>retro_hsap_3716
TCCATAGGAATTCACAAGAAGGGCTCTGAGCTCCTGAAGGAGAAGCTGCACAAAGCTCACAAGGAGCTGCAGCTGAAGGG
CGAAGACTGTGAGCAGCTGTTCCTAGTGCAGGAGCAGCTGCACGGGAGCTGGAGGAGCTGATGACTAGCCTGTTTGAGGA
AGCCCACAAGATGGTGTGGGAAGCCAGCATACAGCAGGCAGTGTCAGAAAAGCAGCTGAATGCGGAGGCATGGGGAAAGA
TAGACATGCTGCAGGCAGAGGTGACAGCTTGAAGACACTGGTCATCATGTCCACACCAGCCTCTCCCAACTACAAGCTCC
ACCTGCACCTGCTGAGCCCCACTAAGGGTGGGCCCTGCAAGGCCCACTGCCAACCTAAGAGCACCAGCAGTGCCCTCTCC
TTGGCCTTGTGCCCCACTGTGAGACATGCCCTCACCTTGGACAAGGAGGTGGATGTGACACTATTGGCAGAGTTCCAAGC
CTGGAAGGAATTACCTACCTTGGACAAGACCTGTTCCTTGCTGCAAAGGGTGTAGTGGGAGGATATGGACCCCTGCCTGG
ACTTCACAGTGCAGAATCTCTTGCCACAGGTGTAGGCCTCTATGGGGGACACCACACTCACTATCAAGCCTGTGGCTCTG
CAGAAGCTGCCTATAGTGAGGGTAACTGTGGTCAATTGTGGCAGTGCCAATATATGTGTCTTGAGCAATTTGGCCCATAC
CTGCCACCACCACCACATCTGGCTTTGTGACTTTGCGAGCCACTACCACATCTCACTGTCTTCTCAGGCCAGGATCACTG
CAGTGTGCAACTTTTTCATCTATATCTGCTACATCCACAAGGCCTGGTGCGACAGGATTTGAAGCCAGTGTTCTGGGAGA
TCACAAAGCTGTGAAAAGAGATACAGCTGGCCAAACTC
ORF - retro_hsap_3716 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: |
64.54 % |
Parental protein coverage: |
80.63 % |
Number of stop codons detected: |
3 |
Number of frameshifts detected |
3 |
Retrocopy - Parental Gene Alignment:
Parental | SMEIREKGSEFLKEELHRAQKELKLKDEECERLSKVREQLE-QELEELTASLFEEAHKMVREANMKQAAS |
| S..I..KGSE.LKE.LH.A.KEL.LK.E.CE.L..V.EQL...ELEEL..SLFEEAHKMV.EA...QA.S |
Retrocopy | SIGIHKKGSELLKEKLHKAHKELQLKGEDCEQLFLVQEQLH<RELEELMTSLFEEAHKMVWEASIQQAVS |
|
Parental | EKQLK-EARGKIDMLQAEVTA-LKTLVITSTPASPNRELHPQLLSPTKAGPRKGHSRHKSTSSTLCPAVC |
| EKQL..EA.GKIDMLQAEVTA.LKTLVI.STPASPN..LH..LLSPTK.GP.K.H...KSTSS.L..A.C |
Retrocopy | EKQLNAEAWGKIDMLQAEVTA<LKTLVIMSTPASPNYKLHLHLLSPTKGGPCKAHCQPKSTSSALSLALC |
|
Parental | PAAGHTLTPDREGKEVDTILFAEFQAWRESPTLDKTCPFLERVYREDVGPCLDFTMQELSVLVRAAVEDN |
| P...H.LT.D...KEVD..L.AEFQAW.E.PTLDKTC..L.RV..ED..PCLDFT.Q.L...V.A...D. |
Retrocopy | PTVRHALTLD---KEVDVTLLAEFQAWKELPTLDKTCSLLQRV*WEDMDPCLDFTVQNLLPQV*ASMGDT |
|
Parental | TLTIEPVASQTLPTVKVAEVDCSSTNTCALSGLTRTC-RHRIRLGDSKSHYYISPSSRARITAVCNFFTY |
| TLTI.PVA.Q.LP.V.V..V.C.S.N.C.LS.L..TC..H.I.L.D..SHY.IS.SS.ARITAVCNFF.Y |
Retrocopy | TLTIKPVALQKLPIVRVTVVNCGSANICVLSNLAHTCHHHHIWLCDFASHYHISLSSQARITAVCNFFIY |
|
Parental | IRYIQ-QGLVRQDAEPMFWEIMRLRKEMSLAKL |
| I.YI..QGLVRQD..P.FWEI..L.KE..LAKL |
Retrocopy | ICYIH<QGLVRQDLKPVFWEITKL*KEIQLAKL |
|
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 .04 RPM |
22 .48 RPM |
bodymap2_adrenal |
0 .00 RPM |
27 .65 RPM |
bodymap2_brain |
0 .00 RPM |
2 .72 RPM |
bodymap2_breast |
0 .02 RPM |
10 .45 RPM |
bodymap2_colon |
0 .00 RPM |
17 .34 RPM |
bodymap2_heart |
0 .02 RPM |
5 .91 RPM |
bodymap2_kidney |
0 .04 RPM |
9 .35 RPM |
bodymap2_liver |
0 .00 RPM |
2 .60 RPM |
bodymap2_lung |
0 .00 RPM |
7 .19 RPM |
bodymap2_lymph_node |
0 .35 RPM |
21 .25 RPM |
bodymap2_ovary |
0 .00 RPM |
40 .81 RPM |
bodymap2_prostate |
0 .21 RPM |
15 .22 RPM |
bodymap2_skeletal_muscle |
0 .00 RPM |
3 .95 RPM |
bodymap2_testis |
0 .00 RPM |
45 .06 RPM |
bodymap2_thyroid |
0 .08 RPM |
7 .63 RPM |
bodymap2_white_blood_cells |
0 .00 RPM |
0 .00 RPM |
RNA Polymerase II actvity near the 5' end of retro_hsap_3716 was not detected
No EST(s) were mapped for retro_hsap_3716 retrocopy.
No TSS is located nearby retro_hsap_3716 retrocopy 5' end.
retro_hsap_3716 was not experimentally validated.
Retrocopy orthology:
Retrocopy
retro_hsap_3716 has 3 orthologous retrocopies within
eutheria group
.
Parental genes homology:
Parental genes homology involve
7 parental genes, and
7 retrocopies.
Expression level across human populations :
Library |
Retrogene expression |
CEU_NA11831 |
0 .09 RPM |
CEU_NA11843 |
0 .03 RPM |
CEU_NA11930 |
0 .00 RPM |
CEU_NA12004 |
0 .00 RPM |
CEU_NA12400 |
0 .04 RPM |
CEU_NA12751 |
0 .00 RPM |
CEU_NA12760 |
0 .00 RPM |
CEU_NA12827 |
0 .00 RPM |
CEU_NA12872 |
0 .03 RPM |
CEU_NA12873 |
0 .00 RPM |
FIN_HG00183 |
0 .00 RPM |
FIN_HG00277 |
0 .04 RPM |
FIN_HG00315 |
0 .03 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 .02 RPM |
GBR_HG00099 |
0 .03 RPM |
GBR_HG00111 |
0 .00 RPM |
GBR_HG00114 |
0 .00 RPM |
GBR_HG00119 |
0 .05 RPM |
GBR_HG00131 |
0 .00 RPM |
GBR_HG00133 |
0 .00 RPM |
GBR_HG00134 |
0 .02 RPM |
GBR_HG00137 |
0 .03 RPM |
GBR_HG00142 |
0 .00 RPM |
GBR_HG00143 |
0 .03 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 .03 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).