RetrogeneDB ID: retro_ocun_1245

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 4:80359869..80360627(+)
• Located in intron of: ENSOCUG00000000881

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_1245
TTGTGGAGTGCAGAGAATGAATGTTTTAAACTCGTTGACTTTGGTTTAGTGTCAAAGAAGGCAATCAGGATGTAAAGTAT
ATTCAGACAGACAGGTATCTTCCAGAAGCAGAGCTGCAAAATTGCTTGGCCCAGGCTGGCCTGCAGAGACACACAGAATG
TACCTCAGCTGTTGATCTGTGGAGCCTTAGAATCATTTTACTGGAAATGTTCTCAGGAATGAAACTGAAACATACAGTCT
GATCTCAGGAATGGAAGACAAACAGTTCTGCTATTACTGACCACAGATTTGCCAGTAGAGCAGTGGTGAATGCTGCAATT
CGAGCCCATCACCTAAGAGACCTTATCAAAGCCTGCTTCATGGTGATCCAAGCAGAATTCCTGCGGAAATGGCATTGTGC
AGTCCATTCTTTAGCATTCCTTTCACCCCTGAAATTGAAGATCTGGTGATGATTCCTACCCCACAGCTAAGACTGCAGAA
CGTACTAGATGATGATTATCTCGAAAGTGAAAAGGAATTCATGAAGATGTTGCAGAAGATGTAAAAGAGGAATGTCAGAA
ATATGGACCAGTGGTATCTCTGCTTGTTCCAAAGGAAAATCCTGGCAGAGGGCAAGTCTTTGTTGAGTATGCCAATGCTG
GTGATTCCAAAGCTGTTCAGGAATGACTGACCTGAGGATGTTTGATGAGAAGTTTGTTGTGGCTACATTCTACCCACTGA
GTGCCTACAAGAGGGGCTATCTGTATCAAACCTTGCTT

Alignment

ORF - retro_ocun_1245 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.46 %
• Parental protein coverage: 60.86 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  LWSAENECFKLIDFGL-SFKEGNQDVKYIQTDGYRAPEAELQNCLAQAGLQSDTECTSAVDLWSLGIILL
          LWSAENECFKL.DFGL.S.KEGNQDVKYIQTD.Y..PEAELQNCLAQAGLQ..TECTSAVDLWSL.IILL
Retrocopy LWSAENECFKLVDFGL<SVKEGNQDVKYIQTDRY-LPEAELQNCLAQAGLQRHTECTSAVDLWSLRIILL

Parental  EMFSGMKLKHTVRSQEWKANSSAIIDHIFASKAVVNAAIPAYHLRDLIK-SMLHDDPSRRIPAEMALCSP
          EMFSGMKLKHTV.SQEWK.NSSAI.DH.FAS.AVVNAAI.A.HLRDLIK.S.LH.DPSR.IPAEMALCSP
Retrocopy EMFSGMKLKHTV*SQEWKTNSSAITDHRFASRAVVNAAIRAHHLRDLIK<SLLHGDPSR-IPAEMALCSP

Parental  FFSIPFAPHIEDLVMLPTPVLRLLNVL-DDDYLENEEE-YEDIVEDVKEECQKYGPVVSLLVPKENPGRG
          FFSIPF.P.IEDLVM.PTP.LRL.NVL.DD......E...ED..EDVKEECQKYGPVVSLLVPKENPGRG
Retrocopy FFSIPFTPEIEDLVMIPTPQLRLQNVLDDDYLESEKEF<HEDVAEDVKEECQKYGPVVSLLVPKENPGRG

Parental  QVFVEYANAGDSKAAQKLLT-GRMFDGKFVVATFYPLSAYKRGYLYQTLL
          QVFVEYANAGDSKA.Q..LT..RMFD.KFVVATFYPLSAYKRGYLYQTLL
Retrocopy QVFVEYANAGDSKAVQE*LT<LRMFDEKFVVATFYPLSAYKRGYLYQTLL

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	0.11 RPM	6.79 RPM
SRP017611_kidney	0.00 RPM	5.37 RPM
SRP017611_liver	0.00 RPM	2.77 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1245 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1245 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1245 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,