RetrogeneDB ID: | retro_hsap_4810 | ||
Retrocopylocation | Organism: | Human (Homo sapiens) | |
Coordinates: | X:40749899..40750805(-) | ||
Located in intron of: | None | ||
Retrocopyinformation | Ensembl ID: | ENSG00000232801 | |
Aliases: | None | ||
Status: | KNOWN_PSEUDOGENE | ||
Parental geneinformation | Parental gene summary: | ||
Parental gene symbol: | SDCBP | ||
Ensembl ID: | ENSG00000137575 | ||
Aliases: | SDCBP, MDA-9, ST1, SYCL, TACIP18 | ||
Description: | syndecan binding protein (syntenin) [Source:HGNC Symbol;Acc:10662] |
Percent Identity: | 89.44 % |
Parental protein coverage: | 94.97 % |
Number of stop codons detected: | 1 |
Number of frameshifts detected | 0 |
Parental | KNPAKMSLYPSLEDLKVDKVIQAQTAFSANPANPAILSEASAPIPHDGNLYPRLYPELSQYMGLSLNEEE |
KNPAKMSLYPSLE.LKVDKVI.AQT.FS.N.ANPAILSEASAPI...GNLYP.LYPELSQYMGLSLNEEE | |
Retrocopy | KNPAKMSLYPSLENLKVDKVIGAQTTFSTNSANPAILSEASAPISQNGNLYPKLYPELSQYMGLSLNEEE |
Parental | IRANVAVVSGAPLQG-LVARPSSINYMVAPVTGNDVGIRRAEIKQGIREVILCKDQDGKIGLRLKSIDNG |
I.ANVA.VSGAP.QG.LVARPSS.NYMVAPVTGNDVGI.RAEIKQGI.EVILCKD..GKIGLRLKSIDNG | |
Retrocopy | ICANVAMVSGAPIQGQLVARPSSMNYMVAPVTGNDVGIHRAEIKQGICEVILCKDHNGKIGLRLKSIDNG |
Parental | IFVQLVQANSPASLVGLRFGDQVLQINGENCAGWSSDKAHKVLKQAFGEKITMTIRDRPFERTITMHKDS |
IFVQLVQANSPASLVGLR..DQVLQIN.ENCAG.SSDKAHKVLKQ.FGE.ITMTI.DRPFE.TITMHKDS | |
Retrocopy | IFVQLVQANSPASLVGLRIEDQVLQINSENCAG*SSDKAHKVLKQNFGE-ITMTIHDRPFEWTITMHKDS |
Parental | TGHVGFIFKNGKITSIVKDSSAARNGLLTEHNICEINGQNVIGLKDSQIADILSTSGTVVTITIMPAFIF |
TGHVGFIFKNG.ITSIVKDSSAARNGLLTEHNICEINGQNVI..KDSQ.ADILSTSGTVVTITIMPAFIF | |
Retrocopy | TGHVGFIFKNGQITSIVKDSSAARNGLLTEHNICEINGQNVIESKDSQTADILSTSGTVVTITIMPAFIF |
Parental | EHIIKRMAPSIMKSLMDHTIPEV |
EHIIK.MAPSIMKSLMDHTI.EV | |
Retrocopy | EHIIKQMAPSIMKSLMDHTISEV |
* | Stop codon |
> | Forward frameshift by one nucleotide |
< | Reverse frameshift by one nucleotide |
Library | Retrocopy expression | Parental gene expression |
---|---|---|
bodymap2_adipose | 0 .02 RPM | 454 .71 RPM |
bodymap2_adrenal | 0 .02 RPM | 260 .60 RPM |
bodymap2_brain | 0 .00 RPM | 171 .89 RPM |
bodymap2_breast | 0 .02 RPM | 291 .15 RPM |
bodymap2_colon | 0 .12 RPM | 376 .18 RPM |
bodymap2_heart | 0 .00 RPM | 155 .39 RPM |
bodymap2_kidney | 0 .04 RPM | 203 .27 RPM |
bodymap2_liver | 0 .00 RPM | 77 .48 RPM |
bodymap2_lung | 0 .00 RPM | 592 .44 RPM |
bodymap2_lymph_node | 0 .00 RPM | 377 .22 RPM |
bodymap2_ovary | 0 .00 RPM | 193 .13 RPM |
bodymap2_prostate | 0 .00 RPM | 248 .23 RPM |
bodymap2_skeletal_muscle | 0 .00 RPM | 71 .77 RPM |
bodymap2_testis | 0 .04 RPM | 178 .84 RPM |
bodymap2_thyroid | 0 .00 RPM | 186 .32 RPM |
bodymap2_white_blood_cells | 0 .02 RPM | 721 .54 RPM |
Species | RetrogeneDB ID |
---|---|
Pan troglodytes | retro_ptro_3200 |
Gorilla gorilla | retro_ggor_2995 |
Pongo abelii | retro_pabe_3738 |
Macaca mulatta | retro_mmul_2564 |
Species | Parental gene accession | Retrocopies number | |
---|---|---|---|
Ailuropoda melanoleuca | ENSAMEG00000006161 | 1 retrocopy | |
Bos taurus | ENSBTAG00000019910 | 2 retrocopies | |
Canis familiaris | ENSCAFG00000007112 | 1 retrocopy | |
Choloepus hoffmanni | ENSCHOG00000003565 | 5 retrocopies | |
Equus caballus | ENSECAG00000015053 | 1 retrocopy | |
Homo sapiens | ENSG00000137575 | 2 retrocopies |
retro_hsap_3971, retro_hsap_4810 ,
|
Gorilla gorilla | ENSGGOG00000009019 | 2 retrocopies | |
Loxodonta africana | ENSLAFG00000010757 | 1 retrocopy | |
Microcebus murinus | ENSMICG00000003968 | 1 retrocopy | |
Myotis lucifugus | ENSMLUG00000004807 | 1 retrocopy | |
Macaca mulatta | ENSMMUG00000017296 | 1 retrocopy | |
Mustela putorius furo | ENSMPUG00000010339 | 5 retrocopies | |
Nomascus leucogenys | ENSNLEG00000001408 | 2 retrocopies | |
Otolemur garnettii | ENSOGAG00000013462 | 1 retrocopy | |
Procavia capensis | ENSPCAG00000016432 | 1 retrocopy | |
Pongo abelii | ENSPPYG00000018612 | 3 retrocopies | |
Pan troglodytes | ENSPTRG00000020277 | 2 retrocopies | |
Tupaia belangeri | ENSTBEG00000013965 | 1 retrocopy |
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 .00 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 .02 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 .03 RPM |
TSI_NA20532 | 0 .00 RPM |
TSI_NA20538 | 0 .00 RPM |
TSI_NA20756 | 0 .00 RPM |
TSI_NA20765 | 0 .02 RPM |
TSI_NA20771 | 0 .00 RPM |
TSI_NA20786 | 0 .03 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 |