>retro_hsap_280
ATGATTGTGTTTGCCGTGCTCCTGTCGTTGGTGGCGGGTGTTTGAGGGAACGAGTTTAGTTCTTGGTCTGTTATTTTCAG
AAATGGAAATTGGCCTATACCGGGAGAGTGAATCCCAGACGTGGCTGCATTGTCCATGGCCTTCTCTGTGAAGGAAAACC
TTTCTTGGCCAGGACTTGCAGTAGGTGACCTATTTCATCGTCCTCGGGCTACCGTCATGGTGATGGTGAAGGGAGTGGAC
AAACTGGCTCTACCACCAGGCAGTGTCATTTCATACCCTTTGGAGAATGCAGTTCCGTTTGGTCTTGGCAGTGTTGCAAA
TTCCATTCGCTCTTTATTTTCTGACGAAACTCCTGTTGTTTTGCAGTTGGCTCCTAGTGAGGAAAGAGTGTATTTGGTAG
GGAAGGCAAACTCAGTGTTTGAAGACCTTTCAGTCACCTTAGGACAGCTCCATAATTACTTGTTTCAGGAAAACTCCATT
CTCAGTTCATTTCCCCTGAATTCTCTGAGTAGGAACAATGGAGTTGACTTGCTCTTTCTTTCTGAACTCCAAGTGCTACA
TGATATTTCAAGCTTGGTGTCTTGTCATAAGCATCTAGCCAAGGATCATTCTCCTGATTTATATTCACTGGAGCTGGCAG
GTTTGGATGAAATTGGGAAGCATTACAGGGAAGACTCTGAACAATTCATAGTTGCTTCTAAAATCCTGTTGACGCTCTGC
AAGAGTTTGCAGATAACATGTACAATCTTTACAGTGGGAATGCAGTGGTAGAGTTAGTCACTATTAAGTCATTTGACACC
TCCCTTATGAGGAAGACAAGGACTATCTTTGAGGCAAAATAAGTGAAGAACCCAGCAAGTCCCTATAACCTTGCGTATAA
TTTTGAATATTCAGTGATTTTCAACATGATACTTTGGATAATGATTGCCTTGGCCCTGGCTGTGATTATCACTTCTTACA
ATATTTGGAACATGGATCCTGGATATGATAGCATCATTTATAGGATTACAAACCAGAAGATTCGAATAGAT
ORF - retro_hsap_280 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: |
86.04 % |
Parental protein coverage: |
100. % |
Number of stop codons detected: |
3 |
Number of frameshifts detected |
1 |
Retrocopy - Parental Gene Alignment:
Parental | MAVFVVLLALVAGVLGNEFSILKSPGSVVFRNGNWPIPGERIPDVAALSMGFSVKEDLSWPGLAVGNLFH |
| M.VF.VLL.LVAGV.GNEF....S..SV.FRNGNWPIPGE.IPDVAALSM.FSVKE.LSWPGLAVG.LFH |
Retrocopy | MIVFAVLLSLVAGV*GNEF----SSWSVIFRNGNWPIPGE*IPDVAALSMAFSVKENLSWPGLAVGDLFH |
|
Parental | RPRATVMVMVKGVNKLALPPGSVISYPLENAVPFSLDSVANSIHSLFSEETPVVLQLAPSEERVYMVGKA |
| RPRATVMVMVKGV.KLALPPGSVISYPLENAVPF.L.SVANSI.SLFS.ETPVVLQLAPSEERVY.VGKA |
Retrocopy | RPRATVMVMVKGVDKLALPPGSVISYPLENAVPFGLGSVANSIRSLFSDETPVVLQLAPSEERVYLVGKA |
|
Parental | NSVFEDLSVTLRQLRNRLFQENSVLSSLPLNSLSRNNEVDLLFLSELQVLHDISSLLSRHKHLAKDHSPD |
| NSVFEDLSVTL.QL.N.LFQENS.LSS.PLNSLSRNN.VDLLFLSELQVLHDISSL.S.HKHLAKDHSPD |
Retrocopy | NSVFEDLSVTLGQLHNYLFQENSILSSFPLNSLSRNNGVDLLFLSELQVLHDISSLVSCHKHLAKDHSPD |
|
Parental | LYSLELAGLDEIGKRYGEDSEQFRDASKIL-VDALQKFADDMYSLYGGNAVVELVTVKSFDTSLIRKTRT |
| LYSLELAGLDEIGK.Y.EDSEQF..ASKIL.VDALQ.FAD.MY.LY.GNAVVELVT.KSFDTSL.RKTRT |
Retrocopy | LYSLELAGLDEIGKHYREDSEQFIVASKIL<VDALQEFADNMYNLYSGNAVVELVTIKSFDTSLMRKTRT |
|
Parental | ILEAKQAKNPASPYNLAYKYNFEYSVVFNMVLWIMIALALAVIITSYNIWNMDPGYDSIIYRMTNQKIRM |
| I.EAK..KNPASPYNLA..YNFEYSV.FNM.LWIMIALALAVIITSYNIWNMDPGYDSIIYR.TNQKIR. |
Retrocopy | IFEAK*VKNPASPYNLA--YNFEYSVIFNMILWIMIALALAVIITSYNIWNMDPGYDSIIYRITNQKIRI |
|
Parental | D |
| D |
Retrocopy | D |
|
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 .00 RPM |
121 .32 RPM |
bodymap2_adrenal |
0 .08 RPM |
115 .88 RPM |
bodymap2_brain |
0 .00 RPM |
238 .46 RPM |
bodymap2_breast |
0 .12 RPM |
161 .66 RPM |
bodymap2_colon |
0 .00 RPM |
168 .43 RPM |
bodymap2_heart |
0 .00 RPM |
45 .82 RPM |
bodymap2_kidney |
0 .00 RPM |
237 .04 RPM |
bodymap2_liver |
0 .00 RPM |
85 .30 RPM |
bodymap2_lung |
0 .00 RPM |
194 .16 RPM |
bodymap2_lymph_node |
0 .00 RPM |
137 .67 RPM |
bodymap2_ovary |
0 .13 RPM |
145 .69 RPM |
bodymap2_prostate |
0 .00 RPM |
157 .49 RPM |
bodymap2_skeletal_muscle |
0 .00 RPM |
28 .63 RPM |
bodymap2_testis |
0 .21 RPM |
124 .98 RPM |
bodymap2_thyroid |
0 .04 RPM |
267 .05 RPM |
bodymap2_white_blood_cells |
0 .00 RPM |
332 .35 RPM |
RNA Polymerase II actvity may be related with retro_hsap_280 in 2 libraries
ENCODE library ID |
Target |
ChIP-Seq Peak coordinates |
ENCFF002DBO |
POLR2A |
1:197191118..197191502 |
ENCFF002DBP |
POLR2A |
1:197191147..197191477 |
No EST(s) were mapped for retro_hsap_280 retrocopy.
No TSS is located nearby retro_hsap_280 retrocopy 5' end.
retro_hsap_280 was not experimentally validated.
Retrocopy orthology:
Retrocopy
retro_hsap_280 has 4 orthologous retrocopies within
eutheria group
.
Parental genes homology:
Parental genes homology involve
8 parental genes, and
8 retrocopies.
Expression level across human populations :
Library |
Retrogene expression |
CEU_NA11831 |
0 .00 RPM |
CEU_NA11843 |
0 .00 RPM |
CEU_NA11930 |
0 .00 RPM |
CEU_NA12004 |
0 .00 RPM |
CEU_NA12400 |
0 .00 RPM |
CEU_NA12751 |
0 .00 RPM |
CEU_NA12760 |
0 .00 RPM |
CEU_NA12827 |
0 .00 RPM |
CEU_NA12872 |
0 .00 RPM |
CEU_NA12873 |
0 .00 RPM |
FIN_HG00183 |
0 .00 RPM |
FIN_HG00277 |
0 .00 RPM |
FIN_HG00315 |
0 .06 RPM |
FIN_HG00321 |
0 .00 RPM |
FIN_HG00328 |
0 .05 RPM |
FIN_HG00338 |
0 .02 RPM |
FIN_HG00349 |
0 .00 RPM |
FIN_HG00375 |
0 .02 RPM |
FIN_HG00377 |
0 .00 RPM |
FIN_HG00378 |
0 .02 RPM |
GBR_HG00099 |
0 .00 RPM |
GBR_HG00111 |
0 .02 RPM |
GBR_HG00114 |
0 .03 RPM |
GBR_HG00119 |
0 .05 RPM |
GBR_HG00131 |
0 .03 RPM |
GBR_HG00133 |
0 .05 RPM |
GBR_HG00134 |
0 .00 RPM |
GBR_HG00137 |
0 .00 RPM |
GBR_HG00142 |
0 .06 RPM |
GBR_HG00143 |
0 .00 RPM |
TSI_NA20512 |
0 .03 RPM |
TSI_NA20513 |
0 .00 RPM |
TSI_NA20518 |
0 .00 RPM |
TSI_NA20532 |
0 .00 RPM |
TSI_NA20538 |
0 .05 RPM |
TSI_NA20756 |
0 .00 RPM |
TSI_NA20765 |
0 .00 RPM |
TSI_NA20771 |
0 .00 RPM |
TSI_NA20786 |
0 .00 RPM |
TSI_NA20798 |
0 .00 RPM |
YRI_NA18870 |
0 .00 RPM |
YRI_NA18907 |
0 .00 RPM |
YRI_NA18916 |
0 .04 RPM |
YRI_NA19093 |
0 .00 RPM |
YRI_NA19099 |
0 .00 RPM |
YRI_NA19114 |
0 .00 RPM |
YRI_NA19118 |
0 .00 RPM |
YRI_NA19213 |
0 .00 RPM |
YRI_NA19214 |
0 .00 RPM |
YRI_NA19223 |
0 .00 RPM |
Indel association:
No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (
PubMed).