>retro_hsap_3973
ATGCGTCCCTCCTCCTCCCCACCTTGTGGCGGGCAGCAGCCCTCTAGCTTTGGCTCCGTGGACTGGCTCTCCCAAAGCAG
CTGCTCAGGGCCGACCCACACCCCCAGGCCTGCCGAGGTCTCCCTGGGGAGCCTCCCTGGCCCGGACCAGGCATCGGGCC
CCGAGGAGCCCCCTCAGGCCGTCAGCATCAAGGAGGCTAGGTCCTCAAATCTGCCTCCGCCAGAGAGGGCTATGGCTGGG
TTGAGGAAAGGGCCAAACGCCTGGCGGGCCCCACTGTGTCCACACAGCCTTCACCACGGAGCAGGTCCGTGGCTTGGAGG
GCATCTTCCAGCACCACCAGTACCTGGGCCCTCTGGAGTGGAAGAGGCTGGCCAGGGAAATGCAGCTGTCGGAGGTCCAG
ATAAAAACCTGGTTTCAAAATCGCCGCATGAAACACGAACGGCAAATGCAGGACTCCCAGCTGAACAGCCTCTTCTCGGA
GTCACTGCACGCACCCCTGGCTTTCCACTCACCGTCTTCTGGCCTTGCCAATGGCCTGCACCTGCTGTGCCCTTGGGCAC
CCCTGCCTGGGCCCCAGACTCTGATGCTGTCCCCTGGCTCCTTCTGGGGTCTCTGCAAGTGGAACAAGAGGCCCTGGCCT
CTGAGTGGGCCTGCTGCTGTGGGCAGCCTCTGGCGTACCACCCCCCAAAGCCCAGGAAGTGGCATGCATACGCTGGGACC
AGCCCTGTCCACGGGGCCCTGGGGCCTGGTGTGCTCTGCCGGAGACGGGA
ORF - retro_hsap_3973 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: |
78.54 % |
Parental protein coverage: |
98.84 % |
Number of stop codons detected: |
0 |
Number of frameshifts detected |
4 |
Retrocopy - Parental Gene Alignment:
Parental | MRLSSSPPRGPQQLSSFGSVDWLSQSSCSGPTHTPRPADFSLGSLPGPGQTSGAREPPQAVSIKEAAGSS |
| MR.SSSPP.G.QQ.SSFGSVDWLSQSSCSGPTHTPRPA..SLGSLPGP.Q.SG..EPPQAVSIKEA..SS |
Retrocopy | MRPSSSPPCGGQQPSSFGSVDWLSQSSCSGPTHTPRPAEVSLGSLPGPDQASGPEEPPQAVSIKEAR-SS |
|
Parental | NLPAPERTMAGLSKEPNTLRAPR-VRTAFTMEQVRTLEGVFQHHQYLSPLERKRLAREMQLSEVQIKTWF |
| NLP.PER.MAGL.K.PN..RAP..V.TAFT.EQVR.LEG.FQHHQYL.PLE.KRLAREMQLSEVQIKTWF |
Retrocopy | NLPPPERAMAGLRKGPNAWRAPL>VHTAFTTEQVRGLEGIFQHHQYLGPLEWKRLAREMQLSEVQIKTWF |
|
Parental | QNRRMKHKRQMQDPQLHSPFSGSLHAPPAFYSTSSGLANGLQLLCPWAPLSGPQALMLPPGSFWGLC-QV |
| QNRRMKH.RQMQD.QL.S.FS.SLHAP.AF.S.SSGLANGL.LLCPWAPL.GPQ.LML.PGSFWGLC.QV |
Retrocopy | QNRRMKHERQMQDSQLNSLFSESLHAPLAFHSPSSGLANGLHLLCPWAPLPGPQTLMLSPGSFWGLC<QV |
|
Parental | AQEALASAGASCCGQPLASH-PPTPGRP--SLGPALSTGPRGL-CAMPQTG |
| .QEALAS..A.CCGQPLA.H.P..PG.....LGPALSTGP.GL.CA.P.TG |
Retrocopy | EQEALASEWACCCGQPLAYH>PQSPGSGMHTLGPALSTGPWGL>CALPETG |
|
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 |
0 .44 RPM |
bodymap2_adrenal |
0 .04 RPM |
0 .53 RPM |
bodymap2_brain |
0 .05 RPM |
0 .28 RPM |
bodymap2_breast |
0 .00 RPM |
0 .53 RPM |
bodymap2_colon |
0 .00 RPM |
0 .10 RPM |
bodymap2_heart |
0 .00 RPM |
0 .59 RPM |
bodymap2_kidney |
0 .00 RPM |
0 .45 RPM |
bodymap2_liver |
0 .00 RPM |
0 .15 RPM |
bodymap2_lung |
0 .04 RPM |
1 .23 RPM |
bodymap2_lymph_node |
0 .00 RPM |
0 .93 RPM |
bodymap2_ovary |
0 .00 RPM |
2 .83 RPM |
bodymap2_prostate |
0 .00 RPM |
0 .40 RPM |
bodymap2_skeletal_muscle |
0 .00 RPM |
0 .09 RPM |
bodymap2_testis |
0 .02 RPM |
0 .60 RPM |
bodymap2_thyroid |
0 .02 RPM |
0 .30 RPM |
bodymap2_white_blood_cells |
0 .00 RPM |
8 .94 RPM |
RNA Polymerase II actvity near the 5' end of retro_hsap_3973 was not detected
No EST(s) were mapped for retro_hsap_3973 retrocopy.
No TSS is located nearby retro_hsap_3973 retrocopy 5' end.
retro_hsap_3973 was not experimentally validated.
Retrocopy orthology:
Retrocopy
retro_hsap_3973 has 2 orthologous retrocopies within
eutheria group
.
Parental genes homology:
Parental genes homology involve
5 parental genes, and
18 retrocopies.
Expression level across human populations :
Library |
Retrogene expression |
CEU_NA11831 |
0 .00 RPM |
CEU_NA11843 |
0 .03 RPM |
CEU_NA11930 |
0 .00 RPM |
CEU_NA12004 |
0 .00 RPM |
CEU_NA12400 |
0 .00 RPM |
CEU_NA12751 |
0 .00 RPM |
CEU_NA12760 |
0 .04 RPM |
CEU_NA12827 |
0 .00 RPM |
CEU_NA12872 |
0 .00 RPM |
CEU_NA12873 |
0 .00 RPM |
FIN_HG00183 |
0 .05 RPM |
FIN_HG00277 |
0 .04 RPM |
FIN_HG00315 |
0 .00 RPM |
FIN_HG00321 |
0 .00 RPM |
FIN_HG00328 |
0 .05 RPM |
FIN_HG00338 |
0 .00 RPM |
FIN_HG00349 |
0 .00 RPM |
FIN_HG00375 |
0 .02 RPM |
FIN_HG00377 |
0 .03 RPM |
FIN_HG00378 |
0 .02 RPM |
GBR_HG00099 |
0 .00 RPM |
GBR_HG00111 |
0 .02 RPM |
GBR_HG00114 |
0 .05 RPM |
GBR_HG00119 |
0 .02 RPM |
GBR_HG00131 |
0 .09 RPM |
GBR_HG00133 |
0 .00 RPM |
GBR_HG00134 |
0 .00 RPM |
GBR_HG00137 |
0 .03 RPM |
GBR_HG00142 |
0 .08 RPM |
GBR_HG00143 |
0 .00 RPM |
TSI_NA20512 |
0 .00 RPM |
TSI_NA20513 |
0 .02 RPM |
TSI_NA20518 |
0 .03 RPM |
TSI_NA20532 |
0 .00 RPM |
TSI_NA20538 |
0 .05 RPM |
TSI_NA20756 |
0 .00 RPM |
TSI_NA20765 |
0 .06 RPM |
TSI_NA20771 |
0 .00 RPM |
TSI_NA20786 |
0 .03 RPM |
TSI_NA20798 |
0 .00 RPM |
YRI_NA18870 |
0 .00 RPM |
YRI_NA18907 |
0 .00 RPM |
YRI_NA18916 |
0 .02 RPM |
YRI_NA19093 |
0 .03 RPM |
YRI_NA19099 |
0 .00 RPM |
YRI_NA19114 |
0 .03 RPM |
YRI_NA19118 |
0 .02 RPM |
YRI_NA19213 |
0 .05 RPM |
YRI_NA19214 |
0 .00 RPM |
YRI_NA19223 |
0 .06 RPM |
Indel association:
No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (
PubMed).