>retro_hsap_1096
CAGCCTCCCGGGCATGCAGGTCCATGATATTCAAAGAACATTTTATGAAGAATACATCCTGTGAAAGATAAAGCTGGTCA
AAAGTGCAAGCCTACCAATGTGTTTGATTTTCCTAATAATTCTGCCGTCTCAAGAATTGGCAGGCTTGGTGAAAATGAGA
AAGATGAAGAACCTTATGAAACCTTTGATCCTCCTTTACACAGCTCATCTATGTATGCCAATGAAGAATTCTCCAAATAT
TGTGGATTATCTACCACTTCAACTCCTGCAGGAAAAGAAGCAAAAAGAAGCTCGAGCACTTCTGAAAATGAAGGAAGTGA
AAACGAATCTGCAAAAATGAGTGCAAAAAGCCAGGAAGAAAACTCAAACTCAGCGATGAGTCTGAAAGCACTGAAGAAAG
TGATGTGAGAAGAAAAGTTAAGTCAGTGGAGAAAATAAAGACCCAACAACACGAGGCTATTCCAACTACAGCATCTTCAG
CCCTTTCAGAGAAACCAGCCGACTCAGTCACTTCCAAAACCATAGGACCCATTAATGCCCAGCCATCTGTTGAAAAAGAC
ACACTGACAACAGAAAGTCAAGCAAAACCCAGAAAAAAGGGAATATATCTTATGGCAAAAGGAAGAAATCAAGAAGTGAA
GCAATAGACTCAGATATTTCCAACATTGTGCATATTTGGTGTCTGGAAGGAAGGAAAACCAACGACATCATGGAATTGAA
TATTGTTTTGCCTGCATTTGAGAAAAACCTCGTCCAGTATAAACATTGAATAGAATCTAAAATTTGTAAGAAACACATCA
ATAAATTTTATTGTACTAGTAAAGAAGAACTCAACAAAATGCTTAAAAAGTCCAGATATTGAAAAATCTGAAAAAGAAGA
ATGCTAAGGTAATTTCAGATATCAAAAAGAAATGACAGCGTTTGACTGAAGTCCAGGATGAGCTGCTTTGGTTAGAGCCA
CCAACTGAAACAACTACAAACAAAATATTATGAACTTAAGGAGAGAACAGTCTTCCCTTAGGAATGCAGCTATTTCTTAT
CTAATTCAAAACAACTCCATCGGAAGTATTCAGATGTTCAGGAGAAAGAACCAAACGTAAAGGAAACATAAGATTCATCC
AGCCTTCCAGGTGTTATTTAAAGTAGGAACACTTTTGGGAGCTGAAAATCTTCTGTAAAATATCAGCCATCAATGAGAGA
AGCTCCTCCACCAG
ORF - retro_hsap_1096 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: |
69.16 % |
Parental protein coverage: |
97.61 % |
Number of stop codons detected: |
8 |
Number of frameshifts detected |
7 |
Retrocopy - Parental Gene Alignment:
Parental | RPHRSEGARRSKNTLERTHSMKDKAGQKCKPIDVFDFPDNSDVSSIGRLGENEKDEETYETFDPPLHSTA |
| .P....G...SKN.L.R.H..KDKAGQKCKP..VFDFP.NS.VS.IGRLGENEKDEE.YETFDPPLHS.. |
Retrocopy | QPPGHAGP*YSKNIL*RIHPVKDKAGQKCKPTNVFDFPNNSAVSRIGRLGENEKDEEPYETFDPPLHSSS |
|
Parental | IYADEEEFSKHCGLSLSSTPPGKEAKRSSDTSGNEASEIESVKISAK-KPGRKLRPISDDSESIEESDTR |
| .YA.EE.FSK.CGLS..STP.GKEAKRSS.TS.NE.SE.ES.K.SAK.KPGRKL...SD.SES.EESD.R |
Retrocopy | MYANEE-FSKYCGLSTTSTPAGKEAKRSSSTSENEGSENESAKMSAK<KPGRKLK-LSDESESTEESDVR |
|
Parental | RKVKSAEKISTQRHEVIRTTASSELSEKPAESVTSKKTGPLSAQPSVEKENLAIESQ-SKTQKKGKISHD |
| RKVKS.EKI.TQ.HE.I.TTASS.LSEKPA.SVTSK..GP..AQPSVEK..L..ESQ.SKTQKKG.IS.. |
Retrocopy | RKVKSVEKIKTQQHEAIPTTASSALSEKPADSVTSKTIGPINAQPSVEKDTLTTESQ<SKTQKKGNISYG |
|
Parental | KRKKSRSKAIGSDTSDIVHIWCPEGMKTSDIKELNIVLPEFEKTHLEHQQRIESKVCKAAIATFYVNVKE |
| KRKKSRS.AI.SD.S.IVHIWC.EG.KT.DI.ELNIVLP.FEK........IESK.CK..I..FY...KE |
Retrocopy | KRKKSRSEAIDSDISNIVHIWCLEGRKTNDIMELNIVLPAFEKNLVQYKH*IESKICKKHINKFYCTSKE |
|
Parental | QFIKMLKES-QMLTNLKRKNAKMISDIEKKRQRMIEVQDELLRLEP-QLKQLQTKYDELKER-KSSLRNA |
| ...KMLK.S.Q.L.NLK.KNAK.ISDI.KK.QR..EVQDELL.LEP.QLKQLQTKY.ELKER..SSLRNA |
Retrocopy | ELNKMLKKS<QILKNLKKKNAKVISDIKKK*QRLTEVQDELLWLEP>QLKQLQTKYYELKER>QSSLRNA |
|
Parental | A-YFLSNLKQLYQDYSDVQAQEPNVKETYDSSSLPALLFKARTLLGA-ESHLRNINHQLEKLLDQ |
| A.YFLSN.KQL...YSDVQ..EPNVKET.DSSSLP......R...G..E..L.NI.HQ.EKLL.Q |
Retrocopy | A<YFLSNSKQLHRKYSDVQEKEPNVKET*DSSSLPGVI-*SRNTFGS>ENLL*NISHQ*EKLLHQ |
|
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 .06 RPM |
1 .37 RPM |
bodymap2_adrenal |
0 .10 RPM |
2 .70 RPM |
bodymap2_brain |
0 .14 RPM |
0 .54 RPM |
bodymap2_breast |
0 .00 RPM |
2 .86 RPM |
bodymap2_colon |
0 .00 RPM |
1 .68 RPM |
bodymap2_heart |
0 .00 RPM |
1 .66 RPM |
bodymap2_kidney |
0 .06 RPM |
1 .26 RPM |
bodymap2_liver |
0 .04 RPM |
0 .76 RPM |
bodymap2_lung |
0 .07 RPM |
1 .11 RPM |
bodymap2_lymph_node |
0 .26 RPM |
2 .27 RPM |
bodymap2_ovary |
0 .00 RPM |
1 .56 RPM |
bodymap2_prostate |
0 .00 RPM |
2 .36 RPM |
bodymap2_skeletal_muscle |
0 .00 RPM |
0 .25 RPM |
bodymap2_testis |
0 .02 RPM |
136 .72 RPM |
bodymap2_thyroid |
0 .00 RPM |
2 .37 RPM |
bodymap2_white_blood_cells |
0 .24 RPM |
2 .46 RPM |
RNA Polymerase II actvity near the 5' end of retro_hsap_1096 was not detected
No EST(s) were mapped for retro_hsap_1096 retrocopy.
No TSS is located nearby retro_hsap_1096 retrocopy 5' end.
retro_hsap_1096 was not experimentally validated.
Retrocopy orthology:
Retrocopy
retro_hsap_1096 has 3 orthologous retrocopies within
eutheria group
.
Parental genes homology:
Parental genes homology involve
8 parental genes, and
8 retrocopies.
Expression level across human populations :
Library |
Retrogene expression |
CEU_NA11831 |
0 .71 RPM |
CEU_NA11843 |
0 .23 RPM |
CEU_NA11930 |
0 .81 RPM |
CEU_NA12004 |
0 .08 RPM |
CEU_NA12400 |
0 .14 RPM |
CEU_NA12751 |
0 .53 RPM |
CEU_NA12760 |
0 .18 RPM |
CEU_NA12827 |
0 .38 RPM |
CEU_NA12872 |
0 .71 RPM |
CEU_NA12873 |
0 .64 RPM |
FIN_HG00183 |
0 .36 RPM |
FIN_HG00277 |
0 .55 RPM |
FIN_HG00315 |
0 .25 RPM |
FIN_HG00321 |
0 .76 RPM |
FIN_HG00328 |
0 .54 RPM |
FIN_HG00338 |
0 .13 RPM |
FIN_HG00349 |
0 .06 RPM |
FIN_HG00375 |
0 .42 RPM |
FIN_HG00377 |
0 .08 RPM |
FIN_HG00378 |
0 .08 RPM |
GBR_HG00099 |
0 .29 RPM |
GBR_HG00111 |
0 .17 RPM |
GBR_HG00114 |
0 .45 RPM |
GBR_HG00119 |
0 .45 RPM |
GBR_HG00131 |
0 .60 RPM |
GBR_HG00133 |
0 .53 RPM |
GBR_HG00134 |
0 .74 RPM |
GBR_HG00137 |
0 .41 RPM |
GBR_HG00142 |
0 .64 RPM |
GBR_HG00143 |
0 .26 RPM |
TSI_NA20512 |
0 .00 RPM |
TSI_NA20513 |
0 .17 RPM |
TSI_NA20518 |
0 .25 RPM |
TSI_NA20532 |
0 .37 RPM |
TSI_NA20538 |
0 .28 RPM |
TSI_NA20756 |
0 .00 RPM |
TSI_NA20765 |
0 .87 RPM |
TSI_NA20771 |
0 .11 RPM |
TSI_NA20786 |
0 .10 RPM |
TSI_NA20798 |
0 .22 RPM |
YRI_NA18870 |
0 .68 RPM |
YRI_NA18907 |
0 .31 RPM |
YRI_NA18916 |
0 .76 RPM |
YRI_NA19093 |
0 .26 RPM |
YRI_NA19099 |
0 .32 RPM |
YRI_NA19114 |
0 .24 RPM |
YRI_NA19118 |
0 .33 RPM |
YRI_NA19213 |
0 .60 RPM |
YRI_NA19214 |
0 .34 RPM |
YRI_NA19223 |
0 .76 RPM |
Indel association:
No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (
PubMed).