RetrogeneDB ID: | retro_hsap_3313 | ||
Retrocopylocation | Organism: | Human (Homo sapiens) | |
Coordinates: | 5:43231916..43233275(-) | ||
Located in intron of: | ENSG00000177453 | ||
Retrocopyinformation | Ensembl ID: | ENSG00000247763 | |
Aliases: | None | ||
Status: | KNOWN_PSEUDOGENE | ||
Parental geneinformation | Parental gene summary: | ||
Parental gene symbol: | TUBA1A | ||
Ensembl ID: | ENSG00000167552 | ||
Aliases: | TUBA1A, B-ALPHA-1, LIS3, TUBA3 | ||
Description: | tubulin, alpha 1a [Source:HGNC Symbol;Acc:20766] |
Percent Identity: | 79.52 % |
Parental protein coverage: | 100. % |
Number of stop codons detected: | 1 |
Number of frameshifts detected | 6 |
Parental | MRECISIH-VGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGKHVPRAVFVD |
MR..ISI...GQAGVQ.GNACWE.YCLEHGIQP.GQMPSDKT..GGDDSFN.FFSETG.GKHVPRAVF.D | |
Retrocopy | MRDRISIS<IGQAGVQVGNACWEPYCLEHGIQPNGQMPSDKTTRGGDDSFNSFFSETGSGKHVPRAVFLD |
Parental | LEPTVID-EVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFLVF |
L.P.VID.EV.TGTY.QLFHPEQLITGKEDA..NYA..HYTIG.EI.DLVLD.I.KLA.QC...QGFL.F | |
Retrocopy | LKPMVIDDEVCTGTYNQLFHPEQLITGKEDASSNYA*RHYTIGQEITDLVLDQICKLAEQCMDRQGFLFF |
Parental | HSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEA |
HSFG.G.GSGFTS.LME.L.VDYGKKSKL.FSIY..PQVSTAVVEPYNSILT.HTTLEHSDC.FMVDNEA | |
Retrocopy | HSFGEGVGSGFTSPLMEQLPVDYGKKSKLQFSIYSPPQVSTAVVEPYNSILTSHTTLEHSDCVFMVDNEA |
Parental | IYDICRR-NLDIERPTYTNLNRLIGQIVSSITASLRFDGALNVDLTEFQTNLVPYPRIHFPLATYA-PVI |
.YDI..R.NLD.ERPTYT.LNRLIGQIVSSITASLRFDG.LNVDLTEFQT.LV.YP.IHF.L.TYA.PVI | |
Retrocopy | TYDIWHR<NLDTERPTYTKLNRLIGQIVSSITASLRFDGVLNVDLTEFQTKLVAYPPIHFRLDTYA<PVI |
Parental | SAEKAYHE-QLSVAEITNACFEPANQMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRTIQFV- |
SAEKAYHE.QLSVAE...ACF.PANQM.KC.P.HGKYMACCL.YRGD.V.KDVNAAIATI.......... | |
Retrocopy | SAEKAYHE>QLSVAETASACFQPANQMMKCEPCHGKYMACCLFYRGDMVLKDVNAAIATINQDQVYHLIC |
Parental | DWCPTGFKVGINYQ-PPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDL-MYAKRAFVHWYVGEG |
...P.GFKVGIN.Q.PPTVV.GGDL.K.QRAVCMLSNTTAIAEAWA.LDHKFDL.MY.K.AFVHWYVGE. | |
Retrocopy | GLVPPGFKVGINCQ>PPTVVTGGDLVKTQRAVCMLSNTTAIAEAWAHLDHKFDL>MYVKSAFVHWYVGER |
Parental | MEEGEFSEAREDMAALEKDYEEVGVDSVEGEGEEEGEEY |
.EEGEFSEA.EDM.ALEKDY.EVGVDSVEGEGEEE.EEY | |
Retrocopy | REEGEFSEASEDMTALEKDYKEVGVDSVEGEGEEEREEY |
* | Stop codon |
> | Forward frameshift by one nucleotide |
< | Reverse frameshift by one nucleotide |
Library | Retrocopy expression | Parental gene expression |
---|---|---|
bodymap2_adipose | 0 .00 RPM | 40 .79 RPM |
bodymap2_adrenal | 0 .00 RPM | 138 .19 RPM |
bodymap2_brain | 0 .07 RPM | 685 .29 RPM |
bodymap2_breast | 0 .00 RPM | 120 .64 RPM |
bodymap2_colon | 0 .00 RPM | 124 .87 RPM |
bodymap2_heart | 0 .04 RPM | 57 .28 RPM |
bodymap2_kidney | 0 .00 RPM | 99 .27 RPM |
bodymap2_liver | 0 .00 RPM | 5 .58 RPM |
bodymap2_lung | 0 .00 RPM | 83 .42 RPM |
bodymap2_lymph_node | 0 .00 RPM | 60 .81 RPM |
bodymap2_ovary | 0 .06 RPM | 189 .07 RPM |
bodymap2_prostate | 0 .00 RPM | 127 .93 RPM |
bodymap2_skeletal_muscle | 0 .00 RPM | 10 .97 RPM |
bodymap2_testis | 0 .00 RPM | 88 .18 RPM |
bodymap2_thyroid | 0 .00 RPM | 23 .80 RPM |
bodymap2_white_blood_cells | 0 .00 RPM | 180 .52 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_154282 | 1047 libraries | 613 libraries | 167 libraries | 2 libraries | 0 libraries |
Species | RetrogeneDB ID |
---|---|
Pan troglodytes | retro_ptro_2158 |
Species | Parental gene accession | Retrocopies number | |
---|---|---|---|
Bos taurus | ENSBTAG00000001489 | 3 retrocopies | |
Callithrix jacchus | ENSCJAG00000020894 | 2 retrocopies | |
Dasypus novemcinctus | ENSDNOG00000004121 | 1 retrocopy | |
Equus caballus | ENSECAG00000013798 | 1 retrocopy | |
Homo sapiens | ENSG00000123416 | 1 retrocopy | |
Homo sapiens | ENSG00000167552 | 1 retrocopy |
retro_hsap_3313 ,
|
Nomascus leucogenys | ENSNLEG00000017836 | 2 retrocopies | |
Oryctolagus cuniculus | ENSOCUG00000027812 | 1 retrocopy | |
Pteropus vampyrus | ENSPVAG00000004645 | 2 retrocopies | |
Rattus norvegicus | ENSRNOG00000004559 | 3 retrocopies | |
Vicugna pacos | ENSVPAG00000005749 | 4 retrocopies |
Library | Retrogene expression |
---|---|
CEU_NA11831 | 0 .00 RPM |
CEU_NA11843 | 0 .00 RPM |
CEU_NA11930 | 0 .03 RPM |
CEU_NA12004 | 0 .00 RPM |
CEU_NA12400 | 0 .00 RPM |
CEU_NA12751 | 0 .02 RPM |
CEU_NA12760 | 0 .00 RPM |
CEU_NA12827 | 0 .05 RPM |
CEU_NA12872 | 0 .03 RPM |
CEU_NA12873 | 0 .00 RPM |
FIN_HG00183 | 0 .03 RPM |
FIN_HG00277 | 0 .00 RPM |
FIN_HG00315 | 0 .00 RPM |
FIN_HG00321 | 0 .06 RPM |
FIN_HG00328 | 0 .05 RPM |
FIN_HG00338 | 0 .02 RPM |
FIN_HG00349 | 0 .00 RPM |
FIN_HG00375 | 0 .00 RPM |
FIN_HG00377 | 0 .00 RPM |
FIN_HG00378 | 0 .02 RPM |
GBR_HG00099 | 0 .00 RPM |
GBR_HG00111 | 0 .00 RPM |
GBR_HG00114 | 0 .00 RPM |
GBR_HG00119 | 0 .02 RPM |
GBR_HG00131 | 0 .00 RPM |
GBR_HG00133 | 0 .02 RPM |
GBR_HG00134 | 0 .00 RPM |
GBR_HG00137 | 0 .00 RPM |
GBR_HG00142 | 0 .03 RPM |
GBR_HG00143 | 0 .00 RPM |
TSI_NA20512 | 0 .00 RPM |
TSI_NA20513 | 0 .00 RPM |
TSI_NA20518 | 0 .00 RPM |
TSI_NA20532 | 0 .03 RPM |
TSI_NA20538 | 0 .00 RPM |
TSI_NA20756 | 0 .00 RPM |
TSI_NA20765 | 0 .02 RPM |
TSI_NA20771 | 0 .00 RPM |
TSI_NA20786 | 0 .00 RPM |
TSI_NA20798 | 0 .06 RPM |
YRI_NA18870 | 0 .03 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 .02 RPM |
YRI_NA19213 | 0 .05 RPM |
YRI_NA19214 | 0 .00 RPM |
YRI_NA19223 | 0 .00 RPM |