>retro_hsap_1742
CTTCAAAGAGATGGAGATGTCATCAGCAAGGCGGTGATGGAAATGCTGGCAAGGACCATCAAGTACCTGGAGCCCAACCC
AGCCTCACAGGCTAAGCTGACCATGCTCAACACAGTGTGAAAGATCCAGGGCCAGGTGAAGAACCCCGGCTACCCGCAGT
CGGAGGGGCTCCTGAGCGAGTGCCTGATCCGCCACCAGAAGGAGCTGGGCAACGAGTCCAACTTCAGTGATGCACTGCTG
GATGCCGGCGAGTCCATGAAGCACCTGGCAGAGGTGAAGGACTCCCTGGACATAGAGGTCAAGCAGAACTTCATTGACCT
CCTCCAGAACCTGTGTGAGAAAGACCTGAAGGGGATCCAGCACCACCTGCAGAAGCTAGAGGGCCGCCGCCTGGACTTTG
ACTAAAAGAAGCGGCAGGGCAAGATCCCCGATGAGGAGCTGCGCCAGGCGCTGGAGAAGTTTGAGGACTCCAAGGAGGTA
GCAGAAACCAGCATGCACAACCTCCTGGAGACCGACATTGAGCAGATGAGTCAACTCCGGGCCCTGGCGGAGGCGCAGCT
GAACGACCACTGGCAGGCCATGCAGATCCTGGACGAGCTGGCAGAGAAGCTCAAGCGCAGGATGCGGGAAGCTTCCTCAC
GCCCCAAGCGGGAGTATAAGCCCAAGTTCTGGGAGCCCTTTGACCTCGGAGAGCCTGAGCAGTCCAACGGGGGCTTCCCC
TGCACCACAGTCCCCAAGATCGCAGCTTCATCCCCTTTCCAATCTTCCAACAAGTCCATCTGTACTCCTAGCAGGAGCAT
GCCGCCCCTAGACCAGCCAAGCTGCAAGGTGCTGTATGACTTCCAGCCTGAGAACCATGGGGAGCTGGGCTTCCATGAGG
GCGACGTCTTCACGCTCATCAACCAGATCAACGAGAACTGGTACCAGGGCATGCTGGACGGCCAGTTGGGCTTCTTCCTG
CTCAGCTACATGGACGTGCTCATGCCTCTGCCC
ORF - retro_hsap_1742 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: |
84.04 % |
Parental protein coverage: |
90.22 % |
Number of stop codons detected: |
2 |
Number of frameshifts detected |
0 |
Retrocopy - Parental Gene Alignment:
Parental | MEKKVDVTSKAVTEVLARTIEYLQPNPASRAKLTMLNTVSKIRGQVKNPGYPQSEGLLGECMIRHGKELG |
| .....DV.SKAV.E.LARTI.YL.PNPAS.AKLTMLNTV.KI.GQVKNPGYPQSEGLL.EC.IRH.KELG |
Retrocopy | LQRDGDVISKAVMEMLARTIKYLEPNPASQAKLTMLNTV*KIQGQVKNPGYPQSEGLLSECLIRHQKELG |
|
Parental | GESNFGDALLDAGESMKRLAEVKDSLDIEVKQNFIDPLQNLCEKDLKEIQHHLKKLEGRRLDFDYKKKRQ |
| .ESNF.DALLDAGESMK.LAEVKDSLDIEVKQNFID.LQNLCEKDLK.IQHHL.KLEGRRLDFD.KK.RQ |
Retrocopy | NESNFSDALLDAGESMKHLAEVKDSLDIEVKQNFIDLLQNLCEKDLKGIQHHLQKLEGRRLDFD*KK-RQ |
|
Parental | GKIPDEELRQALEKFEESKEVAETSMHNLLETDIEQVSQLSALVDAQLDYHRQAVQILDELAEKLKRRMR |
| GKIPDEELRQALEKFE.SKEVAETSMHNLLETDIEQ.SQL.AL..AQL..H.QA.QILDELAEKLKRRMR |
Retrocopy | GKIPDEELRQALEKFEDSKEVAETSMHNLLETDIEQMSQLRALAEAQLNDHWQAMQILDELAEKLKRRMR |
|
Parental | EASSRPKREYKPKPREPFDLGEPEQSNGGFPCTTAPKIAASSSFRSSDKPIRTPSRSMPPLDQPSCKALY |
| EASSRPKREYKPK..EPFDLGEPEQSNGGFPCTT.PKIAASS.F.SS.K.I.TPSRSMPPLDQPSCK.LY |
Retrocopy | EASSRPKREYKPKFWEPFDLGEPEQSNGGFPCTTVPKIAASSPFQSSNKSICTPSRSMPPLDQPSCKVLY |
|
Parental | DFEPENDGELGFHEGDVITLTNQIDENWYEGMLDGQSGFFPLSYVEVLVPLP |
| DF.PEN.GELGFHEGDV.TL.NQI.ENWY.GMLDGQ.GFF.LSY..VL.PLP |
Retrocopy | DFQPENHGELGFHEGDVFTLINQINENWYQGMLDGQLGFFLLSYMDVLMPLP |
|
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 .10 RPM |
61 .30 RPM |
bodymap2_adrenal |
0 .47 RPM |
44 .54 RPM |
bodymap2_brain |
0 .14 RPM |
14 .81 RPM |
bodymap2_breast |
0 .04 RPM |
32 .30 RPM |
bodymap2_colon |
0 .14 RPM |
39 .72 RPM |
bodymap2_heart |
0 .02 RPM |
7 .38 RPM |
bodymap2_kidney |
0 .15 RPM |
19 .61 RPM |
bodymap2_liver |
0 .08 RPM |
12 .63 RPM |
bodymap2_lung |
0 .04 RPM |
33 .98 RPM |
bodymap2_lymph_node |
0 .15 RPM |
28 .95 RPM |
bodymap2_ovary |
0 .31 RPM |
59 .89 RPM |
bodymap2_prostate |
0 .10 RPM |
36 .20 RPM |
bodymap2_skeletal_muscle |
0 .00 RPM |
12 .70 RPM |
bodymap2_testis |
0 .30 RPM |
41 .36 RPM |
bodymap2_thyroid |
0 .32 RPM |
31 .96 RPM |
bodymap2_white_blood_cells |
0 .04 RPM |
20 .04 RPM |
RNA Polymerase II actvity near the 5' end of retro_hsap_1742 was not detected
1 EST(s) were mapped to retro_hsap_1742 retrocopy
EST ID |
Start |
End |
Identity |
Match |
Mis-match |
Score |
CV361858 |
28951833 |
28952185 |
99.4 |
162 |
1 |
158 |
No TSS is located nearby retro_hsap_1742 retrocopy 5' end.
retro_hsap_1742 was not experimentally validated.
Retrocopy orthology:
Retrocopy
retro_hsap_1742 has 1 orthologous retrocopies within
eutheria group
.
Parental genes homology:
Parental genes homology involve
6 parental genes, and
16 retrocopies.
Expression level across human populations :
Library |
Retrogene expression |
CEU_NA11831 |
0 .06 RPM |
CEU_NA11843 |
0 .17 RPM |
CEU_NA11930 |
0 .36 RPM |
CEU_NA12004 |
0 .04 RPM |
CEU_NA12400 |
0 .18 RPM |
CEU_NA12751 |
0 .27 RPM |
CEU_NA12760 |
0 .22 RPM |
CEU_NA12827 |
0 .05 RPM |
CEU_NA12872 |
0 .27 RPM |
CEU_NA12873 |
0 .22 RPM |
FIN_HG00183 |
0 .36 RPM |
FIN_HG00277 |
0 .37 RPM |
FIN_HG00315 |
0 .06 RPM |
FIN_HG00321 |
0 .15 RPM |
FIN_HG00328 |
0 .26 RPM |
FIN_HG00338 |
0 .06 RPM |
FIN_HG00349 |
0 .11 RPM |
FIN_HG00375 |
0 .15 RPM |
FIN_HG00377 |
0 .10 RPM |
FIN_HG00378 |
0 .15 RPM |
GBR_HG00099 |
0 .09 RPM |
GBR_HG00111 |
0 .11 RPM |
GBR_HG00114 |
0 .26 RPM |
GBR_HG00119 |
0 .14 RPM |
GBR_HG00131 |
0 .20 RPM |
GBR_HG00133 |
0 .19 RPM |
GBR_HG00134 |
0 .61 RPM |
GBR_HG00137 |
0 .14 RPM |
GBR_HG00142 |
0 .22 RPM |
GBR_HG00143 |
0 .10 RPM |
TSI_NA20512 |
0 .00 RPM |
TSI_NA20513 |
0 .17 RPM |
TSI_NA20518 |
0 .17 RPM |
TSI_NA20532 |
0 .41 RPM |
TSI_NA20538 |
0 .32 RPM |
TSI_NA20756 |
0 .09 RPM |
TSI_NA20765 |
0 .52 RPM |
TSI_NA20771 |
0 .09 RPM |
TSI_NA20786 |
0 .05 RPM |
TSI_NA20798 |
0 .09 RPM |
YRI_NA18870 |
0 .47 RPM |
YRI_NA18907 |
0 .24 RPM |
YRI_NA18916 |
0 .32 RPM |
YRI_NA19093 |
0 .18 RPM |
YRI_NA19099 |
0 .19 RPM |
YRI_NA19114 |
0 .10 RPM |
YRI_NA19118 |
0 .27 RPM |
YRI_NA19213 |
0 .22 RPM |
YRI_NA19214 |
0 .10 RPM |
YRI_NA19223 |
0 .36 RPM |
Indel association:
No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (
PubMed).