>retro_hsap_4062
AGCAGAATTCGAGAACTAAGCAAATTAGCTGAGACCACAATAAAGTCAAACAAGGCTTTTCGGAAGAATTTGAGACACTA
CAACAACAGGAGTGCATACTTCTCTACGGCCGAAAAGAGGGTAAAAGGCAAGAAAACAAAAACAAAAATAGATATAAAAA
TAACCTGCCCTTTGATCATACCAGGGTTGTCCTACACGATGGTGATCCCAACGAGCCTGTTTCAGATGACATCAATGCAA
ATATCATCATGCCCAAATTTGAAACCAAGTGTAACAATTCAAAGCCCAAGAAGAGTTACATTGCCACACAAGGCTGCCTG
CAAAACATGGTGAACGACTTTTGGCGGATGGTATTCCAAGAAAACTCCTGAGTGATTGTCATGACAACGAAAGAAGTGGA
GAGAGGATAGAGTAAATGTGTCAAATACTGGCCTGATGAGTATGCTCTAAAAGAATATGGCATCATGCGTGTTAGGAATA
TCAGAGAAAGCACCGCTCACAACTATATGCTAAGAGAACTTAAACTTTCAAAGGTTGGGCAAGGGAATATGGAGAGAATG
GTCTGGCAATACCACTTTTGGACCTGGCCGGACCACGGAGTGCCCATTGACCCCAGGGGTGTGCTGGACTTCCTGGAGGA
GGTGCACCATAAGCAGGAACGCATCATGCATGCAAGGCCAGTCGTGGTGCACGGCAGTGCTGGAATTGGCCGGACAGGGA
CATACGTTGTGATTGATATTCTGACTGACATCAACAGAGAGAAAGGTGTTGACTGCAACATTGACGTTCTCAAAACTATC
CAGATGGTGCAGTCTCAGAGGTCAGGGATGGTCCAGACAGAAACACAGTACCGATTTATCTATATGGCGGTCCAGCATTA
TACTGAAACACTACAGCGCAGGATTGAAGAAGAGCAGAAAAGCAAGAGGAAAGGTCATGAATATACAAATATTAAGTATT
CTCTAGCGGACCAGACGAGTGGAGATCAG
ORF - retro_hsap_4062 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: |
83.99 % |
Parental protein coverage: |
55.65 % |
Number of stop codons detected: |
2 |
Number of frameshifts detected |
1 |
Retrocopy - Parental Gene Alignment:
Parental | SRVRELSKLAETT-DKVKQGFWEEFETLQQQECKLLYSRKEGQRQENKNKNRYKNILPFDHTRVVLHDGD |
| SR.RELSKLAETT..KVKQGF.EEFETLQQQEC.LLY...................LPFDHTRVVLHDGD |
Retrocopy | SRIRELSKLAETT<NKVKQGFSEEFETLQQQECILLYGXXXXXXXXXXXXXXXXXXLPFDHTRVVLHDGD |
|
Parental | PNEPVSDYINANIIMPEFETKCNNSKPKKSYIATQGCLQNTVNDFWRMVFQENSRVIVMTTKEVERGKSK |
| PNEPVSD.INANIIMP.FETKCNNSKPKKSYIATQGCLQN.VNDFWRMVFQENS.VIVMTTKEVERG.SK |
Retrocopy | PNEPVSDDINANIIMPKFETKCNNSKPKKSYIATQGCLQNMVNDFWRMVFQENS*VIVMTTKEVERG*SK |
|
Parental | CVKYWPDEYALKEYGVMRVRNVKESAAHDYTLRELKLSKVGQGNTERTVWQYHFRTWPDHGVPSDPGGVL |
| CVKYWPDEYALKEYG.MRVRN..ES.AH.Y.LRELKLSKVGQGN.ER.VWQYHF.TWPDHGVP.DP.GVL |
Retrocopy | CVKYWPDEYALKEYGIMRVRNIRESTAHNYMLRELKLSKVGQGNMERMVWQYHFWTWPDHGVPIDPRGVL |
|
Parental | DFLEEVHHKQESIMDAGPVVVHCSAGIGRTGTFIVIDILIDIIREKGVDCDIDVPKTIQMVRSQRSGMVQ |
| DFLEEVHHKQE.IM.A.PVVVH.SAGIGRTGT..VIDIL.DI.REKGVDC.IDV.KTIQMV.SQRSGMVQ |
Retrocopy | DFLEEVHHKQERIMHARPVVVHGSAGIGRTGTYVVIDILTDINREKGVDCNIDVLKTIQMVQSQRSGMVQ |
|
Parental | TEAQYRFIYMAVQHYIETLQRRIEEEQKSKRKGHEYTNIKYSLADQTSGDQ |
| TE.QYRFIYMAVQHY.ETLQRRIEEEQKSKRKGHEYTNIKYSLADQTSGDQ |
Retrocopy | TETQYRFIYMAVQHYTETLQRRIEEEQKSKRKGHEYTNIKYSLADQTSGDQ |
|
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 |
263 .94 RPM |
bodymap2_adrenal |
0 .06 RPM |
132 .33 RPM |
bodymap2_brain |
0 .28 RPM |
394 .29 RPM |
bodymap2_breast |
0 .00 RPM |
407 .53 RPM |
bodymap2_colon |
0 .00 RPM |
244 .85 RPM |
bodymap2_heart |
0 .00 RPM |
230 .25 RPM |
bodymap2_kidney |
0 .15 RPM |
164 .18 RPM |
bodymap2_liver |
0 .00 RPM |
136 .31 RPM |
bodymap2_lung |
0 .11 RPM |
155 .10 RPM |
bodymap2_lymph_node |
0 .15 RPM |
127 .17 RPM |
bodymap2_ovary |
0 .00 RPM |
141 .82 RPM |
bodymap2_prostate |
0 .02 RPM |
171 .56 RPM |
bodymap2_skeletal_muscle |
0 .00 RPM |
276 .40 RPM |
bodymap2_testis |
0 .02 RPM |
163 .74 RPM |
bodymap2_thyroid |
0 .11 RPM |
231 .81 RPM |
bodymap2_white_blood_cells |
0 .47 RPM |
123 .01 RPM |
RNA Polymerase II actvity near the 5' end of retro_hsap_4062 was not detected
No EST(s) were mapped for retro_hsap_4062 retrocopy.
No TSS is located nearby retro_hsap_4062 retrocopy 5' end.
retro_hsap_4062 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_hsap_4062 has 0 orthologous retrocopies within eutheria group .
Parental genes homology:
Parental genes homology involve
7 parental genes, and
22 retrocopies.
Expression level across human populations :
Library |
Retrogene expression |
CEU_NA11831 |
0 .11 RPM |
CEU_NA11843 |
0 .09 RPM |
CEU_NA11930 |
0 .16 RPM |
CEU_NA12004 |
0 .00 RPM |
CEU_NA12400 |
0 .00 RPM |
CEU_NA12751 |
0 .15 RPM |
CEU_NA12760 |
0 .04 RPM |
CEU_NA12827 |
0 .09 RPM |
CEU_NA12872 |
0 .16 RPM |
CEU_NA12873 |
0 .13 RPM |
FIN_HG00183 |
0 .11 RPM |
FIN_HG00277 |
0 .15 RPM |
FIN_HG00315 |
0 .00 RPM |
FIN_HG00321 |
0 .06 RPM |
FIN_HG00328 |
0 .05 RPM |
FIN_HG00338 |
0 .04 RPM |
FIN_HG00349 |
0 .00 RPM |
FIN_HG00375 |
0 .05 RPM |
FIN_HG00377 |
0 .00 RPM |
FIN_HG00378 |
0 .08 RPM |
GBR_HG00099 |
0 .03 RPM |
GBR_HG00111 |
0 .06 RPM |
GBR_HG00114 |
0 .13 RPM |
GBR_HG00119 |
0 .12 RPM |
GBR_HG00131 |
0 .23 RPM |
GBR_HG00133 |
0 .10 RPM |
GBR_HG00134 |
0 .09 RPM |
GBR_HG00137 |
0 .00 RPM |
GBR_HG00142 |
0 .08 RPM |
GBR_HG00143 |
0 .13 RPM |
TSI_NA20512 |
0 .00 RPM |
TSI_NA20513 |
0 .07 RPM |
TSI_NA20518 |
0 .03 RPM |
TSI_NA20532 |
0 .14 RPM |
TSI_NA20538 |
0 .09 RPM |
TSI_NA20756 |
0 .23 RPM |
TSI_NA20765 |
0 .04 RPM |
TSI_NA20771 |
0 .03 RPM |
TSI_NA20786 |
0 .05 RPM |
TSI_NA20798 |
0 .06 RPM |
YRI_NA18870 |
0 .14 RPM |
YRI_NA18907 |
0 .03 RPM |
YRI_NA18916 |
0 .15 RPM |
YRI_NA19093 |
0 .10 RPM |
YRI_NA19099 |
0 .00 RPM |
YRI_NA19114 |
0 .03 RPM |
YRI_NA19118 |
0 .08 RPM |
YRI_NA19213 |
0 .07 RPM |
YRI_NA19214 |
0 .05 RPM |
YRI_NA19223 |
0 .06 RPM |
Indel association:
No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (
PubMed).