RetrogeneDB ID: | retro_hsap_4762 | ||
Retrocopylocation | Organism: | Human (Homo sapiens) | |
Coordinates: | X:135929542..135930187(+) | ||
Located in intron of: | None | ||
Retrocopyinformation | Ensembl ID: | ENSG00000225400 | |
Aliases: | None | ||
Status: | KNOWN_PSEUDOGENE | ||
Parental geneinformation | Parental gene summary: | ||
Parental gene symbol: | RAB28 | ||
Ensembl ID: | ENSG00000157869 | ||
Aliases: | RAB28, CORD18 | ||
Description: | RAB28, member RAS oncogene family [Source:HGNC Symbol;Acc:9768] |
Percent Identity: | 72.89 % |
Parental protein coverage: | 99.55 % |
Number of stop codons detected: | 2 |
Number of frameshifts detected | 5 |
Parental | MSDSEEESQDRQ-LKIVVLGDGASGKTSLTTC-FAQETFGKQYKQTIGLDFF-LRRITLPGNLNVTL-QI |
M.DS.EESQD...LKI.VLG...S.KTSL.T..F....F.....QTIGLDFF.LRRITLPGNLNVTL... | |
Retrocopy | M*DSKEESQDQH<LKIIVLGNSTSRKTSLATD<FCSKNF-QEPVQTIGLDFF<LRRITLPGNLNVTL<LV |
Parental | WDIGGQTIGGKMLDKYIYGAQGVLLVYDITNYQSFENLEDWYTV-VKKVSEESETQPLVALVGNKIDLEH |
WD.GG.TI..KMLD..IYGAQ...LVY.IT...S....E......VKKVSEESETQPLV.LVGNKIDLEH | |
Retrocopy | WDTGGRTIRSKMLDRSIYGAQEIILVYGIT---SYQSFENF*KI>VKKVSEESETQPLVTLVGNKIDLEH |
Parental | MRTIKPEKHLRFCQENGFSSHFVSAKTGDSVFLCFQKVAAEILGIKLNKAEIEQSQRVVKADIVNYNQEP |
..T.KPEKHLRFCQENGF.SHFVSAK..DSVFLCFQKV.AEILGIKLNKAEIEQSQRVVKADIVNYNQEP | |
Retrocopy | NQTVKPEKHLRFCQENGFNSHFVSAKARDSVFLCFQKVVAEILGIKLNKAEIEQSQRVVKADIVNYNQEP |
Parental | MSRTVNPPRSSMCAV |
M.R.VNP.RSS.CAV | |
Retrocopy | MARAVNPSRSSVCAV |
* | Stop codon |
> | Forward frameshift by one nucleotide |
< | Reverse frameshift by one nucleotide |
Library | Retrocopy expression | Parental gene expression |
---|---|---|
bodymap2_adipose | 0 .50 RPM | 14 .67 RPM |
bodymap2_adrenal | 1 .21 RPM | 14 .02 RPM |
bodymap2_brain | 2 .18 RPM | 20 .72 RPM |
bodymap2_breast | 0 .97 RPM | 17 .24 RPM |
bodymap2_colon | 3 .38 RPM | 17 .42 RPM |
bodymap2_heart | 0 .98 RPM | 15 .67 RPM |
bodymap2_kidney | 0 .62 RPM | 17 .85 RPM |
bodymap2_liver | 0 .06 RPM | 5 .20 RPM |
bodymap2_lung | 2 .06 RPM | 24 .05 RPM |
bodymap2_lymph_node | 0 .69 RPM | 17 .93 RPM |
bodymap2_ovary | 1 .95 RPM | 29 .67 RPM |
bodymap2_prostate | 3 .24 RPM | 20 .94 RPM |
bodymap2_skeletal_muscle | 1 .84 RPM | 6 .00 RPM |
bodymap2_testis | 0 .94 RPM | 48 .40 RPM |
bodymap2_thyroid | 1 .28 RPM | 19 .09 RPM |
bodymap2_white_blood_cells | 0 .32 RPM | 19 .33 RPM |
ENCODE library ID | Target | ChIP-Seq Peak coordinates |
---|---|---|
ENCFF002CZW | POLR2A | X:135929709..135930459 |
Species | RetrogeneDB ID |
---|---|
Gorilla gorilla | retro_ggor_2966 |
Pongo abelii | retro_pabe_3707 |
Species | Parental gene accession | Retrocopies number | |
---|---|---|---|
Choloepus hoffmanni | ENSCHOG00000001523 | 1 retrocopy | |
Callithrix jacchus | ENSCJAG00000012136 | 2 retrocopies | |
Dasypus novemcinctus | ENSDNOG00000007750 | 4 retrocopies | |
Dipodomys ordii | ENSDORG00000012378 | 1 retrocopy | |
Homo sapiens | ENSG00000157869 | 7 retrocopies |
retro_hsap_4166, retro_hsap_4259, retro_hsap_4261, retro_hsap_4263, retro_hsap_4265, retro_hsap_4317, retro_hsap_4762 ,
|
Gorilla gorilla | ENSGGOG00000024190 | 1 retrocopy | |
Macropus eugenii | ENSMEUG00000006792 | 4 retrocopies | |
Macaca mulatta | ENSMMUG00000022025 | 1 retrocopy | |
Nomascus leucogenys | ENSNLEG00000016243 | 1 retrocopy | |
Pongo abelii | ENSPPYG00000014610 | 1 retrocopy | |
Pan troglodytes | ENSPTRG00000015920 | 2 retrocopies | |
Rattus norvegicus | ENSRNOG00000017074 | 1 retrocopy | |
Sarcophilus harrisii | ENSSHAG00000009274 | 1 retrocopy | |
Sus scrofa | ENSSSCG00000022358 | 2 retrocopies | |
Ictidomys tridecemlineatus | ENSSTOG00000004135 | 1 retrocopy | |
Tarsius syrichta | ENSTSYG00000010939 | 2 retrocopies |
Library | Retrogene expression |
---|---|
CEU_NA11831 | 0 .30 RPM |
CEU_NA11843 | 0 .37 RPM |
CEU_NA11930 | 0 .55 RPM |
CEU_NA12004 | 0 .27 RPM |
CEU_NA12400 | 0 .18 RPM |
CEU_NA12751 | 0 .34 RPM |
CEU_NA12760 | 0 .49 RPM |
CEU_NA12827 | 0 .38 RPM |
CEU_NA12872 | 0 .35 RPM |
CEU_NA12873 | 0 .45 RPM |
FIN_HG00183 | 0 .38 RPM |
FIN_HG00277 | 0 .41 RPM |
FIN_HG00315 | 0 .14 RPM |
FIN_HG00321 | 0 .42 RPM |
FIN_HG00328 | 0 .43 RPM |
FIN_HG00338 | 0 .17 RPM |
FIN_HG00349 | 0 .31 RPM |
FIN_HG00375 | 0 .54 RPM |
FIN_HG00377 | 0 .13 RPM |
FIN_HG00378 | 0 .36 RPM |
GBR_HG00099 | 0 .26 RPM |
GBR_HG00111 | 0 .26 RPM |
GBR_HG00114 | 0 .16 RPM |
GBR_HG00119 | 0 .29 RPM |
GBR_HG00131 | 0 .57 RPM |
GBR_HG00133 | 0 .31 RPM |
GBR_HG00134 | 0 .24 RPM |
GBR_HG00137 | 0 .33 RPM |
GBR_HG00142 | 0 .50 RPM |
GBR_HG00143 | 0 .32 RPM |
TSI_NA20512 | 0 .23 RPM |
TSI_NA20513 | 0 .24 RPM |
TSI_NA20518 | 0 .11 RPM |
TSI_NA20532 | 0 .48 RPM |
TSI_NA20538 | 0 .60 RPM |
TSI_NA20756 | 0 .26 RPM |
TSI_NA20765 | 0 .50 RPM |
TSI_NA20771 | 0 .26 RPM |
TSI_NA20786 | 0 .08 RPM |
TSI_NA20798 | 0 .47 RPM |
YRI_NA18870 | 0 .61 RPM |
YRI_NA18907 | 0 .31 RPM |
YRI_NA18916 | 0 .27 RPM |
YRI_NA19093 | 0 .16 RPM |
YRI_NA19099 | 0 .45 RPM |
YRI_NA19114 | 0 .37 RPM |
YRI_NA19118 | 0 .29 RPM |
YRI_NA19213 | 0 .41 RPM |
YRI_NA19214 | 0 .27 RPM |
YRI_NA19223 | 0 .36 RPM |