RetrogeneDB ID: retro_ocun_1535

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: AAGW02079214:53729..54571(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UHMK1
• Ensembl ID: ENSOCUG00000012411
• Aliases: None
• Description: U2AF homology motif (UHM) kinase 1 [Source:HGNC Symbol;Acc:19683]

Sequence

>retro_ocun_1535
TCCAGAGATGTTCTGGAAGGCCTTGCTCTCCTTCATCATGAGGGTCGTGTCCACGCAGACCTCAAACCGCAGAACATACT
GTGGAGTGCAGAGAACGAATGTTTTAAACTCACTGACTTTGGACTTAGCTTCAAAGAAGGCACTCCGGGTGTAAAGTACA
TTCAAACAGACGGGTGTCGTGCTCCAGAAGCAGAGCTGAAAAATCACGTGGCCCAGGCTGGCCTGCAGAGTGATACATAA
TGTAGCTCGGCTGCTGGTCTGCGGAGCCTAGGAATCATTTTACTGGAAATGTTCTCAGGAACGAAGCTGAAGCATACAGT
CCGATCTCAGGAATGGAAGGCAAGCAGTTCTGCTGTTGTTGATGAGATATTTGCCGGTAAAGCAGTGGTGAATGCCACAA
TTCCAACCCGTCACCTAAGAGACCTTATCAAAAGCATGCTTCATGATGATCCAAGCAGAAGAGTTCCTGCTGAAATGGCA
TCGCGCAGCCCATTCGTTAGCATTCCTTTTGCCCCTCATGTTGAAGATCTGATGGTAGTTCCTACCCCACTGCTAAGACT
GCTGAGCATGCTAGATGATGATCATCTTGAGAATGAAGAGGAACATGAAGATATTGTAGAAGATGTAAAAGAGGAATGCC
AGAAATATGGACCCGTGATATCTCTGCTTGTCCAAAGGAAAATCCTGGCAGAGGGCAAGTCTTTGTCGAGTATGCCAATG
CTGGTGGTTCCAAAGATGCTCAGGAATTACTGACCGGAAGGATGTTTGATGGGAAGTTTGTCATGGCTACATTCTACCCG
CAGAGTGCCTACAAGAGGGGATATCTGTATCAAACCTTGCTT

Alignment

ORF - retro_ocun_1535 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.33 %
• Parental protein coverage: 67.06 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ARDVLEALAFLHHEGYVHADLKPRNILWSAENECFKLIDFGLSFKEGNQDVKYIQTDGYRAPEAELQNCL
          .RDVLE.LA.LHHEG.VHADLKP.NILWSAENECFKL.DFGLSFKEG...VKYIQTDG.RAPEAEL.N..
Retrocopy SRDVLEGLALLHHEGRVHADLKPQNILWSAENECFKLTDFGLSFKEGTPGVKYIQTDGCRAPEAELKNHV

Parental  AQAGLQSDTECTSAVDLWSLGIILLEMFSGMKLKHTVRSQEWKANSSAIIDHIFASKAVVNAAIPAYHLR
          AQAGLQSDT.C.SA..L.SLGIILLEMFSG.KLKHTVRSQEWKA.SSA..D.IFA.KAVVNA.IP..HLR
Retrocopy AQAGLQSDT*CSSAAGLRSLGIILLEMFSGTKLKHTVRSQEWKASSSAVVDEIFAGKAVVNATIPTRHLR

Parental  DLIKSMLHDDPSRRIPAEMALCSPFFSIPFAPHIEDLVMLPTPVLRLLNVLDDDYLENEEEYEDIVEDVK
          DLIKSMLHDDPSRR.PAEMA..SPF.SIPFAPH.EDL...PTP.LRLL..LDDD.LENEEE.EDIVEDVK
Retrocopy DLIKSMLHDDPSRRVPAEMASRSPFVSIPFAPHVEDLMVVPTPLLRLLSMLDDDHLENEEEHEDIVEDVK

Parental  EECQKYGPVVSLLV-PKENPGRGQVFVEYANAGDSKAAQKLLTGRMFDGKFVVATFYPLSAYKRGYLYQT
          EECQKYGPV.SLLV.PKENPGRGQVFVEYANAG.SK.AQ.LLTGRMFDGKFV.ATFYP.SAYKRGYLYQT
Retrocopy EECQKYGPVISLLV<PKENPGRGQVFVEYANAGGSKDAQELLTGRMFDGKFVMATFYPQSAYKRGYLYQT

Parental  LL
          LL
Retrocopy LL

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	0.55 RPM	6.79 RPM
SRP017611_kidney	1.32 RPM	5.37 RPM
SRP017611_liver	0.15 RPM	2.77 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1535 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1535 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1535 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000001048	1 retrocopy	retro_mdom_103,
Oryctolagus cuniculus	ENSOCUG00000012411	3 retrocopies	retro_ocun_1245, retro_ocun_1535 , retro_ocun_1547,
Rattus norvegicus	ENSRNOG00000002941	1 retrocopy	retro_rnor_1274,