RetrogeneDB ID:

retro_ocun_349

Retrocopy
location
Organism:Rabbit (Oryctolagus cuniculus)
Coordinates:1:21114979..21117198(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:CUL4B
Ensembl ID:ENSOCUG00000015633
Aliases:None
Description:cullin 4B [Source:HGNC Symbol;Acc:2555]


Retrocopy-Parental alignment summary:






>retro_ocun_349
TCCTCCTTCTGCCTGGGGCTTTACATGGCTACTTCTAGCCACGTACCAATATAGAAAAAGGTGCATTTTGAAAAAATCCT
GGAGCTTGTAGTGTTTGATATGAAGTTGGCTGAGGAATCCTCCTCCATCTCTTCCTCTTCATCTTCACCAACTGCTGCAA
CATCTCAGCAGCAGTAACTTAAAAATAAACTATATTCGTCTTTTCTGTGGCTTTGGTGCATCATGCAAACAGCCCAGCCA
AATCTTGTACCATCAACTCTAGCTTTGCTAATAGCAAGCCTGCCTCTCCTAAGAAGTTAGTGATCAAGAACTTTAAAGAT
AAGCCTAAATTACCAGAAAACAACACAGATGAAACTTGGCAGAAACTGAAAGAAGCAGTGGAAGCTATTCAGAATAGTAC
TTCAGTTGAGTATAATTAGAACTCTACTAGGCTATAGAAAATCTCTGTTGTTACGGATTCTCAACAAACGTGTACGAACA
GCTGGGACAGATTTGTGATGATCACATCAGAACACAAATTCATCAGTTCAGAAAAGATTCACAGGATAGTGTCCTTTTCC
TAAAGAAGATTGATAGGTGCTCGCAGAACCATTGCAGACAAATGATCATAATCAGGAGCATCTTTTTGTTTCTGGATAGA
ACTTGTGTTCTTCAGAATTCAGTGCTGCCCTCCATTCGGGACGTGGGACTGGCGTTATTTAGGGCACATATTATAAGTGA
TCAGAAAGTCCAGAATAAGACAACTGATGGCATGGCTTCTCTTGACAGAGGGAAAGGAATTGTGAAGCAATTGATAGACG
TTTACCCCTAAGCCTTTTAAGTATGCTCTCTGATTTGCACATTTATCAAGATTCTTTTGAACAAGGATTTTTGAAGGAAA
CTAACTGGCTCTACACAGCTGAAGGCCAAAAATTAATGCAGGAAAGACAGGTTCCTGAATATCTTCATCATGTTAACAAA
CATCTAGAAGAAGAACTAGGTAGACTTATTACATACTTAGATCAGACTACCTAGAAATCATTGATTGCTCATGCAGAAAA
ACAACCTCTAGACAAACACTTAACAGCATTTTTAAGAAACGTTTAAATAATCTCCTTGATGGTAACTTAATTCAAGATTT
ATTTCTCCTGTATCAGCTCTTCAGTAGAGTTCGAGGTGGTGTTCAGATTCTCTTGTAATAGTGGACTGACTGCATCAAGG
TATTGGCAGCACTATTGTAATCAATCTTGAAAAAGGTAAAACCATGGCTCAAGCACTGCTGGATTTTAAAGATAAAGTTG
ATCATATAATTGATATCTGCTTTCTGAAGAATTAAATATTTATCAATACCATGAAATGTACATTTGAAACATTCATTACA
AAAGATCAAATAAATCTGAGCTCATAGCCAAGTATATAGATTCAAACTTTGTGCAGGCAACAAAGAAGCTACAGATGAAG
AACTTGAGAAAATGTAGAATAATATTATGATCATATTTAGATTTATTTATGGCAAGGGCGTTTTTGAGGACTTCTATAAA
AAAGATTTATTAGCCAAGTGTCTGTTATTTCGGAAGAGTCCATTTGTAGATGCTAAAAAATCAATGCCGTCCAAACTCAA
ACATCAACATGGAACTGCTTTCACCAGCAAGCTTGAAGGGATATTTCAAGACATGGATATTTCTAAAGATATCATGGTTC
AGTTCAAACAGTATATGCAGAATCAGAATGTACCTGGAAATATTGAATGAACTGTGAATATCCTGACAATGAGTCATTGG
CCAACATATGTGCCTATGGACATCCATTTACCACCAGGGATGGTAAAACTTCAAGAAATTTTTAAGACATTTTACCAAGG
TAAAAACAGTGGCAGAAAACTTCAATGGCAGTCAACCCTAGGACACTGTGTGCTAAAAGCAAAGTTTAAAAAGGGCAAAA
AAAATCAACAACAACAAATCCAGGTCTCTCTTTTTAAATGTTGCTGCTAATGTTTAATGAGAAAGTGGAGTTCAGTTTAA
AAGAGATCAAACAGGCTACTGGAATCGAGGCTGGAGAGTTAGAGTTAAGGAGAAAATTTACAGGCATCAGCCTGTGGCAA
CTAGAGTTCTGGTGAAAAAAATCTGAAGAGCAAAGATATTGAAGATGTTGACATATTCATTTGTAATGATGATTTCAAGC
ACAAACTTTTCAGGATAAAGACCAATCAAATTCAGATGAAAGAGATGAGGAATAAGCAA

ORF - retro_ocun_349 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 76.26 %
Parental protein coverage: 78.05 %
Number of stop codons detected: 10
Number of frameshifts detected 9


Retrocopy - Parental Gene Alignment:

ParentalSSFCLGVSVATSSHVPIQKKLRFEDTLEFVGFDAKMAEESSS-SSSSSSPTAATSQQQQLKNK-SILISS
SSFCLG...ATSSHVPI.KK..FE..LE.V.FD.K.AEESSS.SSSSSSPTAATSQQQ.LKNK..I...S
RetrocopySSFCLGLYMATSSHVPI*KKVHFEKILELVVFDMKLAEESSSISSSSSSPTAATSQQQ*LKNK<TIFVFS
ParentalVASVHHANGLAKSTTV-SSFANSKPGSAKKLVIKNFKDKPKLPENYTDETWQKLKEAVEAIQNSTSIKYN
VA.VHHAN..AKS.T..SSFANSKP.S.KKLVIKNFKDKPKLPEN.TDETWQKLKEAVEAIQNSTS..YN
RetrocopyVALVHHANSPAKSCTINSSFANSKPASPKKLVIKNFKDKPKLPENNTDETWQKLKEAVEAIQNSTSVEYN
Parental-LEELYQAVENLCSYKISANLYKQLRQICEDHIKAQIHQFREDSLDSVLFLKKIDRCWQNHCRQMIMIRS
.LE.LY.A.ENLC.Y..S.N.Y.QL.QIC.DHI..QIHQFR.DS.DSVLFLKKIDRC.QNHCRQMI.IRS
Retrocopy<LE-LY*AIENLCCYGFSTNVYEQLGQICDDHIRTQIHQFRKDSQDSVLFLKKIDRCSQNHCRQMIIIRS
ParentalIFLFLDRTYVLQNSMLPSIWDMGLELFRAHIISDQKVQNKTIDGILLLI-ERERNGEAIDRSLLRSLLSM
IFLFLDRT.VLQNS.LPSI.D.GL.LFRAHIISDQKVQNKT.DG...L...RERN.EAIDR.L..SLLSM
RetrocopyIFLFLDRTCVLQNSVLPSIRDVGLALFRAHIISDQKVQNKTTDGMASLD<QRERNCEAIDRRLPLSLLSM
ParentalLSDLQIYQDSFEQRFLEETNRLYAAEGQKLMQEREVPEYLHHVNKRLEEEADRLITYLDQTTQKSLIATV
LSDL.IYQDSFEQ.FL.ETN.LY.AEGQKLMQER.VPEYLHHVNK.LEEE..RLITYLDQTT.KSLIA..
RetrocopyLSDLHIYQDSFEQGFLKETNWLYTAEGQKLMQERQVPEYLHHVNKHLEEELGRLITYLDQTT*KSLIAHA
ParentalEKQLLGEHLTA-ILQKGLNNLLDENRIQDLSLLYQLFSRVRGGVQVLLQQWIEYIK-AFGSTIVINPEKD
EKQ.L..HLTA.I..K.LNNLLD.N.IQDL.LLYQLFSRVRGGVQ.LL..W...IK...GSTIVIN.EK.
RetrocopyEKQPLDKHLTA<IFKKRLNNLLDGNLIQDLFLLYQLFSRVRGGVQILL**WTDCIK<GIGSTIVINLEKG
ParentalKTMVQELLDFKDKVDHIIDICFLKNEKFINAMKEAFETFIN-KRPNKPAELIAKYVDS-KLRAGNKEATD
KTM.Q.LLDFKDKVDHIIDICFLKN..FIN.MK..FETFI..KR.NK..ELIAKY.DS.KL.AGNKEATD
RetrocopyKTMAQALLDFKDKVDHIIDICFLKN*IFINTMKCTFETFIT<KRSNK-SELIAKYIDS<KLCAGNKEATD
ParentalEELEKMLDKIMIIFRFIYGKDVFEAFYKKD-LAKRLLVGKSASVDAEKSMLSKLKHECGAAFTSKLEGMF
EELEKM...IMIIFRFIYGK.VFE.FYKKD.LAK.LL..KS..VDA.KSM.SKLKH..G.AFTSKLEG.F
RetrocopyEELEKM*NNIMIIFRFIYGKGVFEDFYKKDLLAKCLLFRKSPFVDAKKSMPSKLKHQHGTAFTSKLEGIF
ParentalKDMELSKDIMIQFKQYMQNQNVPGNIELTVNILTMGYWPTYVPMEVHLPPEMVKLQEIFKTFYLGKHSGR
.DM..SKDIM.QFKQYMQNQNVPGNIE.TVNILTM..WPTYVPM..HLPP.MVKLQEIFKTFY.GK.SGR
RetrocopyQDMDISKDIMVQFKQYMQNQNVPGNIE*TVNILTMSHWPTYVPMDIHLPPGMVKLQEIFKTFYQGKNSGR
ParentalKLQWQSTLGHCVLKAEFKEGKK----ELQVSLFQ-TLVLLMFNEGEEFSLEEIKQATGIEDG--ELRR-T
KLQWQSTLGHCVLKA.FK.GKK......QVSLF...L.L.MFNE..EFSL.EIKQATGIE.G..ELRR..
RetrocopyKLQWQSTLGHCVLKAKFKKGKKNQQQQIQVSLFK<MLLL-MFNEKVEFSLKEIKQATGIEAGELELRR>N
ParentalLQSLACGKARVLAKNPKGKDIEDGDKFICNDDFKHKLFRIKINQIQMKETVEEQ
LQ..ACG......KN.K.KDIED.D.FICNDDFKHKLFRIK.NQIQMKE....Q
RetrocopyLQASACGN*SSGEKNLKSKDIEDVDIFICNDDFKHKLFRIKTNQIQMKEMRNKQ

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






RNA-Seq - click to see more details

(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
SRP017611_brain 0 .00 RPM 56 .02 RPM
SRP017611_kidney 0 .20 RPM 38 .01 RPM
SRP017611_liver 0 .00 RPM 19 .58 RPM

ChIP-Seq - click to see more details

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_ocun_349 retrocopy.

TSS - click to see more details

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab - click to see more details

retro_ocun_349 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ocun_349 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species Parental gene accession Retrocopies number
Monodelphis domestica ENSMODG000000103451 retrocopy
retro_mdom_793,
Oryctolagus cuniculus ENSOCUG00000015633 1 retrocopy
retro_ocun_349 ,
Otolemur garnettii ENSOGAG000000012822 retrocopies
retro_ogar_2069, retro_ogar_2642,
Sarcophilus harrisii ENSSHAG000000114261 retrocopy
retro_shar_682,


Copyright © RetrogeneDB 2014-2017