>retro_hsap_2350
ATGCCGATGGTAGAGGAGCTTTACGGCAACTATGGCATCATGGCCGATACCACGGAGCGAGTGGGCCAGCATAAAGATGC
CTATCAAGTGATACTGGATGGTGTGAAAGGTGGTACTAAGGAAAAACGATTAGCAGCTCAATTTATTCTGAAATTCTTTA
AGCATTTTACAGAATTGGCTGATTCTGCTATCAATGCACAGTTAGACCTCTGTGAAGATGAAGATGTATCTATTTGACGT
CAAGCAATTAAAGAACTGCCTCAATTTACCACTGGAGAAAATCTTCCTCGAGTGGCAGATATACTAATGCAACTTTTGGA
GTCAGATGGCTCTGCAGAATTTAACCTAGTGAACAATGCCCTGTTGAGTATATTTAACATGGATGGAAAAGGGACTTTAG
GTTCATTGTTCAGCCAAATACTTCAAGGAGAGGACATTGTTAGAGAATGAGCAATTAAATTCCTTTCTACAAAACTTAAG
ACTTTACCAGATGAAGTATTAACAAAGGAAGTGGAAGAGCTTATACTAACTGAATCCAAACACGTCCTAGAAGATGTGAC
TCATGAAGAATTTGTTCTATTCATGAATTACTGTCTGGGTTAAAAAGCTTACAGACAGTAAGTGGAAGACAGCAACTTGT
AAAGTTGGTGGCTGAACAGGCCGACCTAGAACAGACCTTCAATCCCTCAGATCCTGAGTGTGTGGGCAGGCTCTTACAGT
GCACTCAGCAGGCAGTACCCTTCTTCTCTAAAACTGTCCATTCCACAAGGTCTGTGACATATTTCTGTGAGCAGGTTCTC
CCTAACCTTGGTATCTTGACTACCGCAGTGGAAGGTCTTGACATACAGTTGGAGGTATTGAAATTGTTGGTGGAGATGAG
TTCATTTTGTGGTGACATGGAAAAACTAGAAACAAATTTAGGGAAACTATTTGATAAGTTATTGGAATACATGCCCCTCC
CTCCAGAAGAAGCAGAAAATGGAGGGAATGCTGGTGATGAAGAACCCAAACTACAGTTCAGTTATGTGGAATGTTTGTTG
TACAGTTTTCACCAGTTGGGCCAAAAACTTCCAGATTTCTTAACAGCCAAACTGAATGCAGAAAAACTCAAAGATTTCAA
AATCAGGCTGCAATACTTTGCACGAGGCCTGCAAGTTTATATCAGACAACTTCACTTAGCTCTCCAGGTGAAACAGGTGA
GAACAGAAAAGAACAGAAAACAGAAGAGAACAAAATTAAAGTTGTTGCATTGAAAGCAACAAACAATATCAATGTTTTAA
TCAAGGATCTCTTCCACATTCCTCCTTCTTGTAAGAGCACAGTAACACTATCCTGGAAACCTGTATAAAAGGTTGAGATT
GGGCAAAAGAGAGCCAGTGAATATACAACTTCAGGTTCACCACCCCAGAAATCTTCAGCAGAACAAAAAAGAGATGCCAG
GCAGATTTATAATCCTCCCAGTGAGAAATATAGCAGCAATTTGGGCAACTTTAATTATGAGAGGAGCCTTCAGGGAAAG
ORF - retro_hsap_2350 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: |
89.78 % |
Parental protein coverage: |
100. % |
Number of stop codons detected: |
3 |
Number of frameshifts detected |
2 |
Retrocopy - Parental Gene Alignment:
Parental | MPTVEELYRNYGILADATEQVGQHKDAYQVILDGVKGGTKEKRLAAQFIPKFFKHFPELADSAINAQLDL |
| MP.VEELY.NYGI.AD.TE.VGQHKDAYQVILDGVKGGTKEKRLAAQFI.KFFKHF.ELADSAINAQLDL |
Retrocopy | MPMVEELYGNYGIMADTTERVGQHKDAYQVILDGVKGGTKEKRLAAQFILKFFKHFTELADSAINAQLDL |
|
Parental | CEDEDVSIRRQAIKELPQFATGENLPRVADILTQLLQTDDSAEFNLVNNALLSIFKMDAKGTLGGLFSQI |
| CEDEDVSI.RQAIKELPQF.TGENLPRVADIL.QLL..D.SAEFNLVNNALLSIF.MD.KGTLG.LFSQI |
Retrocopy | CEDEDVSI*RQAIKELPQFTTGENLPRVADILMQLLESDGSAEFNLVNNALLSIFNMDGKGTLGSLFSQI |
|
Parental | LQGEDIVRERAIKFLSTKLKTLPDEVLTKEVEELILTESKKVLEDVTGEEFVLFM-KILSGLKSLQTVSG |
| LQGEDIVRE.AIKFLSTKLKTLPDEVLTKEVEELILTESK.VLEDVT.EEFVLFM...LSGLKSLQTVSG |
Retrocopy | LQGEDIVRE*AIKFLSTKLKTLPDEVLTKEVEELILTESKHVLEDVTHEEFVLFM<ELLSGLKSLQTVSG |
|
Parental | RQQLVELVAEQADLEQTFNPSDPDCVDRLLQCTRQAVPLFSKNVHSTRFVTYFCEQVLPNLGTLTTPVEG |
| RQQLV.LVAEQADLEQTFNPSDP.CV.RLLQCT.QAVP.FSK.VHSTR.VTYFCEQVLPNLG.LTT.VEG |
Retrocopy | RQQLVKLVAEQADLEQTFNPSDPECVGRLLQCTQQAVPFFSKTVHSTRSVTYFCEQVLPNLGILTTAVEG |
|
Parental | LDIQLEVLKLLAEMSSFCGDMEKLETNLRKLFDKLLEYMPLPPEEAENGENAGNEEPKLQFSYVECLLYS |
| LDIQLEVLKLL.EMSSFCGDMEKLETNL.KLFDKLLEYMPLPPEEAENG.NAG.EEPKLQFSYVECLLYS |
Retrocopy | LDIQLEVLKLLVEMSSFCGDMEKLETNLGKLFDKLLEYMPLPPEEAENGGNAGDEEPKLQFSYVECLLYS |
|
Parental | FHQLGRKLPDFLTAKLNAEKLKDFKIRLQYFARGLQVYIRQLRLALQ-GKTGEALK---TEENKIKVVAL |
| FHQLG.KLPDFLTAKLNAEKLKDFKIRLQYFARGLQVYIRQL.LALQ.G.TGE..K...TEENKIKVVAL |
Retrocopy | FHQLGQKLPDFLTAKLNAEKLKDFKIRLQYFARGLQVYIRQLHLALQ<GETGENRKEQKTEENKIKVVAL |
|
Parental | KITNNINVLIKDLFHIPPSYKSTVTLSWKPVQKVEIGQKRASEDTTSGSPPKKSSAGPKRDARQIYNPPS |
| K.TNNINVLIKDLFHIPPS.KSTVTLSWKPV.KVEIGQKRASE.TTSGSPP.KSSA..KRDARQIYNPPS |
Retrocopy | KATNNINVLIKDLFHIPPSCKSTVTLSWKPV*KVEIGQKRASEYTTSGSPPQKSSAEQKRDARQIYNPPS |
|
Parental | GKYSSNLGNFNYERSLQGK |
| .KYSSNLGNFNYERSLQGK |
Retrocopy | EKYSSNLGNFNYERSLQGK |
|
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 |
91 .62 RPM |
bodymap2_adrenal |
0 .00 RPM |
98 .66 RPM |
bodymap2_brain |
0 .00 RPM |
138 .51 RPM |
bodymap2_breast |
0 .00 RPM |
80 .31 RPM |
bodymap2_colon |
0 .00 RPM |
120 .50 RPM |
bodymap2_heart |
0 .00 RPM |
43 .05 RPM |
bodymap2_kidney |
0 .06 RPM |
120 .96 RPM |
bodymap2_liver |
0 .02 RPM |
63 .65 RPM |
bodymap2_lung |
0 .00 RPM |
71 .01 RPM |
bodymap2_lymph_node |
0 .00 RPM |
96 .56 RPM |
bodymap2_ovary |
0 .00 RPM |
119 .56 RPM |
bodymap2_prostate |
0 .00 RPM |
114 .04 RPM |
bodymap2_skeletal_muscle |
0 .00 RPM |
51 .00 RPM |
bodymap2_testis |
0 .00 RPM |
95 .10 RPM |
bodymap2_thyroid |
0 .00 RPM |
144 .59 RPM |
bodymap2_white_blood_cells |
0 .00 RPM |
156 .10 RPM |
RNA Polymerase II actvity near the 5' end of retro_hsap_2350 was not detected
1 EST(s) were mapped to retro_hsap_2350 retrocopy
EST ID |
Start |
End |
Identity |
Match |
Mis-match |
Score |
AA668659 |
178862785 |
178863171 |
99.5 |
383 |
2 |
380 |
No TSS is located nearby retro_hsap_2350 retrocopy 5' end.
retro_hsap_2350 was not experimentally validated.
Retrocopy orthology:
Retrocopy
retro_hsap_2350 has 3 orthologous retrocopies within
eutheria group
.
Parental genes homology:
Parental genes homology involve
5 parental genes, and
8 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 .02 RPM |
CEU_NA12760 |
0 .00 RPM |
CEU_NA12827 |
0 .00 RPM |
CEU_NA12872 |
0 .03 RPM |
CEU_NA12873 |
0 .00 RPM |
FIN_HG00183 |
0 .03 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 .03 RPM |
FIN_HG00375 |
0 .00 RPM |
FIN_HG00377 |
0 .00 RPM |
FIN_HG00378 |
0 .00 RPM |
GBR_HG00099 |
0 .03 RPM |
GBR_HG00111 |
0 .04 RPM |
GBR_HG00114 |
0 .00 RPM |
GBR_HG00119 |
0 .00 RPM |
GBR_HG00131 |
0 .00 RPM |
GBR_HG00133 |
0 .00 RPM |
GBR_HG00134 |
0 .00 RPM |
GBR_HG00137 |
0 .00 RPM |
GBR_HG00142 |
0 .03 RPM |
GBR_HG00143 |
0 .00 RPM |
TSI_NA20512 |
0 .00 RPM |
TSI_NA20513 |
0 .00 RPM |
TSI_NA20518 |
0 .03 RPM |
TSI_NA20532 |
0 .03 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).