RetrogeneDB ID:

retro_ocun_1239

Retrocopy
location
Organism:Rabbit (Oryctolagus cuniculus)
Coordinates:4:73185239..73186514(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSOCUG00000026122
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:SF3B4
Ensembl ID:ENSOCUG00000004614
Aliases:None
Description:splicing factor 3b, subunit 4, 49kDa [Source:HGNC Symbol;Acc:10771]


Retrocopy-Parental alignment summary:






>retro_ocun_1239
ATGGCTGCCGGGCCGATCTCCGAGCGGAACCAGGATGCTACTGTGTACGTGGGGGGCCTGGACGAGAAGGTTAGCAAACC
TCTGCTGTGGGAGCTCTTCCTGCAGGCAGGACCGGTGGTCAACACTCACATGCCGAAGGACAGAGTCACTGGCCAGCACC
AAGGCTATGGCTTTGTGGAATTCTTGAGTGAAGAAGATGCTGACTATGCCATTAAGATCATGAACATGATCAAACTCTAT
GGGAAGCCAATACGAGTGAACAAGGCATCAGCTCACAACAAAAACCTGGATGTGGGGGCCAACATTTTCATCGGGAACCT
GGACCCGGAGATTGACGAGAAGCTGCTTTACGATACTTTTAGCGCCTTTGGGGTCATCTTACAACCCCCAAGATCATGCG
GGACCCTGACACAGGCAACTCCAAAGGTTATGCCTTTATTAATTTCGCTTCATTTGATGCCTCGGATGCAGCAATTGAGG
CCATGAATGGGCAGTACCTCTGTAACCGCCCCATCACCGTGTCTTATGCCTTCAAGAAGGACTCCAAGGGTGAGCGCCAT
GGCTCCGCAGCTGAACGACTTCTGGCAGCCCAGAACCCACTCTCCCAGGCTGATCGCCCGCATCAGCTGTTTGCAGATGC
ACCCCCTCCACCCTCTGCTCCCAACCCTGTGGTATCATCACTGGGGTCTGGGCTTCCTCCACCAGGCATGCCTCCTCCTG
GCTCTTTCCCACCCCCAGTGCCGCCTCCTGGAGCCCTCCCACCTGGAATACCTCCAGCCATGCCCCCCCCACCAATGCCT
CCTGGGGCTGGAGGACATGGCCCTCCATCAGCAGGCACCCCGGGGGCTGGACATCCTGGTCATGGACACTCACATCCTCA
CCCCTTCCCACCAGGTGGCATGCCCCATCCAGGGATGTCTCAGATGCAGCTGGCCCACCATGGCCCTCATGGCTTAGGAC
ACCCCCATGCTGGGCCCCCAGGCTCTGGGGGACAGCCACCACCACGCCCACCTCCTGGAATGCCTGCCTCATCCTGGACC
TCCTCCAATGGGCATGCCCCCCAGAGGACCTCCGTTTGGATCTCCCATGGGTCACCCAGGCCCTATGCCTCCACATGGTA
TGCGAGGACCCCCTCCACTGATGCCGCCTCATGGGTACACTGGTCCTCCACGGCCCCCGCCCTATGGCTACCAGCGGGGC
CCCCTTCCTCCACCCAGACCCACTCCCCGGCCTCCAGTTCCCCCTCGAGGCCCACTTCGGGGCCCTCTTCCTCAA

ORF - retro_ocun_1239 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 98.13 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 0
Number of frameshifts detected: 2


Retrocopy - Parental Gene Alignment:

ParentalMAAGPISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYA
MAAGPISERNQDATVYVGGLDEKVS.PLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYA
RetrocopyMAAGPISERNQDATVYVGGLDEKVSKPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYA
ParentalIKIMNMIKLYGKPIRVNKASAHNKNLDVGANIFIGNLDPEIDEKLLYDTFSAFGVILQ-TPKIMRDPDTG
IKIMNMIKLYGKPIRVNKASAHNKNLDVGANIFIGNLDPEIDEKLLYDTFSAFGVILQ.TPKIMRDPDTG
RetrocopyIKIMNMIKLYGKPIRVNKASAHNKNLDVGANIFIGNLDPEIDEKLLYDTFSAFGVILQ<TPKIMRDPDTG
ParentalNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKDSKGERHGSAAERLLAAQNPLSQADRPHQ
NSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKDSKGERHGSAAERLLAAQNPLSQADRPHQ
RetrocopyNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKDSKGERHGSAAERLLAAQNPLSQADRPHQ
ParentalLFADAPPPPSAPNPVVSSLGSGLPPPGMPPPGSFPPPVPPPGALPPGIPPAMPPPPMPPGAGGHGPPSAG
LFADAPPPPSAPNPVVSSLGSGLPPPGMPPPGSFPPPVPPPGALPPGIPPAMPPPPMPPGAGGHGPPSAG
RetrocopyLFADAPPPPSAPNPVVSSLGSGLPPPGMPPPGSFPPPVPPPGALPPGIPPAMPPPPMPPGAGGHGPPSAG
ParentalTPGAGHPGHGHSHPHPFPPGGMPHPGMSQMQLAHHGPHGLGHPHAGPPGSGGQPPPRPPPGMPHPG-PPP
TPGAGHPGHGHSHPHPFPPGGMPHPGMSQMQLAHHGPHGLGHPHAGPPGSGGQPPPRPPPGMP.....PP
RetrocopyTPGAGHPGHGHSHPHPFPPGGMPHPGMSQMQLAHHGPHGLGHPHAGPPGSGGQPPPRPPPGMPASS>GPP
Parental-MGMPPRGPPFGSPMGHPGPMPPHGMRGPPPLMPPHGYTGPPRPPPYGYQRGPLPPPRPTPRPPVPPRGP
.MGMPPRGPPFGSPMGHPGPMPPHGMRGPPPLMPPHGYTGPPRPPPYGYQRGPLPPPRPTPRPPVPPRGP
RetrocopyPMGMPPRGPPFGSPMGHPGPMPPHGMRGPPPLMPPHGYTGPPRPPPYGYQRGPLPPPRPTPRPPVPPRGP
ParentalLRGPLPQ
LRGPLPQ
RetrocopyLRGPLPQ

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 .61 RPM 24 .78 RPM
SRP017611_kidney 2 .53 RPM 18 .14 RPM
SRP017611_liver 0 .15 RPM 7 .40 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_1239 retrocopy.

TSS - click to see more details

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab - click to see more details

retro_ocun_1239 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ocun_1239 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 16 parental genes, and 23 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000124952 retrocopies
retro_btau_1385, retro_btau_592,
Canis familiaris ENSCAFG000000116173 retrocopies
retro_cfam_585, retro_cfam_711, retro_cfam_729,
Callithrix jacchus ENSCJAG000000007933 retrocopies
retro_cjac_1297, retro_cjac_1909, retro_cjac_638,
Cavia porcellus ENSCPOG000000082671 retrocopy
retro_cpor_234,
Echinops telfairi ENSETEG000000089631 retrocopy
retro_etel_1310,
Homo sapiens ENSG000001433681 retrocopy
retro_hsap_1356,
Gorilla gorilla ENSGGOG000000047611 retrocopy
retro_ggor_1056,
Macaca mulatta ENSMMUG000000072561 retrocopy
retro_mmul_2191,
Mustela putorius furoENSMPUG000000055632 retrocopies
retro_mputfur_1105, retro_mputfur_648,
Oryctolagus cuniculus ENSOCUG000000033421 retrocopy
retro_ocun_924,
Oryctolagus cuniculus ENSOCUG00000004614 1 retrocopy
retro_ocun_1239 ,
Pongo abelii ENSPPYG000000009121 retrocopy
retro_pabe_1124,
Pan troglodytes ENSPTRG000000012431 retrocopy
retro_ptro_930,
Pteropus vampyrus ENSPVAG000000141711 retrocopy
retro_pvam_931,
Rattus norvegicus ENSRNOG000000211811 retrocopy
retro_rnor_2350,
Ictidomys tridecemlineatus ENSSTOG000000006842 retrocopies
retro_itri_1153, retro_itri_487,


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