RetrogeneDB ID: | retro_hsap_1356 | ||
Retrocopylocation | Organism: | Human (Homo sapiens) | |
Coordinates: | 14:67665778..67667041(+) | ||
Located in intron of: | ENSG00000172717 | ||
Retrocopyinformation | Ensembl ID: | ENSG00000258988 | |
Aliases: | None | ||
Status: | KNOWN_PSEUDOGENE | ||
Parental geneinformation | Parental gene summary: | ||
Parental gene symbol: | SF3B4 | ||
Ensembl ID: | ENSG00000143368 | ||
Aliases: | SF3B4, AFD1, Hsh49, SAP49, SF3b49 | ||
Description: | splicing factor 3b, subunit 4, 49kDa [Source:HGNC Symbol;Acc:10771] |
Percent Identity: | 91.1 % |
Parental protein coverage: | 100. % |
Number of stop codons detected: | 1 |
Number of frameshifts detected | 3 |
Parental | MAAGPISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFV-EFLSEEDADY |
MA..PISERNQDATVYVGGL.EKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGY.FV.EFLSE.DADY | |
Retrocopy | MATRPISERNQDATVYVGGLNEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYDFV<EFLSEDDADY |
Parental | AIKIMNMIKLYGKPIRVNKASAHNKNLDVGANIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTG |
AIKIMNMI.LYGKPIRVNKASAHNKNLDVGANIF.GNLDPEIDEKLLYDTFSAFGVILQTPKIM.DPDTG | |
Retrocopy | AIKIMNMIRLYGKPIRVNKASAHNKNLDVGANIFNGNLDPEIDEKLLYDTFSAFGVILQTPKIMWDPDTG |
Parental | NSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKDSKGERHGSAAERLLAAQNPLSQADRPHQ |
NSKGYAFINFASFDAS.AAIEAMNGQYLCN.PITVSYAF.KDSKGERHG.AA.RLLAAQNPLSQ.DRPHQ | |
Retrocopy | NSKGYAFINFASFDASVAAIEAMNGQYLCNHPITVSYAFEKDSKGERHGLAAGRLLAAQNPLSQPDRPHQ |
Parental | LFADAPPPPSAPNPVVSSLGSGLPPPGMPPPGSFPPPVPPPGALPPGIPPAMP-PPPMPPGAAGHGPPSA |
LFADAPP.PSAPNPVVSSLGSGLPPPGMPPPGSFPPPV.PPGALPPGIPPAMP.PPPMPPGAAGHGPPSA | |
Retrocopy | LFADAPPSPSAPNPVVSSLGSGLPPPGMPPPGSFPPPVLPPGALPPGIPPAMP<PPPMPPGAAGHGPPSA |
Parental | GTPGAGHPGHGHSHPHPFPPGGMPHPGMSQMQLAHHGPHGLGHPHAGPPGSGGQPPPRPPPGMPHPGPPP |
GTPGAGHPGHGHS..HPFPPGG.PHPGMSQMQLAHHGPHGLGHPH.G.PGSGGQPPP.PPPGMP.PGPPP | |
Retrocopy | GTPGAGHPGHGHSQAHPFPPGGVPHPGMSQMQLAHHGPHGLGHPHSGHPGSGGQPPPQPPPGMPYPGPPP |
Parental | MGMPPRGPPFGSPMGHPGPMPPHGMRGPPPLMP-PHGYTGPPRPPPYGYQRGPLPPPRPTPRPPVPPRGP |
MGMPPR.PPF.SPMGHPGPMPPHGMRG.PPLMP.PHGYTGPP.P.PYGYQ..PLPP.RPTP.PPV.PRGP | |
Retrocopy | MGMPPRRPPF*SPMGHPGPMPPHGMRGLPPLMP<PHGYTGPPQPTPYGYQ--PLPPTRPTPQPPVAPRGP |
Parental | LRGPLPQ |
L..PLPQ | |
Retrocopy | LWSPLPQ |
* | Stop codon |
> | Forward frameshift by one nucleotide |
< | Reverse frameshift by one nucleotide |
Library | Retrocopy expression | Parental gene expression |
---|---|---|
bodymap2_adipose | 0 .02 RPM | 26 .46 RPM |
bodymap2_adrenal | 0 .00 RPM | 37 .93 RPM |
bodymap2_brain | 0 .00 RPM | 14 .28 RPM |
bodymap2_breast | 0 .02 RPM | 23 .29 RPM |
bodymap2_colon | 0 .00 RPM | 18 .83 RPM |
bodymap2_heart | 0 .02 RPM | 13 .24 RPM |
bodymap2_kidney | 0 .12 RPM | 29 .32 RPM |
bodymap2_liver | 0 .09 RPM | 13 .27 RPM |
bodymap2_lung | 0 .00 RPM | 27 .13 RPM |
bodymap2_lymph_node | 0 .00 RPM | 22 .86 RPM |
bodymap2_ovary | 0 .00 RPM | 53 .94 RPM |
bodymap2_prostate | 0 .00 RPM | 35 .06 RPM |
bodymap2_skeletal_muscle | 0 .00 RPM | 16 .21 RPM |
bodymap2_testis | 1 .90 RPM | 58 .84 RPM |
bodymap2_thyroid | 0 .04 RPM | 30 .79 RPM |
bodymap2_white_blood_cells | 0 .04 RPM | 59 .20 RPM |
Species | RetrogeneDB ID |
---|---|
Pan troglodytes | retro_ptro_930 |
Gorilla gorilla | retro_ggor_1056 |
Macaca mulatta | retro_mmul_2191 |
Species | Parental gene accession | Retrocopies number | |
---|---|---|---|
Bos taurus | ENSBTAG00000012495 | 2 retrocopies | |
Canis familiaris | ENSCAFG00000011617 | 3 retrocopies | |
Callithrix jacchus | ENSCJAG00000000793 | 3 retrocopies | |
Cavia porcellus | ENSCPOG00000008267 | 1 retrocopy | |
Echinops telfairi | ENSETEG00000008963 | 1 retrocopy | |
Homo sapiens | ENSG00000076053 | 1 retrocopy | |
Homo sapiens | ENSG00000143368 | 1 retrocopy |
retro_hsap_1356 ,
|
Gorilla gorilla | ENSGGOG00000004761 | 1 retrocopy | |
Macaca mulatta | ENSMMUG00000007256 | 1 retrocopy | |
Mustela putorius furo | ENSMPUG00000005563 | 2 retrocopies | |
Oryctolagus cuniculus | ENSOCUG00000004614 | 1 retrocopy | |
Pongo abelii | ENSPPYG00000000912 | 1 retrocopy | |
Pan troglodytes | ENSPTRG00000001243 | 1 retrocopy | |
Pteropus vampyrus | ENSPVAG00000014171 | 1 retrocopy | |
Rattus norvegicus | ENSRNOG00000021181 | 1 retrocopy | |
Ictidomys tridecemlineatus | ENSSTOG00000000684 | 2 retrocopies |
Library | Retrogene expression |
---|---|
CEU_NA11831 | 0 .11 RPM |
CEU_NA11843 | 0 .09 RPM |
CEU_NA11930 | 0 .07 RPM |
CEU_NA12004 | 0 .04 RPM |
CEU_NA12400 | 0 .07 RPM |
CEU_NA12751 | 0 .17 RPM |
CEU_NA12760 | 0 .04 RPM |
CEU_NA12827 | 0 .05 RPM |
CEU_NA12872 | 0 .11 RPM |
CEU_NA12873 | 0 .16 RPM |
FIN_HG00183 | 0 .14 RPM |
FIN_HG00277 | 0 .00 RPM |
FIN_HG00315 | 0 .03 RPM |
FIN_HG00321 | 0 .09 RPM |
FIN_HG00328 | 0 .28 RPM |
FIN_HG00338 | 0 .00 RPM |
FIN_HG00349 | 0 .03 RPM |
FIN_HG00375 | 0 .07 RPM |
FIN_HG00377 | 0 .03 RPM |
FIN_HG00378 | 0 .02 RPM |
GBR_HG00099 | 0 .06 RPM |
GBR_HG00111 | 0 .06 RPM |
GBR_HG00114 | 0 .08 RPM |
GBR_HG00119 | 0 .12 RPM |
GBR_HG00131 | 0 .11 RPM |
GBR_HG00133 | 0 .12 RPM |
GBR_HG00134 | 0 .20 RPM |
GBR_HG00137 | 0 .08 RPM |
GBR_HG00142 | 0 .08 RPM |
GBR_HG00143 | 0 .06 RPM |
TSI_NA20512 | 0 .03 RPM |
TSI_NA20513 | 0 .12 RPM |
TSI_NA20518 | 0 .06 RPM |
TSI_NA20532 | 0 .07 RPM |
TSI_NA20538 | 0 .00 RPM |
TSI_NA20756 | 0 .03 RPM |
TSI_NA20765 | 0 .08 RPM |
TSI_NA20771 | 0 .03 RPM |
TSI_NA20786 | 0 .08 RPM |
TSI_NA20798 | 0 .00 RPM |
YRI_NA18870 | 0 .03 RPM |
YRI_NA18907 | 0 .00 RPM |
YRI_NA18916 | 0 .04 RPM |
YRI_NA19093 | 0 .03 RPM |
YRI_NA19099 | 0 .05 RPM |
YRI_NA19114 | 0 .03 RPM |
YRI_NA19118 | 0 .02 RPM |
YRI_NA19213 | 0 .02 RPM |
YRI_NA19214 | 0 .05 RPM |
YRI_NA19223 | 0 .14 RPM |