>retro_hsap_2952
AAACTACTAGAGGAGTTGTCTATTCTTTATAATAGTCATACTGGCTCTATGTGACCATCTTCCAAAACATTTCCAACTTG
AGGGATGTCTTCTACAGGGAAATGAGCAAACTGAACCACAATCTCTCCGAGGTGATGAGCAAACTGGAGAAGCAACATTC
CAGTAAAGTCTTTGTGGTGAAGAGACTATCAAGCAGCAGCAGGCGCTCTTTAGTCATTTCTCCCCCAGTTCGAACATCTA
CAGTCTCCAGTCCACTTACCTCACCTACTAGTCCCTCTACACTTTCCTCGAAGAGTAAGAGTGAATCTGTCTCAGCAACT
GAAGATCTGGCACCTGATGCAGCCCAGGGGGAAGACAATTCTGAGATCAAGGAGCTCTTAGAAGATGAGGAAATAGGGAA
GGAAGGATCTGAAGCAAGCTCCTCTGAGGAAGAAGAGCCTCTACTAACCTGCAACGGCCCCTCCCAGGCCCAGCCCTCTC
CTATCATTGAGAGTGCCAGGTCCCAGGAAGAAGTTCCCCCCAGCTCCCCTGCTCTATCACCAGGTGGAGCCCTAAGCCCT
TCAGGACACCCTTTATCATCTGCCGCAGAAGTAGTCCTCCGAACCCGCACCGCAGGTGACAAATCTGAACAATCAAAGAA
GAGAGCCTCTATCCAGAGGACCTCAGCACCCCCTAGTAGGCCTCCTCCACCCAGAGCCACTGCAAGCCCCAGGCCCTCCT
CAGGGAACATACCCTCCAGCCCTCCAGCCTCTGGAGGGGGTTCACCCACCAGCCCTAGGGCCTCCTTGGGGACTGGGACT
CCAAGTCCTAGGACCTCCCTAGAGGTCTCTCCTAATCCAGAACCACCAGAGAAGCCAGTAAGAACTCCTGAGGCCAAAGA
AAATGAAAACATCCACAATCAGAACCTCGAAGAACTTTGTACTTCCCCCACCTTAATGACATCTCACATTGCTTCAGAGC
CTGGAGAGGCAAAGAAGATGGAAGACAAGGAAAATGATAACAAGCTTGTCTCAGCTGACTCCTCGGAGGGCCAAGACCAG
CTTAAAGTCTCCACAGTACCAGACAAGAGCAACCTCACAGCACCTGAACCTCAAGAAGAGGTATCTACAAGTGAAAATGC
ACAACTC
ORF - retro_hsap_2952 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: |
87.53 % |
Parental protein coverage: |
70.54 % |
Number of stop codons detected: |
0 |
Number of frameshifts detected |
1 |
Retrocopy - Parental Gene Alignment:
Parental | ELLEELPILYNSRIGC-YVTIFQNISNLRDVFYREMSKLNHNLYEVMSKLEKQHSNKVFVVKGLSSSSRR |
| .LLEEL.ILYNS..G..YVTIFQNISNLRDVFYREMSKLNHNL.EVMSKLEKQHS.KVFVVK.LSSSSRR |
Retrocopy | KLLEELSILYNSHTGS<YVTIFQNISNLRDVFYREMSKLNHNLSEVMSKLEKQHSSKVFVVKRLSSSSRR |
|
Parental | SLVISPPVRTATVSSPLTSPTSPSTLSLKSESESVSATEDLAPDAAQGEDNSEIKELLEEEEIEKEGSEA |
| SLVISPPVRT.TVSSPLTSPTSPSTLS.KS.SESVSATEDLAPDAAQGEDNSEIKELLE.EEI.KEGSEA |
Retrocopy | SLVISPPVRTSTVSSPLTSPTSPSTLSSKSKSESVSATEDLAPDAAQGEDNSEIKELLEDEEIGKEGSEA |
|
Parental | SSSEEDEPLPACNGPAQAQPSPTTERAKSQEEVLPSSTTPSPGGALSPSGQPSSSATEVVLRTRTASEGS |
| SSSEE.EPL..CNGP.QAQPSP..E.A.SQEEV.PSS...SPGGALSPSG.P.SSA.EVVLRTRTA...S |
Retrocopy | SSSEEEEPLLTCNGPSQAQPSPIIESARSQEEVPPSSPALSPGGALSPSGHPLSSAAEVVLRTRTAGDKS |
|
Parental | EQPKKRASIQRTSAPPSRPPPPRATASPRPSSGNIPSSPTASGGGSPTSPRASLGTGTASPRTSLEVSPN |
| EQ.KKRASIQRTSAPPSRPPPPRATASPRPSSGNIPSSP.ASGGGSPTSPRASLGTGT.SPRTSLEVSPN |
Retrocopy | EQSKKRASIQRTSAPPSRPPPPRATASPRPSSGNIPSSPPASGGGSPTSPRASLGTGTPSPRTSLEVSPN |
|
Parental | PEPPEKPVRTPEAKENENIHNQNPEELCTSPTLMTSQVASEPGEAKKMEDKEKDNKLISANSSEGQDQLQ |
| PEPPEKPVRTPEAKENENIHNQN.EELCTSPTLMTS..ASEPGEAKKMEDKE.DNKL.SA.SSEGQDQL. |
Retrocopy | PEPPEKPVRTPEAKENENIHNQNLEELCTSPTLMTSHIASEPGEAKKMEDKENDNKLVSADSSEGQDQLK |
|
Parental | VSMVPENNNLTAPEPQEEVSTSENPQL |
| VS.VP...NLTAPEPQEEVSTSEN.QL |
Retrocopy | VSTVPDKSNLTAPEPQEEVSTSENAQL |
|
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 |
8 .81 RPM |
bodymap2_adrenal |
0 .02 RPM |
33 .84 RPM |
bodymap2_brain |
0 .00 RPM |
3 .05 RPM |
bodymap2_breast |
0 .00 RPM |
2 .76 RPM |
bodymap2_colon |
0 .00 RPM |
2 .32 RPM |
bodymap2_heart |
0 .00 RPM |
1 .83 RPM |
bodymap2_kidney |
0 .00 RPM |
2 .09 RPM |
bodymap2_liver |
0 .00 RPM |
4 .06 RPM |
bodymap2_lung |
0 .00 RPM |
22 .20 RPM |
bodymap2_lymph_node |
0 .00 RPM |
36 .77 RPM |
bodymap2_ovary |
0 .00 RPM |
3 .62 RPM |
bodymap2_prostate |
0 .00 RPM |
4 .24 RPM |
bodymap2_skeletal_muscle |
0 .00 RPM |
0 .60 RPM |
bodymap2_testis |
0 .00 RPM |
11 .97 RPM |
bodymap2_thyroid |
0 .00 RPM |
1 .75 RPM |
bodymap2_white_blood_cells |
0 .45 RPM |
321 .50 RPM |
RNA Polymerase II actvity near the 5' end of retro_hsap_2952 was not detected
No EST(s) were mapped for retro_hsap_2952 retrocopy.
No TSS is located nearby retro_hsap_2952 retrocopy 5' end.
retro_hsap_2952 was not experimentally validated.
Retrocopy orthology:
Retrocopy
retro_hsap_2952 has 2 orthologous retrocopies within
eutheria group
.
Parental genes homology:
Parental genes homology involve
6 parental genes, and
9 retrocopies.
Expression level across human populations :
Library |
Retrogene expression |
CEU_NA11831 |
0 .02 RPM |
CEU_NA11843 |
0 .03 RPM |
CEU_NA11930 |
0 .03 RPM |
CEU_NA12004 |
0 .04 RPM |
CEU_NA12400 |
0 .00 RPM |
CEU_NA12751 |
0 .05 RPM |
CEU_NA12760 |
0 .00 RPM |
CEU_NA12827 |
0 .05 RPM |
CEU_NA12872 |
0 .00 RPM |
CEU_NA12873 |
0 .06 RPM |
FIN_HG00183 |
0 .00 RPM |
FIN_HG00277 |
0 .00 RPM |
FIN_HG00315 |
0 .06 RPM |
FIN_HG00321 |
0 .00 RPM |
FIN_HG00328 |
0 .00 RPM |
FIN_HG00338 |
0 .00 RPM |
FIN_HG00349 |
0 .00 RPM |
FIN_HG00375 |
0 .00 RPM |
FIN_HG00377 |
0 .05 RPM |
FIN_HG00378 |
0 .00 RPM |
GBR_HG00099 |
0 .06 RPM |
GBR_HG00111 |
0 .06 RPM |
GBR_HG00114 |
0 .00 RPM |
GBR_HG00119 |
0 .00 RPM |
GBR_HG00131 |
0 .06 RPM |
GBR_HG00133 |
0 .02 RPM |
GBR_HG00134 |
0 .00 RPM |
GBR_HG00137 |
0 .03 RPM |
GBR_HG00142 |
0 .00 RPM |
GBR_HG00143 |
0 .00 RPM |
TSI_NA20512 |
0 .00 RPM |
TSI_NA20513 |
0 .00 RPM |
TSI_NA20518 |
0 .00 RPM |
TSI_NA20532 |
0 .03 RPM |
TSI_NA20538 |
0 .00 RPM |
TSI_NA20756 |
0 .00 RPM |
TSI_NA20765 |
0 .04 RPM |
TSI_NA20771 |
0 .00 RPM |
TSI_NA20786 |
0 .00 RPM |
TSI_NA20798 |
0 .00 RPM |
YRI_NA18870 |
0 .03 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 .02 RPM |
Indel association:
No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (
PubMed).