>retro_hsap_3704
AGAACCTGCAGTGTAATGACACTAGTTAAGTCCAGGCCTTTTCGGGAAAAGCAAGGGAAGATACTGCCGAAAGGTCGCAG
GCTCATTGCAGACGATCTGAAGGCTGGAGCTGTGCTGAAAGTTTTCTTCTCTAGCCATCTATAATACATAAAGAAGCTGC
TCATCGATAAGCTGAAGGGTGTCAGCTTCATTAAGATGAAATTCGAGGACATCAAGGATTGGTCCAACCTAGTAATGCCA
CGAGAATAATGGGGATTTTTGCCAAACCTGACCATGCTAACATGACATATCCAAAGACTCAGCTTTAGCACTCACTGCCT
TTATTATTGATTTGTGACAATCTCTGCGACCCTGGGAACCTGGGGACAATTCTGAGATCTCCAGCTGGGGAAGGCTGCAG
CAAAGTGTTACTCACTTTGAAAGGATGTGTGGATGCCTGGGAGCCCAAAGTGCTACAGGCGGGTATGGGTGCACATTTCC
AAGTGCCCATTATCGATAATCTGAAAACGAAACAGTGCCAAATTACCTGCCCCCTGACACCCAGGTCTGTGTGGCTGACA
ACTGAAGCCTTTATGCTCAGGCTCAGATGTCTAATAAAGCCAGTGACCATGGCTGGGTGTAGGATTGGCGATTCCTGAAG
TTTCACAAGTATGAAGAAAAGCAAGGTCTAGAAACTGGAGCCAGTAAAGGTTTGCTGCCTGTTATTGAGGTTCAGAGTTA
TGACTTGGACTGGACAGAGGCACCAGCAGCTGTAATGGTTGGTGGCGTGACCTACGGCATGATCCTGGAATCTCTGTAGT
TTGCCGAGAGCCCTGCGGGCAAGAGGCTGCTGATCCCTGTTGCACCTGGAGTGGACAGCCTCAACTCAGCCATGGCTGCA
CGCATCCTGTTTTTTGAAGGGAAAAGACAACTGCGGGTGAGGGCGGAACACTTGAGCAGGGACAGGAGTTACCAC
ORF - retro_hsap_3704 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: |
78.5 % |
Parental protein coverage: |
75.71 % |
Number of stop codons detected: |
5 |
Number of frameshifts detected |
2 |
Retrocopy - Parental Gene Alignment:
Parental | RLSSVMTIVKSRPFREKQGKILLEGRRLISDALKAGAVPKMFFFSRLEYLKELPVDKLKGVSLIKVKFED |
| R..SVMT.VKSRPFREKQGKIL..GRRLI.D.LKAGAV.K.FF.S.L.Y.K.L..DKLKGVS.IK.KFED |
Retrocopy | RTCSVMTLVKSRPFREKQGKILPKGRRLIADDLKAGAVLKVFFSSHL*YIKKLLIDKLKGVSFIKMKFED |
|
Parental | IKDWSDLVTPQG-IMGIFAKPDHVKMTYPKTQLQHSLPLLLICDNLRDPGNLGTILRSAAGAGCSKVLLT |
| IKDWS.LV.P...IMGIFAKPDH..MTYPKTQL.HSLPLLLICDNL.DPGNLGTILRS.AG.GCSKVLLT |
Retrocopy | IKDWSNLVMPRE<IMGIFAKPDHANMTYPKTQL*HSLPLLLICDNLCDPGNLGTILRSPAGEGCSKVLLT |
|
Parental | -KGCVDAWEPKVLRAGMGAHFRMPIINNL-EWETVPNYLPPDTRVYVADNCGLYAQAEMSNKASDHGWVC |
| .KGCVDAWEPKVL.AGMGAHF..PII.NL.E.ETVPNYLPPDT.V.VADN..LYAQA.MSNKASDHGWV. |
Retrocopy | LKGCVDAWEPKVLQAGMGAHFQVPIIDNL<ENETVPNYLPPDTQVCVADN*SLYAQAQMSNKASDHGWV* |
|
Parental | DQRVMKFHKYEEEEDVETGASQDWLPHVEVQSYDSDWTEAPAAVVIGGETYGVSLESLQLAESTGGKRLL |
| D.R..KFHKYEE....ETGAS...LP..EVQSYD.DWTEAPAAV..GG.TYG..LESL..AES..GKRLL |
Retrocopy | DWRFLKFHKYEEKQGLETGASKGLLPVIEVQSYDLDWTEAPAAVMVGGVTYGMILESL*FAESPAGKRLL |
|
Parental | IPVVPGVDSLNSAMAASILLFEGKRQLRGRAEDLSRDRSYH |
| IPV.PGVDSLNSAMAA.IL.FEGKRQLR.RAE.LSRDRSYH |
Retrocopy | IPVAPGVDSLNSAMAARILFFEGKRQLRVRAEHLSRDRSYH |
|
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 |
6 .82 RPM |
bodymap2_adrenal |
0 .00 RPM |
11 .03 RPM |
bodymap2_brain |
0 .00 RPM |
5 .84 RPM |
bodymap2_breast |
0 .00 RPM |
10 .21 RPM |
bodymap2_colon |
0 .00 RPM |
7 .68 RPM |
bodymap2_heart |
0 .00 RPM |
9 .80 RPM |
bodymap2_kidney |
0 .00 RPM |
9 .78 RPM |
bodymap2_liver |
0 .00 RPM |
11 .41 RPM |
bodymap2_lung |
0 .00 RPM |
4 .91 RPM |
bodymap2_lymph_node |
0 .00 RPM |
6 .94 RPM |
bodymap2_ovary |
0 .00 RPM |
9 .10 RPM |
bodymap2_prostate |
0 .00 RPM |
11 .08 RPM |
bodymap2_skeletal_muscle |
0 .00 RPM |
12 .09 RPM |
bodymap2_testis |
0 .00 RPM |
21 .53 RPM |
bodymap2_thyroid |
0 .00 RPM |
14 .93 RPM |
bodymap2_white_blood_cells |
0 .00 RPM |
8 .23 RPM |
RNA Polymerase II actvity near the 5' end of retro_hsap_3704 was not detected
No EST(s) were mapped for retro_hsap_3704 retrocopy.
No TSS is located nearby retro_hsap_3704 retrocopy 5' end.
retro_hsap_3704 was not experimentally validated.
Retrocopy orthology:
Retrocopy
retro_hsap_3704 has 4 orthologous retrocopies within
eutheria group
.
Parental genes homology:
Parental genes homology involve
6 parental genes, and
6 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 .03 RPM |
FIN_HG00183 |
0 .00 RPM |
FIN_HG00277 |
0 .00 RPM |
FIN_HG00315 |
0 .00 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 .00 RPM |
FIN_HG00378 |
0 .00 RPM |
GBR_HG00099 |
0 .00 RPM |
GBR_HG00111 |
0 .00 RPM |
GBR_HG00114 |
0 .00 RPM |
GBR_HG00119 |
0 .00 RPM |
GBR_HG00131 |
0 .00 RPM |
GBR_HG00133 |
0 .02 RPM |
GBR_HG00134 |
0 .00 RPM |
GBR_HG00137 |
0 .00 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 .00 RPM |
TSI_NA20538 |
0 .00 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 .00 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).