>retro_hsap_4046 ATGGCAGCAGCGGAGGAGGAGGACGGGGGCCCCGAGGGGCCAAATCGCGAGCGGGGCGGGGCGGGCGCGACCTTCGAATG
TAATATATGTTTGGAGACTGCTCGGGAAGCTGTGGTCAGTGTGTGTGGCCACCTGTACTGTTGGCCATGTCTTCATCAGT
GGCTGGCACGGCCAGAACGGCAAGAGTGTCCAGTATGTAAAGCTGGGATCAGCAGAGAGAAGGTTGTCCCGCTTTATGGG
CGAGGGAGCCAGAAGCCCCAGGATCCCAGATTGAAAACTCCACCCCGCCCCCAGGGCCAGAGACCAGCTCCAGAGAGCAG
AGGGGGATTCCAGCCATTTGGTGATACCGGGGGCTTCCACTTCTCATTTGGTGTTGGTGCTTTTCCCTTTGGCTTTTTCA
CCATCGTCTTCAATGCCCATGAGCCTTTCCGCCGGGGTACAGGTGTGGATCTGGGACAGGGTCACCCGGCCTCCAGCTGA
CAGGATTCCCTCTTCCTGTTTCTCGCCATCTTCTTCTTTTTTTGGCTGCTCAGTATT
ORF - retro_hsap_4046 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity:
97.78 %
Parental protein coverage:
100. %
Number of stop codons detected:
1
Number of frameshifts detected
0
Retrocopy - Parental Gene Alignment:
Parental MAAAEEEDGGPEGPNRERGGAGATFECNICLETAREAVVSVCGHLYCWPCLHQWLETRPERQECPVCKAG
MAAAEEEDGGPEGPNRERGGAGATFECNICLETAREAVVSVCGHLYCWPCLHQWL..RPERQECPVCKAG
Retrocopy MAAAEEEDGGPEGPNRERGGAGATFECNICLETAREAVVSVCGHLYCWPCLHQWL-ARPERQECPVCKAG Parental ISREKVVPLYGRGSQKPQDPRLKTPPRPQGQRPAPESRGGFQPFGDTGGFHFSFGVGAFPFGFFTTVFNA
ISREKVVPLYGRGSQKPQDPRLKTPPRPQGQRPAPESRGGFQPFGDTGGFHFSFGVGAFPFGFFT.VFNA
Retrocopy ISREKVVPLYGRGSQKPQDPRLKTPPRPQGQRPAPESRGGFQPFGDTGGFHFSFGVGAFPFGFFTIVFNA Parental HEPFRRGTGVDLGQGHPASSWQDSLFLFLAIFFFFWLLSI
HEPFRRGTGVDLGQGHPASS.QDSLFLFLAIFFFFWLLSI
Retrocopy HEPFRRGTGVDLGQGHPASS* QDSLFLFLAIFFFFWLLSI
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
4 .75 RPM
0 .00 RPM
bodymap2_adrenal
0 .78 RPM
0 .00 RPM
bodymap2_brain
0 .16 RPM
0 .00 RPM
bodymap2_breast
4 .75 RPM
0 .00 RPM
bodymap2_colon
5 .72 RPM
0 .00 RPM
bodymap2_heart
0 .28 RPM
0 .00 RPM
bodymap2_kidney
0 .21 RPM
0 .00 RPM
bodymap2_liver
0 .25 RPM
0 .00 RPM
bodymap2_lung
0 .23 RPM
0 .00 RPM
bodymap2_lymph_node
1 .39 RPM
0 .00 RPM
bodymap2_ovary
0 .77 RPM
0 .00 RPM
bodymap2_prostate
0 .14 RPM
0 .00 RPM
bodymap2_skeletal_muscle
0 .24 RPM
0 .00 RPM
bodymap2_testis
0 .17 RPM
0 .00 RPM
bodymap2_thyroid
1 .00 RPM
0 .00 RPM
bodymap2_white_blood_cells
0 .24 RPM
0 .00 RPM
RNA Polymerase II actvity near the 5' end of retro_hsap_4046 was not detected
No EST(s) were mapped for retro_hsap_4046 retrocopy.
TSS No.
TSS Name
TSS expression level (Expr) in TPM range:
no expression
0 < Expr ≤ 1
1 < Expr ≤ 5
5 < Expr ≤ 10
Expr > 10
TSS #1
TSS_184554 757 libraries 733 libraries 329 libraries 8 libraries 2 libraries
The graphical summary, for retro_hsap_4046
TSS expression levels > 0 TPM .
TSS expression levels were studied across 1829 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)
retro_hsap_4046 was not experimentally validated.
Retrocopy orthology: Retrocopy
retro_hsap_4046 has 1 orthologous retrocopies within
eutheria group
.
Parental genes homology: Parental genes homology involve
1 parental gene, and
1 retrocopy.
Expression level across human populations :
image/svg+xml
GBR_HG00142
GBR_HG00099
GBR_HG00114
GBR_HG00143
GBR_HG00131
GBR_HG00137
GBR_HG00133
GBR_HG00119
GBR_HG00111
GBR_HG00134
FIN_HG00378
FIN_HG00338
FIN_HG00349
FIN_HG00375
FIN_HG00315
FIN_HG00277
FIN_HG00328
FIN_HG00321
FIN_HG00377
FIN_HG00183
TSI_NA20756
TSI_NA20538
TSI_NA20798
TSI_NA20532
TSI_NA20765
TSI_NA20518
TSI_NA20513
TSI_NA20512
TSI_NA20771
TSI_NA20786
YRI_NA19114
YRI_NA19099
YRI_NA18870
YRI_NA18907
YRI_NA19223
YRI_NA19214
YRI_NA18916
YRI_NA19093
YRI_NA19118
YRI_NA19213
Toscani in Italia:
Finnish in Finland:
British in England and Scotland:
Utah Residents (CEPH) with Northern and Western European Ancestry:
Yoruba in Ibadan, Nigeria:
CEU_NA12760
CEU_NA12827
CEU_NA12872
CEU_NA12751
CEU_NA12873
CEU_NA12400
CEU_NA11930
CEU_NA12004
CEU_NA11831
CEU_NA11843
No expression ( = 0 RPM )
> 0 RPM
= 4.66 RPM
Legend:
Show / hide detail expression values
Library
Retrogene expression
CEU_NA11831
4 .43 RPM
CEU_NA11843
1 .08 RPM
CEU_NA11930
3 .78 RPM
CEU_NA12004
3 .84 RPM
CEU_NA12400
1 .02 RPM
CEU_NA12751
3 .81 RPM
CEU_NA12760
4 .04 RPM
CEU_NA12827
0 .94 RPM
CEU_NA12872
4 .35 RPM
CEU_NA12873
1 .02 RPM
FIN_HG00183
0 .85 RPM
FIN_HG00277
1 .11 RPM
FIN_HG00315
4 .47 RPM
FIN_HG00321
0 .85 RPM
FIN_HG00328
0 .88 RPM
FIN_HG00338
0 .79 RPM
FIN_HG00349
3 .56 RPM
FIN_HG00375
4 .30 RPM
FIN_HG00377
1 .66 RPM
FIN_HG00378
0 .53 RPM
GBR_HG00099
3 .84 RPM
GBR_HG00111
4 .66 RPM
GBR_HG00114
3 .71 RPM
GBR_HG00119
3 .76 RPM
GBR_HG00131
3 .56 RPM
GBR_HG00133
0 .70 RPM
GBR_HG00134
0 .68 RPM
GBR_HG00137
3 .19 RPM
GBR_HG00142
0 .92 RPM
GBR_HG00143
3 .80 RPM
TSI_NA20512
0 .73 RPM
TSI_NA20513
0 .82 RPM
TSI_NA20518
0 .67 RPM
TSI_NA20532
0 .61 RPM
TSI_NA20538
0 .64 RPM
TSI_NA20756
0 .81 RPM
TSI_NA20765
0 .73 RPM
TSI_NA20771
4 .43 RPM
TSI_NA20786
0 .89 RPM
TSI_NA20798
0 .87 RPM
YRI_NA18870
1 .18 RPM
YRI_NA18907
1 .07 RPM
YRI_NA18916
0 .93 RPM
YRI_NA19093
0 .94 RPM
YRI_NA19099
0 .88 RPM
YRI_NA19114
1 .02 RPM
YRI_NA19118
4 .25 RPM
YRI_NA19213
0 .88 RPM
YRI_NA19214
0 .76 RPM
YRI_NA19223
0 .48 RPM
Hide detail expression values Indel association: No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (
PubMed ).