RetrogeneDB ID: retro_ocun_563

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 12:57691706..57692451(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBXN2B
• Ensembl ID: ENSOCUG00000023461
• Aliases: None
• Description: UBX domain protein 2B [Source:HGNC Symbol;Acc:27035]

Sequence

>retro_ocun_563
AAGTTTTATTCAGGTGAACATGAATACGGTGGATTACATATAGTTCAACTTCAACTGGGAAAATTGTGAGTAAACTTTTC
AAAGAGGCAAGGGAGCATGGGGCTGTCCTCTGAATGAAGCCACTAGATCTTCAAGTGATGACAAATATAAGTCCTTTCCA
GGTGGAGGATACAGATTGGGAAATTCCTTTTGTAAGCAGTCTGAATACATCTATGGAGAAAATCAGCTGCAAGGTGTTCA
GATTTTGCTTAACCTATGGAGCAATGGTTTCAGCTTAGATGATGGAGAATTGAAACGTTACTGTGACCCAGTAAATGCTC
AATTTTGGGAGTCTTAAAAGAGGAGAGATTCCTTTGGAGCTTCAGTGAATGATTCATGGGGGCCAACTGAGTTTGGATGT
GGAGGATCATCAGGATCAAGAATATATAAAACCTACAATGAGGTGCAATGCTTTCAGTGGGGAAGGGCAAAACCTTGGAC
ACCTTACCCTGCAATAGTCAGAACACCTTCCTCTCCAGAAGAGGATAAGTCAGTGCTTAATTCAGTTATTCATATTAATG
ATTCAGTGCCAACAACAAAAATTCAAATCAGATTAGCAGATGGGAGTCATTTGATACAAAGATTCAACAGTATACACAGA
ATCCTGGATGTCCGGGACTTTATTGTACAGTCTCGTCCTGAATTTGCAGCTCTTTACTTTATTCTTGTGACTTCATTTCC
AAATAAAGATCTAACAGATGAAAAC

Alignment

ORF - retro_ocun_563 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.69 %
• Parental protein coverage: 75.83 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  RFYSGEHEYRGLHIVR-PSTGKIVNELFKEAREHGAV-PLNEATRSSSDDKSKSFTGGGYRLGNSFCKRS
          .FYSGEHEY.GLHIV...STGKIV..LFKEAREHGAV.PLNEATRSSSDDK.KSF.GGGYRLGNSFCK.S
Retrocopy KFYSGEHEYGGLHIVQ<TSTGKIVSKLFKEAREHGAV<PLNEATRSSSDDKYKSFPGGGYRLGNSFCKQS

Parental  EYIYGENQLQDVQVLLKLWSNGFSLDDGELRPYSD-PTNAQFLE-SVKRGEIPLELQRLVHEGQLSLDME
          EYIYGENQLQ.VQ.LL.LWSNGFSLDDGEL..Y.D.P.....L..S.KRGEIPLELQ...H.GQLSLD.E
Retrocopy EYIYGENQLQGVQILLNLWSNGFSLDDGELKRYCD<PSKCSILG<SLKRGEIPLELQ*MIHGGQLSLDVE

Parental  DHQDQEYVKPRLRFKAFSGEGQKLGSLT-PEIVSTPSSPEEEDKSILNAVVHIDDSVPTTKIQIRLADGS
          DHQDQEY.KP..R..AFSGEGQ.LG.LT.P.IV.TPSSPEE.DKS.LN.V.HI.DSVPTTKIQIRLADGS
Retrocopy DHQDQEYIKPTMRCNAFSGEGQNLGHLT<PAIVRTPSSPEE-DKSVLNSVIHINDSVPTTKIQIRLADGS

Parental  RLIQRFNCTHRILDVRNFIVQSRPEFAALDFILVTSFPNKDLTDES
          .LIQRFN..HRILDVR.FIVQSRPEFAAL.FILVTSFPNKDLTDE.
Retrocopy HLIQRFNSIHRILDVRDFIVQSRPEFAALYFILVTSFPNKDLTDEN

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	5.96 RPM
SRP017611_kidney	0.00 RPM	9.93 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_563 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_563 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_563 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryctolagus cuniculus	ENSOCUG00000008783	1 retrocopy	retro_ocun_207,
Oryctolagus cuniculus	ENSOCUG00000023461	1 retrocopy	retro_ocun_563 ,