>retro_hsap_1534
ATGTGTGATAACAGAGAACTGGAAGACAAGCCTCCAGCACCTCCCGTGCGAATGAGCAGGACCATCTTTAGCACTGGGGG
CAAAGACCCTTTGTCAGCCAATCACAGTTTGAAACCTTTGCCTTCTGTTCCAGAGGAGAAAAAGCCCAGGCATAAAATCA
TCTCCATATTCTCAGGCACAGAGAAAGGAAGTAAAAAGAAAGAAAAGGAACGGCCAGAAATTTCTCCTCCATCTGATTTT
GAACACACCATCCATGTTGGCTTTGATGCTGTTACTGGAGAATTCACTGGCATGCCAGAACACTGGGCTCGATTACTACA
GACCTCAAATATCACCAAACTAGAGCAAAAGAAGAATCCTCAGGCTGTGCTGGATGTCTACGACTCCAACACAGTGAAGC
AGAAGTATCTGAGTTTTACTCCTCCTGAGAAAGATGGCTTCCCTTCTGGAACACCAGCACTGAATGCCGAGGGAACAGAA
GCACCTGCAGTAGTGACAGAGGAGGAGGACGATGATGAAGAGACTGCCCCTCCCATTATTGCCCCACCACCGGATCATAT
GAAATCAATTTACACACGGTCTGTAATTGACCCTGTTCCTGCACCAGTTGGTGATTCAAATGTTGATGGTGGTGCCAAGT
CTTTAGACAAACAGAAAAAGAAGACTAAGATGACAGATGAAGAGATTATGGAGAAACTAAGAACTATTGTGAGCATAGGT
GACCCTAAGAAAAAAATATACAAGATATGAAAAAATTGGACAAGGGGCTTCTGGTACAGTTTTCACTGCTACTGACGTTG
CACTGGGACAGAAGGTTGCTATCAAACAAATTAATTTACAGAAACAGCCAAAGAAGGAATTGATCATTAATGAGATTCTG
GTAATGAAAGAATTAAAAAATCCCAACATAGTTAACTTCTTGGACAGTTACCTGGTAGGAGATGAATTGTTTGTGGTCGT
GGAATACCTTGCTAGGGGGTCACTCACTGATGTGGTAACAGAAACCTGCATGGATGAAGCACAGATTGCCGCTGTATGCA
GAGAGAGTTTACAGGCATTGGAGTTTTTACATGCTAATCAAGTGATCCACAGAGACATCAAAAGTGACAGTGTACTTTTG
GGAATGGAAGGATCGGTTAAGCTCACTGACTTTGGTTTCTGTGCCCAGATCACCCCTGAGCAGAGCAAACGCAGTACCGT
GGTCAGAACGCCATACTGGATGGCACCAGAAGTGGTTACACGGAAGGCTTATGGCCCTAAAGTCAATGTATGGTCTCTGG
GTATCATGGCTACTGAGATGGTAGAAGGAGAGCCTCCATACCTCAATGAAAATCCCTTGAGGGCCTTGTGCCTAATAGCA
ACTAATGGAATCCCAGAACTTCAGAATCCAGAGACACTTTCCCCAATATTTCGGGATTTCTTAAATCGATGTTTGGAAAC
AGATGTGGAAAAAAGGGGTTCAGCCAAAGAATTATTACAGCATCTTTTCCTGAAACTAGCCAAACTGTTATCTAGCTTGA
CACCACTGATCATGGCAGCTAAAGAAGCAATGAAGAGTAACCGT
ORF - retro_hsap_1534 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: |
94.29 % |
Parental protein coverage: |
100. % |
Number of stop codons detected: |
0 |
Number of frameshifts detected |
1 |
Retrocopy - Parental Gene Alignment:
Parental | MSDNGELEDKPPAPPVRMSSTIFSTGGKDPLSANHSLKPLPSVPEEKKPRHKIISIFSGTEKGSKKKEKE |
| M.DN.ELEDKPPAPPVRMS.TIFSTGGKDPLSANHSLKPLPSVPEEKKPRHKIISIFSGTEKGSKKKEKE |
Retrocopy | MCDNRELEDKPPAPPVRMSRTIFSTGGKDPLSANHSLKPLPSVPEEKKPRHKIISIFSGTEKGSKKKEKE |
|
Parental | RPEISPPSDFEHTIHVGFDAVTGEFTGMPEQWARLLQTSNITKLEQKKNPQAVLDVLKFYDSNTVKQKYL |
| RPEISPPSDFEHTIHVGFDAVTGEFTGMPE.WARLLQTSNITKLEQKKNPQAVLDV...YDSNTVKQKYL |
Retrocopy | RPEISPPSDFEHTIHVGFDAVTGEFTGMPEHWARLLQTSNITKLEQKKNPQAVLDV---YDSNTVKQKYL |
|
Parental | SFTPPEKDGFPSGTPALNAKGTEAPAVVTEEEDDDEETAPPVIAPRPDHTKSIYTRSVIDPVPAPVGDSH |
| SFTPPEKDGFPSGTPALNA.GTEAPAVVTEEEDDDEETAPP.IAP.PDH.KSIYTRSVIDPVPAPVGDS. |
Retrocopy | SFTPPEKDGFPSGTPALNAEGTEAPAVVTEEEDDDEETAPPIIAPPPDHMKSIYTRSVIDPVPAPVGDSN |
|
Parental | VDGAAKSLDKQKKKTKMTDEEIMEKLRTIVSIGDPKKK-YTRYEKIGQGASGTVFTATDVALGQEVAIKQ |
| VDG.AKSLDKQKKKTKMTDEEIMEKLRTIVSIGDPKKK.YTRYEKIGQGASGTVFTATDVALGQ.VAIKQ |
Retrocopy | VDGGAKSLDKQKKKTKMTDEEIMEKLRTIVSIGDPKKK>YTRYEKIGQGASGTVFTATDVALGQKVAIKQ |
|
Parental | INLQKQPKKELIINEILVMKELKNPNIVNFLDSYLVGDELFVVMEYLAGGSLTDVVTETCMDEAQIAAVC |
| INLQKQPKKELIINEILVMKELKNPNIVNFLDSYLVGDELFVV.EYLA.GSLTDVVTETCMDEAQIAAVC |
Retrocopy | INLQKQPKKELIINEILVMKELKNPNIVNFLDSYLVGDELFVVVEYLARGSLTDVVTETCMDEAQIAAVC |
|
Parental | RECLQALEFLHANQVIHRDIKSDNVLLGMEGSVKLTDFGFCAQITPEQSKRSTMVGTPYWMAPEVVTRKA |
| RE.LQALEFLHANQVIHRDIKSD.VLLGMEGSVKLTDFGFCAQITPEQSKRST.V.TPYWMAPEVVTRKA |
Retrocopy | RESLQALEFLHANQVIHRDIKSDSVLLGMEGSVKLTDFGFCAQITPEQSKRSTVVRTPYWMAPEVVTRKA |
|
Parental | YGPKVDIWSLGIMAIEMVEGEPPYLNENPLRALYLIATNGTPELQNPEKLSPIFRDFLNRCLEMDVEKRG |
| YGPKV..WSLGIMA.EMVEGEPPYLNENPLRAL.LIATNG.PELQNPE.LSPIFRDFLNRCLE.DVEKRG |
Retrocopy | YGPKVNVWSLGIMATEMVEGEPPYLNENPLRALCLIATNGIPELQNPETLSPIFRDFLNRCLETDVEKRG |
|
Parental | SAKELLQHPFLKLAKPLSSLTPLIMAAKEAMKSNR |
| SAKELLQH.FLKLAK.LSSLTPLIMAAKEAMKSNR |
Retrocopy | SAKELLQHLFLKLAKLLSSLTPLIMAAKEAMKSNR |
|
Legend:
* | Stop codon |
> | Forward frameshift by one nucleotide |
< | Reverse frameshift by one nucleotide |
(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)
Expression validation based on RNA-Seq data:
Library |
Retrocopy expression |
Parental gene expression |
bodymap2_adipose |
0 .22 RPM |
212 .34 RPM |
bodymap2_adrenal |
0 .37 RPM |
148 .08 RPM |
bodymap2_brain |
0 .40 RPM |
114 .95 RPM |
bodymap2_breast |
0 .58 RPM |
142 .04 RPM |
bodymap2_colon |
0 .31 RPM |
157 .88 RPM |
bodymap2_heart |
0 .18 RPM |
90 .99 RPM |
bodymap2_kidney |
0 .27 RPM |
126 .77 RPM |
bodymap2_liver |
0 .00 RPM |
91 .13 RPM |
bodymap2_lung |
0 .05 RPM |
155 .20 RPM |
bodymap2_lymph_node |
0 .48 RPM |
155 .73 RPM |
bodymap2_ovary |
1 .50 RPM |
140 .47 RPM |
bodymap2_prostate |
0 .26 RPM |
125 .71 RPM |
bodymap2_skeletal_muscle |
0 .33 RPM |
119 .51 RPM |
bodymap2_testis |
1 .17 RPM |
104 .24 RPM |
bodymap2_thyroid |
0 .90 RPM |
108 .41 RPM |
bodymap2_white_blood_cells |
0 .16 RPM |
424 .00 RPM |
RNA Polymerase II actvity near the 5' end of retro_hsap_1534 was not detected
4 EST(s) were mapped to retro_hsap_1534 retrocopy
EST ID |
Start |
End |
Identity |
Match |
Mis-match |
Score |
CD251902 |
21936617 |
21937444 |
98.2 |
827 |
0 |
819 |
DA320145 |
21936527 |
21937099 |
99.5 |
569 |
3 |
566 |
DN990003 |
21936740 |
21937421 |
99.5 |
523 |
3 |
518 |
DR001344 |
21936472 |
21937271 |
99.5 |
793 |
4 |
788 |
No TSS is located nearby retro_hsap_1534 retrocopy 5' end.
retro_hsap_1534 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_hsap_1534 has 0 orthologous retrocopies within eutheria group .
Parental genes homology:
Parental genes homology involve
3 parental genes, and
3 retrocopies.
Expression level across human populations :
Library |
Retrogene expression |
CEU_NA11831 |
0 .02 RPM |
CEU_NA11843 |
0 .03 RPM |
CEU_NA11930 |
0 .33 RPM |
CEU_NA12004 |
0 .11 RPM |
CEU_NA12400 |
0 .04 RPM |
CEU_NA12751 |
0 .12 RPM |
CEU_NA12760 |
0 .04 RPM |
CEU_NA12827 |
0 .14 RPM |
CEU_NA12872 |
0 .14 RPM |
CEU_NA12873 |
0 .06 RPM |
FIN_HG00183 |
0 .11 RPM |
FIN_HG00277 |
0 .18 RPM |
FIN_HG00315 |
0 .06 RPM |
FIN_HG00321 |
0 .18 RPM |
FIN_HG00328 |
0 .31 RPM |
FIN_HG00338 |
0 .11 RPM |
FIN_HG00349 |
0 .06 RPM |
FIN_HG00375 |
0 .20 RPM |
FIN_HG00377 |
0 .03 RPM |
FIN_HG00378 |
0 .06 RPM |
GBR_HG00099 |
0 .03 RPM |
GBR_HG00111 |
0 .06 RPM |
GBR_HG00114 |
0 .00 RPM |
GBR_HG00119 |
0 .10 RPM |
GBR_HG00131 |
0 .06 RPM |
GBR_HG00133 |
0 .10 RPM |
GBR_HG00134 |
0 .17 RPM |
GBR_HG00137 |
0 .30 RPM |
GBR_HG00142 |
0 .28 RPM |
GBR_HG00143 |
0 .19 RPM |
TSI_NA20512 |
0 .00 RPM |
TSI_NA20513 |
0 .15 RPM |
TSI_NA20518 |
0 .22 RPM |
TSI_NA20532 |
0 .48 RPM |
TSI_NA20538 |
0 .09 RPM |
TSI_NA20756 |
0 .17 RPM |
TSI_NA20765 |
0 .46 RPM |
TSI_NA20771 |
0 .14 RPM |
TSI_NA20786 |
0 .00 RPM |
TSI_NA20798 |
0 .12 RPM |
YRI_NA18870 |
0 .95 RPM |
YRI_NA18907 |
0 .10 RPM |
YRI_NA18916 |
0 .06 RPM |
YRI_NA19093 |
0 .05 RPM |
YRI_NA19099 |
0 .11 RPM |
YRI_NA19114 |
0 .13 RPM |
YRI_NA19118 |
0 .17 RPM |
YRI_NA19213 |
0 .33 RPM |
YRI_NA19214 |
0 .22 RPM |
YRI_NA19223 |
0 .48 RPM |
Indel association:
No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (
PubMed).