RetrogeneDB ID:

retro_btau_1385

Retrocopy
location
Organism:Cow (Bos taurus)
Coordinates:5:66127245..66128518(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSBTAG00000012793
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:SF3B4
Ensembl ID:ENSBTAG00000012495
Aliases:None
Description:splicing factor 3B subunit 4 [Source:RefSeq peptide;Acc:NP_001192513]


Retrocopy-Parental alignment summary:






>retro_btau_1385
ATGGCGGCCGGGACGATCTCCGAGTGAAACCAGGATGCCACTGTGTACGTGGGGGGCCTCTATAAGAAGGTTAGCGAACC
ACTGTTGTGGGAACTATTTCTCCAGGCAGGGCCAGTAGTGAACACGCACATGCCAAAAGATAGAGTCACTGGTCAGCACC
AAGGCTATGGCTTTGTGGAATTCTTGAGTGAGGAAGATGCTGACTATGCCATTAAGATCATGAACATGATCAAACTCTAT
GGGAAGCCAATACGGGTGAACAAAGCATCAGCTCACAACAAAAACCTGGATGTGGGGCCTAACATTTTTATTGGGAACCT
GGACCCAGAGATTGATGAGAAGTTGCTTTATGATACTTTTAGCGCCTTTGGGGCCATCTTACAAACCCCTAAGATTATGC
GGGACCCTGACACAGGCAACTCCAAAGGTTATGCCTTTATTAATTTTGCTTCATTTGATGCTTCAGATGCAGCGATTGAG
GCCATGAATGGGCAGTACCTCTGTAACCGCCCAATCACTGTGTCCTATGCATTCAAGAAGGACTCCAAGGGTGAGCGCCA
TGGCTCAGCCGCTGAAAGACTTCTGGCAGCACAGAACCCGCTCTCCCAGCCTGACCGCCCTCATCAGCTGTTTGCAGATG
CACCTCCTCCACCATCTGCTCCCAATCCTGTGGTATCATCATTGGGATCTGGGCTTCCTCCACCAGGCATGCCTCCTCCT
GGCTCCTTCCCACCTCCAGTACCGCCTCCTGGAGCCCTTCCTCCTGGGATACCCCCAGCCATGCCACCACCATCTATGCC
TCCTGGGGCTGGAGGACATGGCCCCCCATCAGTGGGAACCCCAGGGGCTGGACATCCTGGACACGGACACTCACATCCTC
ACCCATTCCCACCAGGTGGGATGCCCCATCCAGGGATGTCTCAGATGCAGCTGGCCCACCATGGCCCTCATGGCTTAGGG
CACCCCCACGCTGGGCCCCCTGGCTCTGGGGGGCAGCCACCACCCCGACCACCACCTGGAATGCCTCATCCTGGACCTCC
TCCAATGGGGATGCCCCCCCGAGGGCCTCCGTTTGGCTCTCCTATGGGTCACCCAGGTCCTATGCCTCCACATGGTATGC
GTGGACCTCCTCCACTGATGCCTCCTCATGGATACACTGGCCCTCCACGACCTCCACCCTATGGCTACCAGCGGGGGGCC
CCTCCCTCCACCCAGACCCACTCCCCGACCTCCAGTGCCCCCTCGAGGCCCACTTCGAGGCCCTCTCCCTCAG

ORF - retro_btau_1385 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 97.65 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMAAGPISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYA
MAAG.ISE.NQDATVYVGGL..KVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYA
RetrocopyMAAGTISE*NQDATVYVGGLYKKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYA
ParentalIKIMNMIKLYGKPIRVNKASAHNKNLDVGANIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGN
IKIMNMIKLYGKPIRVNKASAHNKNLDVG.NIFIGNLDPEIDEKLLYDTFSAFG.ILQTPKIMRDPDTGN
RetrocopyIKIMNMIKLYGKPIRVNKASAHNKNLDVGPNIFIGNLDPEIDEKLLYDTFSAFGAILQTPKIMRDPDTGN
ParentalSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKDSKGERHGSAAERLLAAQNPLSQADRPHQL
SKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKDSKGERHGSAAERLLAAQNPLSQ.DRPHQL
RetrocopySKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKDSKGERHGSAAERLLAAQNPLSQPDRPHQL
ParentalFADAPPPPSAPNPVVSSLGSGLPPPGMPPPGSFPPPVPPPGALPPGIPPAMPPPPMPPGAGGHGPPSAGT
FADAPPPPSAPNPVVSSLGSGLPPPGMPPPGSFPPPVPPPGALPPGIPPAMPPP.MPPGAGGHGPPS.GT
RetrocopyFADAPPPPSAPNPVVSSLGSGLPPPGMPPPGSFPPPVPPPGALPPGIPPAMPPPSMPPGAGGHGPPSVGT
ParentalPGAGHPGHGHSHPHPFPPGGMPHPGMSQMQLAHHGPHGLGHPHAGPPGSGGQPPPRPPPGMPHPGPPPMG
PGAGHPGHGHSHPHPFPPGGMPHPGMSQMQLAHHGPHGLGHPHAGPPGSGGQPPPRPPPGMPHPGPPPMG
RetrocopyPGAGHPGHGHSHPHPFPPGGMPHPGMSQMQLAHHGPHGLGHPHAGPPGSGGQPPPRPPPGMPHPGPPPMG
ParentalMPPRGPPFGSPMGHPGPMPPHGMRGPPPLMPPHGYTGPPRPPPYGYQRG-PLPPPRPTPRPPVPPRGPLR
MPPRGPPFGSPMGHPGPMPPHGMRGPPPLMPPHGYTGPPRPPPYGYQRG.PLPPPRPTPRPPVPPRGPLR
RetrocopyMPPRGPPFGSPMGHPGPMPPHGMRGPPPLMPPHGYTGPPRPPPYGYQRG>PLPPPRPTPRPPVPPRGPLR
ParentalGPLPQ
GPLPQ
RetrocopyGPLPQ

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
ERP005899_liver 0 .00 RPM 8 .44 RPM
ERP005899_muscle 0 .00 RPM 22 .75 RPM
SRP017611_brain 0 .23 RPM 24 .48 RPM
SRP017611_kidney 0 .24 RPM 30 .58 RPM
SRP017611_liver 0 .15 RPM 12 .31 RPM
SRP030211_testis 0 .32 RPM 85 .73 RPM

ChIP-Seq - click to see more details

Bos taurus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_btau_1385 retrocopy.

TSS - click to see more details

Bos taurus was not studied using FANTOM5 data.

Lab - click to see more details

retro_btau_1385 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_btau_1385 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 18 parental genes, and 27 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG00000012495 2 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,
Felis catus ENSFCAG000000101061 retrocopy
retro_fcat_1607,
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,
Mus musculus ENSMUSG000000688561 retrocopy
retro_mmus_1406,
Oryctolagus cuniculus ENSOCUG000000046141 retrocopy
retro_ocun_1239,
Otolemur garnettii ENSOGAG000000062653 retrocopies
retro_ogar_2227, retro_ogar_2388, retro_ogar_2804,
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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