RetrogeneDB ID: | retro_hsap_109 | ||
Retrocopylocation | Organism: | Human (Homo sapiens) | |
Coordinates: | 4:135121061..135122348(-) | ||
Located in intron of: | None | ||
Retrocopyinformation | Ensembl ID: | ENSG00000254535 | |
Aliases: | None | ||
Status: | KNOWN_PROTEIN_CODING | ||
Parental geneinformation | Parental gene summary: | ||
Parental gene symbol: | PABPC4 | ||
Ensembl ID: | ENSG00000090621 | ||
Aliases: | PABPC4, APP-1, APP1, PABP4, iPABP | ||
Description: | poly(A) binding protein, cytoplasmic 4 (inducible form) [Source:HGNC Symbol;Acc:8557] |
Percent Identity: | 75.41 % |
Parental protein coverage: | 60.16 % |
Number of stop codons detected: | 0 |
Number of frameshifts detected | 0 |
Parental | MNAAASSYPMASLYVGDLHSDVTEAMLYEKFSPAGPVLSIRVCRDMITRRSLGYAYVNFQQPADAERALD |
MN.AA..Y.MASLYVGDLH.DVTE..L..KFS..GPVLSIR.CRD..TRRSLGYAYVNF.Q.ADA..ALD | |
Retrocopy | MNVAAK-YRMASLYVGDLHADVTEDLLFRKFSTVGPVLSIRICRDQVTRRSLGYAYVNFLQLADAQKALD |
Parental | TMNFDVIKGKPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGY |
TMNFD.IKGK.IR.MWSQRD..LR.SG.GNVFIKNLDKSIDNK.LY..FSAFG.ILS.KV..D..GSKGY | |
Retrocopy | TMNFDIIKGKSIRLMWSQRDAYLRRSGIGNVFIKNLDKSIDNKTLYEHFSAFGKILSSKVMSDDQGSKGY |
Parental | AFVHFETQEAADKAIEKMNGMLLNDRKVFVGRFKSRKEREAELGAKAKEFTNVYIKNFGEEVDDESLKEL |
AFVHF..Q.AAD.AIE.MNG.LL...KVFVGRFK.RK.REAEL..KA.EFTNVYIKNFG...DDE.LK.. | |
Retrocopy | AFVHFQNQSAADRAIEEMNGKLLKGCKVFVGRFKNRKDREAELRSKASEFTNVYIKNFGGDMDDERLKDV |
Parental | FSQFGKTLSVKVMRDPNGKSKGFGFVSYEKHEDANKAVEEMNGKEISGKIIFVGRAQKKVERQAELKRKF |
FS..GKTLSVKVM.D..GKSKGFGFVS...HE.A.KAVEEMNG..I.G..IFVGRAQKKVERQAELK..F | |
Retrocopy | FSKYGKTLSVKVMTDSSGKSKGFGFVSFDSHEAAKKAVEEMNGRDINGQLIFVGRAQKKVERQAELKQMF |
Parental | EQLKQERISRYQGVNLYIKNLDDTIDDEKLRKEFSPFGSITSAKVMLEDGRSKGFGFVCFSSPEEATKAV |
EQLK.ERI...QGV.LYIKNLDDTIDDEKLR.EFS.FGSI...KVM.E.G.SKGFG..CFSSPE.ATKA. | |
Retrocopy | EQLKRERIRGCQGVKLYIKNLDDTIDDEKLRNEFSSFGSISRVKVMQEEGQSKGFGLICFSSPEDATKAM |
Parental | TEMNGRIVGSKPLYVALAQR |
TEMNGRI.GSKPL..ALAQR | |
Retrocopy | TEMNGRILGSKPLSIALAQR |
* | Stop codon |
> | Forward frameshift by one nucleotide |
< | Reverse frameshift by one nucleotide |
Library | Retrocopy expression | Parental gene expression |
---|---|---|
bodymap2_adipose | 1 .63 RPM | 159 .98 RPM |
bodymap2_adrenal | 0 .70 RPM | 108 .10 RPM |
bodymap2_brain | 0 .07 RPM | 45 .36 RPM |
bodymap2_breast | 0 .95 RPM | 121 .50 RPM |
bodymap2_colon | 1 .01 RPM | 144 .98 RPM |
bodymap2_heart | 0 .52 RPM | 106 .45 RPM |
bodymap2_kidney | 0 .50 RPM | 70 .11 RPM |
bodymap2_liver | 0 .02 RPM | 60 .43 RPM |
bodymap2_lung | 0 .07 RPM | 96 .19 RPM |
bodymap2_lymph_node | 0 .40 RPM | 123 .71 RPM |
bodymap2_ovary | 1 .25 RPM | 152 .23 RPM |
bodymap2_prostate | 1 .07 RPM | 126 .78 RPM |
bodymap2_skeletal_muscle | 0 .02 RPM | 882 .33 RPM |
bodymap2_testis | 1 .53 RPM | 252 .48 RPM |
bodymap2_thyroid | 1 .41 RPM | 153 .78 RPM |
bodymap2_white_blood_cells | 0 .00 RPM | 134 .07 RPM |
TSS No. | TSS Name | TSS expression level (Expr) in TPM range: | ||||
---|---|---|---|---|---|---|
no expression | 0 < Expr ≤ 1 | 1 < Expr ≤ 5 | 5 < Expr ≤ 10 | Expr > 10 | ||
TSS #1 | TSS_139782 | 1452 libraries | 321 libraries | 53 libraries | 3 libraries | 0 libraries |
Library | Retrogene expression |
---|---|
CEU_NA11831 | 0 .00 RPM |
CEU_NA11843 | 0 .00 RPM |
CEU_NA11930 | 0 .00 RPM |
CEU_NA12004 | 0 .00 RPM |
CEU_NA12400 | 0 .00 RPM |
CEU_NA12751 | 0 .02 RPM |
CEU_NA12760 | 0 .00 RPM |
CEU_NA12827 | 0 .00 RPM |
CEU_NA12872 | 0 .00 RPM |
CEU_NA12873 | 0 .00 RPM |
FIN_HG00183 | 0 .00 RPM |
FIN_HG00277 | 0 .00 RPM |
FIN_HG00315 | 0 .00 RPM |
FIN_HG00321 | 0 .00 RPM |
FIN_HG00328 | 0 .00 RPM |
FIN_HG00338 | 0 .00 RPM |
FIN_HG00349 | 0 .00 RPM |
FIN_HG00375 | 0 .00 RPM |
FIN_HG00377 | 0 .00 RPM |
FIN_HG00378 | 0 .00 RPM |
GBR_HG00099 | 0 .00 RPM |
GBR_HG00111 | 0 .00 RPM |
GBR_HG00114 | 0 .00 RPM |
GBR_HG00119 | 0 .00 RPM |
GBR_HG00131 | 0 .00 RPM |
GBR_HG00133 | 0 .00 RPM |
GBR_HG00134 | 0 .00 RPM |
GBR_HG00137 | 0 .00 RPM |
GBR_HG00142 | 0 .00 RPM |
GBR_HG00143 | 0 .00 RPM |
TSI_NA20512 | 0 .00 RPM |
TSI_NA20513 | 0 .00 RPM |
TSI_NA20518 | 0 .00 RPM |
TSI_NA20532 | 0 .00 RPM |
TSI_NA20538 | 0 .00 RPM |
TSI_NA20756 | 0 .00 RPM |
TSI_NA20765 | 0 .00 RPM |
TSI_NA20771 | 0 .00 RPM |
TSI_NA20786 | 0 .00 RPM |
TSI_NA20798 | 0 .00 RPM |
YRI_NA18870 | 0 .00 RPM |
YRI_NA18907 | 0 .00 RPM |
YRI_NA18916 | 0 .00 RPM |
YRI_NA19093 | 0 .00 RPM |
YRI_NA19099 | 0 .00 RPM |
YRI_NA19114 | 0 .00 RPM |
YRI_NA19118 | 0 .00 RPM |
YRI_NA19213 | 0 .00 RPM |
YRI_NA19214 | 0 .00 RPM |
YRI_NA19223 | 0 .00 RPM |