RetrogeneDB ID: | retro_hsap_835 | ||
Retrocopylocation | Organism: | Human (Homo sapiens) | |
Coordinates: | 11:243121..243508(-) | ||
Located in intron of: | ENSG00000185627 | ||
Retrocopyinformation | Ensembl ID: | None | |
Aliases: | None | ||
Status: | NOVEL | ||
Parental geneinformation | Parental gene summary: | ||
Parental gene symbol: | SRP19 | ||
Ensembl ID: | ENSG00000153037 | ||
Aliases: | None | ||
Description: | signal recognition particle 19kDa [Source:HGNC Symbol;Acc:11300] |
Percent Identity: | 67.91 % |
Parental protein coverage: | 90.28 % |
Number of stop codons detected: | 2 |
Number of frameshifts detected | 4 |
Parental | ARSPADQDRFICIYPAYLNNKKTIAEGRRIPISKAVENPTATEIQDVCSA-VGLNVFLEK-NKMYSREWN |
AR......RFICI.P..LNNK.TI.EGR.IPISK.VENPTA.......S....L..FL.K.NKM.SREWN | |
Retrocopy | ARDSRSMFRFICICPTHLNNK-TIVEGR*IPISKTVENPTARDSRSMFSS<LDLMHFLRK<NKMFSREWN |
Parental | RDVQYRGRVRVQLKQEDGSLCLVQFPSR-KSVMLYAAEMIPKLKTRTQ-KTGGADQSLQQGEGS |
RDVQY..R...QLKQE.GSL.LV.FP.R.KSVML.AA.MIPKLKTRTQ.KTGG.DQSLQQGEGS | |
Retrocopy | RDVQYKSRIWAQLKQENGSLYLVHFPPR>KSVMLCAA*MIPKLKTRTQ>KTGGGDQSLQQGEGS |
* | Stop codon |
> | Forward frameshift by one nucleotide |
< | Reverse frameshift by one nucleotide |
Library | Retrocopy expression | Parental gene expression |
---|---|---|
bodymap2_adipose | 0 .78 RPM | 18 .80 RPM |
bodymap2_adrenal | 1 .88 RPM | 29 .13 RPM |
bodymap2_brain | 0 .52 RPM | 28 .64 RPM |
bodymap2_breast | 0 .37 RPM | 27 .08 RPM |
bodymap2_colon | 0 .17 RPM | 15 .04 RPM |
bodymap2_heart | 0 .20 RPM | 8 .40 RPM |
bodymap2_kidney | 0 .99 RPM | 19 .79 RPM |
bodymap2_liver | 0 .21 RPM | 20 .21 RPM |
bodymap2_lung | 0 .39 RPM | 13 .57 RPM |
bodymap2_lymph_node | 0 .62 RPM | 18 .27 RPM |
bodymap2_ovary | 0 .10 RPM | 26 .24 RPM |
bodymap2_prostate | 0 .00 RPM | 16 .28 RPM |
bodymap2_skeletal_muscle | 0 .00 RPM | 9 .71 RPM |
bodymap2_testis | 0 .32 RPM | 32 .03 RPM |
bodymap2_thyroid | 0 .34 RPM | 35 .38 RPM |
bodymap2_white_blood_cells | 0 .26 RPM | 20 .53 RPM |
Experiment type: | PCR amplification |
---|---|
Forward primer: | TTCTCTCCCTGTGGCTTCCGGG (22 nt long) |
Reverse primer: | CTGCGCCCGGATGGTTACGTC (21 nt long) |
Anneling temperature: | 61 °C |
(Expected) product size: | 609 |
Electrophoresis gel image: | |
Additional comment: | Red arrow indicates PCR product of retrogene in pooled cDNA from 16 human tissues (Clontech). Red number of lane indicates particular retrogene; L - GeneRuler 100 bp DNA Ladder (Thermo Fisher Scientific); N - No template control (water instead of cDNA) |
Library | Retrogene expression |
---|---|
CEU_NA11831 | 0 .49 RPM |
CEU_NA11843 | 0 .20 RPM |
CEU_NA11930 | 0 .46 RPM |
CEU_NA12004 | 0 .04 RPM |
CEU_NA12400 | 0 .18 RPM |
CEU_NA12751 | 0 .56 RPM |
CEU_NA12760 | 0 .49 RPM |
CEU_NA12827 | 0 .14 RPM |
CEU_NA12872 | 0 .33 RPM |
CEU_NA12873 | 0 .22 RPM |
FIN_HG00183 | 0 .66 RPM |
FIN_HG00277 | 0 .44 RPM |
FIN_HG00315 | 0 .30 RPM |
FIN_HG00321 | 0 .85 RPM |
FIN_HG00328 | 0 .92 RPM |
FIN_HG00338 | 0 .17 RPM |
FIN_HG00349 | 0 .09 RPM |
FIN_HG00375 | 0 .44 RPM |
FIN_HG00377 | 0 .48 RPM |
FIN_HG00378 | 0 .38 RPM |
GBR_HG00099 | 0 .20 RPM |
GBR_HG00111 | 0 .30 RPM |
GBR_HG00114 | 0 .34 RPM |
GBR_HG00119 | 0 .57 RPM |
GBR_HG00131 | 0 .92 RPM |
GBR_HG00133 | 0 .17 RPM |
GBR_HG00134 | 0 .92 RPM |
GBR_HG00137 | 0 .71 RPM |
GBR_HG00142 | 1 .83 RPM |
GBR_HG00143 | 0 .10 RPM |
TSI_NA20512 | 0 .03 RPM |
TSI_NA20513 | 0 .75 RPM |
TSI_NA20518 | 0 .19 RPM |
TSI_NA20532 | 0 .92 RPM |
TSI_NA20538 | 0 .46 RPM |
TSI_NA20756 | 0 .20 RPM |
TSI_NA20765 | 0 .87 RPM |
TSI_NA20771 | 0 .34 RPM |
TSI_NA20786 | 0 .08 RPM |
TSI_NA20798 | 0 .44 RPM |
YRI_NA18870 | 0 .51 RPM |
YRI_NA18907 | 0 .31 RPM |
YRI_NA18916 | 0 .32 RPM |
YRI_NA19093 | 0 .26 RPM |
YRI_NA19099 | 0 .53 RPM |
YRI_NA19114 | 0 .10 RPM |
YRI_NA19118 | 0 .37 RPM |
YRI_NA19213 | 0 .43 RPM |
YRI_NA19214 | 0 .44 RPM |
YRI_NA19223 | 0 .78 RPM |