>retro_hsap_3056
ATGCCTGGGCACTTACAGGAAGGCTTCGGCTGTGTGGTCACCAACCGATTCGACCAGTTATTTGACGACGAATCGGACCC
CTTCGAGGTGCTGAAGGCAGCGGAGAACAAGAAAAAAGAAGCCGGCAGGGGTGGCGTTGGGGGCCCTGGGGCCAAGAGCG
CAGCTCAGGCGGCGGCCCAGACCAACTCCAACGCGGCAGGCAAACAGCTGCGCAAGGAGTCCCAGAAAGACCGCAAGAAC
CCGCTGCCCCGCAGCGTTGGCGTGGTTGACAAGAAAGAGGAGACGCAGCCGCCCGTGGCGCTTAAGAAAGAAGGAATAAG
ACGAGTTGGAAGAAGACCTGATCAACAACTTCAGGGTGAGGGGAAAATAATTGATAGAAGACCAGAAAGGCAACCACCTT
GTGAACGAAGATTCGAAAAGCCACTTGAAGAAAAGGGTGAAGGAGGCTAATTTTCAGTTGATAGACCGATTATTGACCGA
CCTATTCGAGGTCGTGGTGGTCTTGGAAGAGGTCGAGGGGGCCGTGGACGTGGAATGGGCCGAGGAGATGGATTTGATTC
TCGTGGCAAACGTGAATTTGATAGGCATAGTGGAAGTGATAGATCTTCTTTTTCACATTACAGTGGCCTGAAGCACGAGG
ACAAACGTGGAGGTAGCGGATCTCACAACTGGGGAACTGTCAAAGACGAATTAACTGACTTGGATCAATCAAATGTGACT
GACGAAACACCTGAAGGTGAAGAACATCATCCAGTGGCAGACACTGAAAATAAGGAGAATGATGTTGAAGAGGTAAAAGA
GGAGGGTCCAAAAGAGATGACTTTGGATGAGTGGAAGGCTATTCAAAATAAGGACCGGGCAAAAGTAGAATTTAATATCT
GAAAACCAAATGAAGGTGCTGATGGGCAGTGGAAGAAGGGATTTGTTTTCATAAATCAAAGAGTGAAGAGGCTTATGCTG
AGGATTCAGTTATGGACCATCATTTCCAGAAGCCAGCAAATGATATAACGTCTCAGCTGGAGATCAATTTTGGAGACCTT
GGCCGCCCAGGACGTGGCGGCAGGGGAGGACAAGGTGGACATGGGCGTGGTGGGCGCCCAAACCGTGGCAGCAGGACCGA
CAAGTCAAGTACTTCTGCTCCTGATGTGGATGACCCAGAGGCATTCCCAGTTCTGGCT
ORF - retro_hsap_3056 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: |
95.94 % |
Parental protein coverage: |
100. % |
Number of stop codons detected: |
2 |
Number of frameshifts detected |
1 |
Retrocopy - Parental Gene Alignment:
Parental | MPGHLQEGFGCVVTNRFDQLFDDESDPFEVLKAAENKKKEAGGGGVGGPGAKSAAQAAAQTNSNAAGKQL |
| MPGHLQEGFGCVVTNRFDQLFDDESDPFEVLKAAENKKKEAG.GGVGGPGAKSAAQAAAQTNSNAAGKQL |
Retrocopy | MPGHLQEGFGCVVTNRFDQLFDDESDPFEVLKAAENKKKEAGRGGVGGPGAKSAAQAAAQTNSNAAGKQL |
|
Parental | RKESQKDRKNPLPPSVGVVDKKEETQPPVALKKEGIRRVGRRPDQQLQGEGKIIDRRPERRPPRERRFEK |
| RKESQKDRKNPLP.SVGVVDKKEETQPPVALKKEGIRRVGRRPDQQLQGEGKIIDRRPER.PP.ERRFEK |
Retrocopy | RKESQKDRKNPLPRSVGVVDKKEETQPPVALKKEGIRRVGRRPDQQLQGEGKIIDRRPERQPPCERRFEK |
|
Parental | PLEEKGEGGEFSVDRPIIDRPIRGRGGLGRGRGGRGRGMGRGDGFDSRGKREFDRHSGSDRSSFSHYSGL |
| PLEEKGEGG.FSVDRPIIDRPIRGRGGLGRGRGGRGRGMGRGDGFDSRGKREFDRHSGSDRSSFSHYSGL |
Retrocopy | PLEEKGEGG*FSVDRPIIDRPIRGRGGLGRGRGGRGRGMGRGDGFDSRGKREFDRHSGSDRSSFSHYSGL |
|
Parental | KHEDKRGGSGSHNWGTVKDELTDLDQSNVTEETPEGEEHHPVADTENKENEVEEVKEEGPKEMTLDEWKA |
| KHEDKRGGSGSHNWGTVKDELTDLDQSNVT.ETPEGEEHHPVADTENKEN.VEEVKEEGPKEMTLDEWKA |
Retrocopy | KHEDKRGGSGSHNWGTVKDELTDLDQSNVTDETPEGEEHHPVADTENKENDVEEVKEEGPKEMTLDEWKA |
|
Parental | IQNKDRAKVEFNIRKPNEGADGQWKKGFV-LHKSKSEEAHAEDSVMDHHFRKPANDITSQLEINFGDLGR |
| IQNKDRAKVEFNI.KPNEGADGQWKKGFV..HKSKSEEA.AEDSVMDHHF.KPANDITSQLEINFGDLGR |
Retrocopy | IQNKDRAKVEFNI*KPNEGADGQWKKGFV<FHKSKSEEAYAEDSVMDHHFQKPANDITSQLEINFGDLGR |
|
Parental | PGRGGRGGRGGRGRGGRPNRGSRTDKSSASAPDVDDPEAFPALA |
| PGRGGRGG.GG.GRGGRPNRGSRTDKSS.SAPDVDDPEAFP.LA |
Retrocopy | PGRGGRGGQGGHGRGGRPNRGSRTDKSSTSAPDVDDPEAFPVLA |
|
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 .26 RPM |
280 .28 RPM |
bodymap2_adrenal |
0 .25 RPM |
259 .94 RPM |
bodymap2_brain |
0 .07 RPM |
141 .41 RPM |
bodymap2_breast |
0 .14 RPM |
247 .26 RPM |
bodymap2_colon |
0 .06 RPM |
385 .44 RPM |
bodymap2_heart |
0 .04 RPM |
165 .85 RPM |
bodymap2_kidney |
0 .10 RPM |
267 .30 RPM |
bodymap2_liver |
0 .04 RPM |
169 .01 RPM |
bodymap2_lung |
0 .00 RPM |
255 .54 RPM |
bodymap2_lymph_node |
0 .18 RPM |
246 .53 RPM |
bodymap2_ovary |
0 .19 RPM |
322 .71 RPM |
bodymap2_prostate |
0 .05 RPM |
279 .30 RPM |
bodymap2_skeletal_muscle |
0 .18 RPM |
342 .10 RPM |
bodymap2_testis |
1 .15 RPM |
334 .21 RPM |
bodymap2_thyroid |
0 .38 RPM |
388 .79 RPM |
bodymap2_white_blood_cells |
0 .06 RPM |
312 .07 RPM |
RNA Polymerase II actvity near the 5' end of retro_hsap_3056 was not detected
No EST(s) were mapped for retro_hsap_3056 retrocopy.
No TSS is located nearby retro_hsap_3056 retrocopy 5' end.
retro_hsap_3056 was not experimentally validated.
Retrocopy orthology:
Retrocopy
retro_hsap_3056 has 1 orthologous retrocopies within
eutheria group
.
Parental genes homology:
Parental genes homology involve
8 parental genes, and
15 retrocopies.
Expression level across human populations :
Library |
Retrogene expression |
CEU_NA11831 |
0 .41 RPM |
CEU_NA11843 |
0 .20 RPM |
CEU_NA11930 |
0 .55 RPM |
CEU_NA12004 |
0 .19 RPM |
CEU_NA12400 |
0 .28 RPM |
CEU_NA12751 |
0 .32 RPM |
CEU_NA12760 |
0 .72 RPM |
CEU_NA12827 |
0 .38 RPM |
CEU_NA12872 |
0 .68 RPM |
CEU_NA12873 |
0 .57 RPM |
FIN_HG00183 |
0 .60 RPM |
FIN_HG00277 |
0 .52 RPM |
FIN_HG00315 |
0 .52 RPM |
FIN_HG00321 |
0 .73 RPM |
FIN_HG00328 |
0 .57 RPM |
FIN_HG00338 |
0 .51 RPM |
FIN_HG00349 |
0 .80 RPM |
FIN_HG00375 |
0 .42 RPM |
FIN_HG00377 |
0 .55 RPM |
FIN_HG00378 |
0 .51 RPM |
GBR_HG00099 |
0 .55 RPM |
GBR_HG00111 |
0 .21 RPM |
GBR_HG00114 |
0 .39 RPM |
GBR_HG00119 |
0 .45 RPM |
GBR_HG00131 |
0 .29 RPM |
GBR_HG00133 |
0 .58 RPM |
GBR_HG00134 |
0 .39 RPM |
GBR_HG00137 |
0 .19 RPM |
GBR_HG00142 |
0 .58 RPM |
GBR_HG00143 |
0 .29 RPM |
TSI_NA20512 |
0 .37 RPM |
TSI_NA20513 |
0 .82 RPM |
TSI_NA20518 |
1 .14 RPM |
TSI_NA20532 |
0 .37 RPM |
TSI_NA20538 |
0 .46 RPM |
TSI_NA20756 |
0 .41 RPM |
TSI_NA20765 |
0 .52 RPM |
TSI_NA20771 |
0 .71 RPM |
TSI_NA20786 |
0 .47 RPM |
TSI_NA20798 |
0 .47 RPM |
YRI_NA18870 |
0 .64 RPM |
YRI_NA18907 |
0 .45 RPM |
YRI_NA18916 |
0 .42 RPM |
YRI_NA19093 |
0 .31 RPM |
YRI_NA19099 |
0 .53 RPM |
YRI_NA19114 |
0 .63 RPM |
YRI_NA19118 |
0 .41 RPM |
YRI_NA19213 |
0 .41 RPM |
YRI_NA19214 |
0 .34 RPM |
YRI_NA19223 |
0 .36 RPM |
Indel association:
No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (
PubMed).