYLHEF.TSAYEDYDIVIWSATNMKWIEAKMK.LGVSTNAN.KITFM
Retrocopy VLDVNYTLFDHRSCAETGVELMRPYLHEFFTSAYEDYDIVIWSATNMKWIEAKMK*LGVSTNANCKITFM

Parental  LDSAAMITVHTPRRGLIDVKPLGVIWGKFSEFYSKKNTIMFDDIGRNFLMNPQNGLKIRPFMKAHLNRDK
          LDSAAMITVHTPRRGLIDVKPLGV.WGKF.EFYSKKNTIMF.DI.RNFLMNPQN.LKIRPFMKAHLNR.K
Retrocopy LDSAAMITVHTPRRGLIDVKPLGVMWGKFLEFYSKKNTIMFYDI*RNFLMNPQNRLKIRPFMKAHLNREK

Parental  DKELLKLTQYLKEIAKLDDFLELNHKYWERYLSKKQGQ
          DKELLKLTQY.KEIAKL.DFLELNHKYWERYLSKK.GQ
Retrocopy DKELLKLTQYFKEIAKLGDFLELNHKYWERYLSKKKGQ

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
SRP017611_brain	0.00 RPM	42.22 RPM
SRP017611_kidney	0.00 RPM	33.45 RPM
SRP017611_liver	0.00 RPM	10.10 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1036 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1036 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1036 has 0 orthologous retrocopies within eutheria group .

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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,