RetrogeneDB ID:

retro_ocun_1794

Retrocopy
location
Organism:Rabbit (Oryctolagus cuniculus)
Coordinates:GL018899:83964..85491(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:TCF7L1
Ensembl ID:ENSOCUG00000008749
Aliases:None
Description:transcription factor 7-like 1 (T-cell specific, HMG-box) [Source:HGNC Symbol;Acc:11640]


Retrocopy-Parental alignment summary:






>retro_ocun_1794
CAGAGCTGCAGCTCGGACTCAGAGGCGGAGAGGCACCCGCAGCCCTCCCGGGACACTTTCCAGAAGCCGCGGGACTATTT
CACCGAAGTGAGAAGGCCCCAGGACGGCGCGTTCTTCAAGGGCCCCCTTACCCTGGGTACCCCTTCCTGATGATCCCGGA
CCTGAGCAACCCCTACCTCTCCAACGGACCCCTGTCTCCGGGAGGAGCATGCATGTACCTGCAGATGAAATGGCCCCTCC
TCGACGTCCCCTCCAGTGCCACAGTCAAGGACACGAGGTCACCGTCTCCGGCACACTTGTCCAATAAAGTTCCTGTTTGT
GCAGCACCCACATCACATGCACCCGTTGACACCGCTCATCACCTAACGCAATGACCACTTCTCCGCCGGCTCCCCTCCAA
CACACCTCTCCCCGGAGATCAATCCAAAGACAGGAATTCCCCGGCCCCCTCATCCATCTGAGCTGTCACTGTATCACCCA
CTGTCCCCAGGAGCTGTCAGACAAATCCCCCACCCCCTTGGCTGGCTCATCCCACAGCAATGACAGCCCATGTACTCCCT
TCCGCCTGGTGGCTTCGGCACCCTTACCCTGCCCTCGCCATGAACCCCTCAATGTCCAGCCTGGTTTCCAGCTGCTTCTC
CCTTCACAGGGTGGCCCCCGCCCATCCTTGCCTGCCCACCTCAGGGATCCTGCACCCCACCATTGTCAAGCAGGAGCCAG
CACCTCCCAGCCTGAGCCCCACGGTGAGCGCGAAGTCACCCGTGACCATGAAGAAGGAGGAGAAGAAACCCCACATGAAG
AAGCCCCTGAATGCCTTCATGTTGTATATGAAGAAGATGAGGGCCAAGGTGGTGGCTGAGTGCACCCTGAAGGAGAGTGC
TGCCATCAACCAGATGCTGGGGAGGAAGTGGCACAACCTGTCGCAGGAAGAACAGGTCAGGCACTAGAAGCTGGCCCAGA
AGGAGCGGCAGCTTCACTCCCAGCTCTACCCGACCAGCTCGGTAGGGACAACTACAGTAAGAAAAAGAAGAGGAAGTGAG
AGAAGCCGCTGTTGCAGACGCAGACGCAGTCACAGCAGCACGTCCAAGAGGCAGAGGGTGCCCTGGCCTCCAAGAGCAAG
AAGCCACGTGTCCAGTACCTGCCCCCCGAGAGGCCTTGTGACAGCCCTGCCTCCTCCCACGGCAGCATGTTGGACTCCCC
TGCCACCCCCTCCACGGCCTTGGACTCACCAGCTGACCCTGCTGCCACCCACTCCAAGCAAGACCAGCCCCTCTCCCACA
CCACCAAGCCAGAGACCTGGGCCCAGCTGGCTCTGCACTCGGCTGCTGTCCTGGCAGCCAAGGCTGCAGCCACGTCCTCC
GGCCAGATGGGCAGCCAGCCTCCCCTCCTGTCCCGGCCCTCCCGCTGGGGTCCGTGCCCACCACTCTGCTGACTTCTCCC
CCCTCTTTCCCAGCCATGCTGCACACCCACCAGACCCTCCCTGTGCTCCAGGCCCAGCCTCTTTCCTTGGTCACCAAGTC
TGCCCAC

ORF - retro_ocun_1794 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 86.15 %
Parental protein coverage: 99.04 %
Number of stop codons detected: 4
Number of frameshifts detected 5


Retrocopy - Parental Gene Alignment:

ParentalRAAALNSEAERRPQPSRDAFQKPRDYFAEVRRPQDGAFFKGP-PYPGYPFLMIPDLSSPYLSNGPLSPGG
......SEAER.PQPSRD.FQKPRDYF.EVRRPQDGAFFKGP.PYPGYPFLMIPDLS.PYLSNGPLSPGG
RetrocopyQSCSSDSEAERHPQPSRDTFQKPRDYFTEVRRPQDGAFFKGP<PYPGYPFLMIPDLSNPYLSNGPLSPGG
ParentalARTYLQMKWPLLDVPSSATVKDARSPSPAHLSNKVPV-VQHPHHMHPLTPLITYSNDHFSPGSPPTHLSP
A..YLQMKWPLLDVPSSATVKD.RSPSPAHLSNKVPV.VQHPHHMHPLTPLIT..NDHFS.GSPPTHLSP
RetrocopyACMYLQMKWPLLDVPSSATVKDTRSPSPAHLSNKVPV>VQHPHHMHPLTPLIT*RNDHFSAGSPPTHLSP
ParentalEIDPKTGIPRPPHPSELSPYYPLSPGAVGQIPHPLGWLVPQQGQPMYSLPPGGF-RHPYPALAMNASMSS
EI.PKTGIPRPPHPSELS.Y.PLSPGAV.QIPHPLGWL.PQQ.QPMYSLPPGGF.RHPYPALAMN.SMSS
RetrocopyEINPKTGIPRPPHPSELSLYHPLSPGAVRQIPHPLGWLIPQQ*QPMYSLPPGGF<RHPYPALAMNPSMSS
ParentalLVSSRFSPHMVAPAHPGLPTSGIPHPAIVSPIVKQEPAPPSLSPAVSAKSPVTVKKEEEKKPHVKKPLNA
LVSS.FS.H.VAPAHP.LPTSGI.HP.....IVKQEPAPPSLSP.VSAKSPVT.KKEE.KKPH.KKPLNA
RetrocopyLVSSCFSLHRVAPAHPCLPTSGILHPT----IVKQEPAPPSLSPTVSAKSPVTMKKEE-KKPHMKKPLNA
ParentalFMLYMKEMRAKVVAECTLKESAAINQILGRKWHNLSREEQAKYYELARKERQLHSQLYPTWSA-RDNYGK
FMLYMK.MRAKVVAECTLKESAAINQ.LGRKWHNLS.EEQ.....LA.KERQLHSQLYPT.S..RDNY.K
RetrocopyFMLYMKKMRAKVVAECTLKESAAINQMLGRKWHNLSQEEQVRH*KLAQKERQLHSQLYPTSSV<RDNYSK
ParentalKKKRKREKQLSQTQTQSQQHVQEAEGALASKSKKPCVQYLPPEKPCDSPASSHGSMLDSPATPSAALASP
KKKRK.EK.L.QTQTQSQQHVQEAEGALASKSKKP.VQYLPPE.PCDSPASSHGSMLDSPATPS.AL.SP
RetrocopyKKKRK*EKPLLQTQTQSQQHVQEAEGALASKSKKPRVQYLPPERPCDSPASSHGSMLDSPATPSTALDSP
ParentalAAPAATHSEQAQPLSLTTKPETRAQLALHSAAFLSAKAAATSPGQMGSQPPLLSRP-LPLGSVPTALLTS
A.PAATHS.Q.QPLS.TTKPET.AQLALHSAA.L.AKAAATS.GQMGSQPPLLSRP.LPLGSVPT.LLTS
RetrocopyADPAATHSKQDQPLSHTTKPETWAQLALHSAAVLAAKAAATSSGQMGSQPPLLSRP<LPLGSVPTTLLTS
ParentalPPSFPATLHAHQTLPVLQAQPLSLVTKSAH
PPSFPA.LH.HQTLPVLQAQPLSLVTKSAH
RetrocopyPPSFPAMLHTHQTLPVLQAQPLSLVTKSAH

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 .33 RPM 9 .77 RPM
SRP017611_kidney 0 .00 RPM 11 .86 RPM
SRP017611_liver 0 .15 RPM 4 .24 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_1794 retrocopy.

TSS - click to see more details

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab - click to see more details

retro_ocun_1794 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ocun_1794 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species Parental gene accession Retrocopies number
Oryctolagus cuniculus ENSOCUG00000008749 1 retrocopy
retro_ocun_1794 ,




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