RetrogeneDB ID:

retro_btau_592

Retrocopy
location
Organism:Cow (Bos taurus)
Coordinates:15:27883640..27884385(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSBTAG00000039673
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_592
CAGAAGGACTCCAAGGGCGAGTGCCATGGCTCAGCAGCTGAACGACTTGTGGCAGCACAGAACCACTCTCCCAGGCTGAC
GACCCTCATCAGCTGTTTGCCGATGCACCATCTCCACCCTCTGCGTCCAATCCTGTGGTATCATCTTTGAGGTCTGGGCT
TCCTCCTCCATGCATGCCTCCTTCTGGCTCTGTCCCACCCCCAGTACTGCCTCCTGGAGCCCTTCCACTCAGGATATCCG
CAGTCATGCCCCCCCACCTATGCCTCCTGGGGCTGGAGGACATGGTCCCCCATCAGCGGGAACCCCAGGGGCTGGACATC
CTGGACACGGACACTCACATCCTCACCCATTCCCACTGGGTGGGATGCTCCATCTAGAGATGTCTCAGATGCAGCTGGTC
CACCATAGCCCTCACGGCTTGGGACAGCCCCATGCTGGGCCCCCTGGCTCTGGAGGGCAGCCATCACCCCAACCACCACC
TGGGATGCGTCACCCTTGACATCTTCTCATGAGCATGCCCCACCCCCACCAGGGGCCTCTGTTTGGCTCTACTGTGGGTC
TCCCAGTCCTATGCCTCCGCATGGTATGCATGGACCTCCTCTACTGATGCCCCCTAACGGATGGATACACTGGCCCTCCA
TGACCTCCACCCTATGGCTACCAGTGGGGGCCGTTCCCTCCACCCAGACCCACTTCCTGGTCTCCAGTTCCCCCTCGAGG
CCCACTTCGAGGCCTTCTCCCTCGG

ORF - retro_btau_592 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 75.89 %
Parental protein coverage: 58.02 %
Number of stop codons detected: 1
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalKKDSKGERHGSAAERLLAAQN-PLSQADRPHQLFADAPPPPSAPNPVVSSLGSGLPPPGMPPPGSFPPPV
.KDSKGE.HGSAAERL.AAQN.PLSQAD.PHQLFADAP.PPSA.NPVVSSL.SGLPPP.MPP.GS.PPPV
RetrocopyQKDSKGECHGSAAERLVAAQN<PLSQADDPHQLFADAPSPPSASNPVVSSLRSGLPPPCMPPSGSVPPPV
ParentalPPPGALPPGIPPAMP-PPPMPPGAGGHGPPSAGTPGAGHPGHGHSHPHPFPPGGMPHPGMSQMQLAHHGP
.PPGALP..I...MP.PPPMPPGAGGHGPPSAGTPGAGHPGHGHSHPHPFP.GGM.H..MSQMQL.HH.P
RetrocopyLPPGALPLRISAVMP<PPPMPPGAGGHGPPSAGTPGAGHPGHGHSHPHPFPLGGMLHLEMSQMQLVHHSP
ParentalHGLGHPHAGPPGSGGQPPPRPPPGMPHPGPPPMGM--PPRGPPFGSPM-GHPGPMPPHGMRGPPPLMPPH
HGLG.PHAGPPGSGGQP.P.PPPGM.HP....M.M..P..GP.FGS...G.P.PMPPHGM.GPP.LMPP.
RetrocopyHGLGQPHAGPPGSGGQPSPQPPPGMRHP*HLLMSMPHPHQGPLFGSTV<GSPSPMPPHGMHGPPLLMPPN
ParentalGYTGPPRP-PP-YGYQRGPLPPPRPTPRPPVPPRGPLRGPLPQ
G....P...PP.YGYQ.GP.PPPRPT...PVPPRGPLRG.LP.
RetrocopyGWIHWPSM>PPPYGYQWGPFPPPRPTSWSPVPPRGPLRGLLPR

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 1 .15 RPM 8 .44 RPM
ERP005899_muscle 0 .05 RPM 22 .75 RPM
SRP017611_brain 0 .00 RPM 24 .48 RPM
SRP017611_kidney 0 .00 RPM 30 .58 RPM
SRP017611_liver 0 .23 RPM 12 .31 RPM
SRP030211_testis 0 .00 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_592 retrocopy.

TSS - click to see more details

Bos taurus was not studied using FANTOM5 data.

Lab - click to see more details

retro_btau_592 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_btau_592 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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