>retro_hsap_2127 TTCAACAAGGGCCCCTCCTACAGGCTCTTGGCGGACGTCCAGAACAGGCTTCTGTTCAAATATGACTCCCAGAAGGAGGC
AGAGCTCCGCAGCTGGATCAAGGGATTCACTGGCCTCTCCATCCGCCCCGACTTCCAGAAGGGCCTGAAGGACGGGATTA
TTTTATGCACACTCGTGAACAAACTGCAGCCGGGCTCAGTCCCCAAGATCAACGGCTTCCGTGTAGAACTGGCACCAGCT
AGAAAACCTCTCCAACATCCTCAAGGCAATGGTCAGCTACGGCATGATCCCGTGGACCTATTTGAGGCCAACGACCTGTT
TGAGAGTGGGAACAATATGCAGGTGCGGGTGTCTCTTCTCGCCCTGGCAGGGAAGGCCAAGACTAAGGGGCTGCAGAGCG
GGGTGGACATCCGTGACAAGTACTCAGAGAAGCAGAACTTCAACGACACCACCATGAAGGCCAGGCTGTGCGTCATCCGG
CTGCAGATTACCAACAAATGTGCCAGCCAGTCAGGCATGACCGCATACGTCACGAGGAGGCATCTCTACGACCCCAAGAA
CCGCATCCTGCCCCCCATGGACAACTCGACCATCAGCCTCCGGATGGGTACAAACAAGTGCGCCAGCCAGGTGGGCATGA
CGGCTCCCGGGAACCAGTGGCACATCTATGACACCAAGTTGGGAATCGACAAGTGTGAGAACTCCTCCATGTCCCTGAAG
ATGGGCTACACGCAGGTCGCCAATCACAGCAGACAGGTCTTTGGCCTAGGCCGGCAAATATATGAACCCAAGTACCAGCC
GGGTGGCCCAGTGGCCCACGGGGCTCCCTCCGCCGGCAACTGCCCAGGGCCAGGGGAGGCCCCTTAGTACCAGGAGGAGA
CCAGCTAC
ORF - retro_hsap_2127 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity:
79.08 %
Parental protein coverage:
98.38 %
Number of stop codons detected:
2
Number of frameshifts detected
2
Retrocopy - Parental Gene Alignment:
Parental FNKGPSYGLSAEVKNRLLSKYDPQKEAELRTWIEGLTGLSIGPDFQKGLKDGTILCTLMNKLQPGSVPKI
FNKGPSY.L.A.V.NRLL.KYD.QKEAELR.WI.G.TGLSI.PDFQKGLKDG.ILCTL.NKLQPGSVPKI
Retrocopy FNKGPSYRLLADVQNRLLFKYDSQKEAELRSWIKGFTGLSIRPDFQKGLKDGIILCTLVNKLQPGSVPKI Parental N-RSMQNWHQLENLSNFIKAMVSYGM-NPVDLFEANDLFESGNMTQVQVSLLALAGKAKTKGLQSGVDIG
N..S..NWHQLENLSN..KAMVSYGM..PVDLFEANDLFESGN..QV.VSLLALAGKAKTKGLQSGVDI.
Retrocopy N> ASV* NWHQLENLSNILKAMVSYGM< DPVDLFEANDLFESGNNMQVRVSLLALAGKAKTKGLQSGVDIR Parental VKYSEKQERNFDDATMKAGQCVIGLQMGTNKCASQSGMTAYGTRRHLYDPKNHILPPMDHSTISLQMGTN
.KYSEKQ..NF.D.TMKA..CVI.LQ..TNKCASQSGMTAY.TRRHLYDPKN.ILPPMD.STISL.MGTN
Retrocopy DKYSEKQ--NFNDTTMKARLCVIRLQI-TNKCASQSGMTAYVTRRHLYDPKNRILPPMDNSTISLRMGTN Parental KCASQVGMTAPGTRRHIYDTKLGTDKCDNSSMSLQMGYTQGANQSGQVFGLGRQIYDPKYCPQGTVADGA
KCASQVGMTAPG...HIYDTKLG.DKC.NSSMSL.MGYTQ.AN.S.QVFGLGRQIY.PKY.P.G.VA.GA
Retrocopy KCASQVGMTAPGNQWHIYDTKLGIDKCENSSMSLKMGYTQVANHSRQVFGLGRQIYEPKYQPGGPVAHGA Parental PSGTGDCPDPGEVPEYPPYYQEEAGY
PS..G.CP.PGE.P.Y....QEE..Y
Retrocopy PS-AGNCPGPGEAP* Y----QEETSY
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
112 .57 RPM
bodymap2_adrenal
0 .00 RPM
74 .98 RPM
bodymap2_brain
0 .26 RPM
7 .85 RPM
bodymap2_breast
0 .12 RPM
71 .30 RPM
bodymap2_colon
0 .00 RPM
53 .46 RPM
bodymap2_heart
0 .00 RPM
21 .03 RPM
bodymap2_kidney
0 .00 RPM
45 .66 RPM
bodymap2_liver
0 .06 RPM
12 .93 RPM
bodymap2_lung
0 .00 RPM
217 .30 RPM
bodymap2_lymph_node
0 .00 RPM
138 .72 RPM
bodymap2_ovary
0 .00 RPM
182 .32 RPM
bodymap2_prostate
0 .00 RPM
86 .83 RPM
bodymap2_skeletal_muscle
0 .00 RPM
7 .91 RPM
bodymap2_testis
0 .06 RPM
39 .76 RPM
bodymap2_thyroid
0 .00 RPM
73 .44 RPM
bodymap2_white_blood_cells
0 .00 RPM
341 .88 RPM
RNA Polymerase II actvity near the 5' end of retro_hsap_2127 was not detected
No EST(s) were mapped for retro_hsap_2127 retrocopy.
No TSS is located nearby retro_hsap_2127 retrocopy 5' end.
Experiment type:
PCR amplification
Forward primer:
GCGAACTAGAAAAAAGACTTAGCTTCC (27 nt long)
Reverse primer:
GGTGTCGTTGAAGTTCTGCTTCT (23 nt long)
Anneling temperature:
60 °C
(Expected) product size:
530
Electrophoresis gel image:
Additional comment:
Red arrow indicates PCR product of retrogene in pooled cDNA from 16 human tissues (Clontech). Red number of lane indicates particular retrogene; L - GeneRuler 100 bp DNA Ladder (Thermo Fisher Scientific); N - No template control (water instead of cDNA)
Retrocopy orthology: Retrocopy retro_hsap_2127 has 0 orthologous retrocopies within eutheria group .
Parental genes homology: Parental genes homology involve
7 parental genes, and
42 retrocopies.
Species
Parental gene accession
Retrocopies number
Homo sapiens ENSG00000064666 16 retrocopies
Show / hide list of retrocopies
retro_hsap_1168 ,
retro_hsap_1575 ,
retro_hsap_1697 ,
retro_hsap_2127 ,
retro_hsap_2495 ,
retro_hsap_255 ,
retro_hsap_2576 ,
retro_hsap_2764 ,
retro_hsap_3505 ,
retro_hsap_4168 ,
retro_hsap_4170 ,
retro_hsap_4175 ,
retro_hsap_4257 ,
retro_hsap_4269 ,
retro_hsap_4326 ,
retro_hsap_943 ,
Homo sapiens ENSG00000117519 1 retrocopy
Show / hide list of retrocopies
Homo sapiens ENSG00000158710 1 retrocopy
Show / hide list of retrocopies
Gorilla gorilla ENSGGOG00000028153 9 retrocopies
Show / hide list of retrocopies
Macaca mulatta ENSMMUG00000015306 1 retrocopy
Show / hide list of retrocopies
Mus musculus ENSMUSG00000004665 2 retrocopies
Show / hide list of retrocopies
Pongo abelii ENSPPYG00000009302 12 retrocopies
Show / hide list of retrocopies
retro_pabe_1299 ,
retro_pabe_1397 ,
retro_pabe_1838 ,
retro_pabe_1920 ,
retro_pabe_2171 ,
retro_pabe_2249 ,
retro_pabe_2900 ,
retro_pabe_3512 ,
retro_pabe_3515 ,
retro_pabe_3543 ,
retro_pabe_3823 ,
retro_pabe_407 ,
Expression level across human populations :
image/svg+xml
GBR_HG00142
GBR_HG00099
GBR_HG00114
GBR_HG00143
GBR_HG00131
GBR_HG00137
GBR_HG00133
GBR_HG00119
GBR_HG00111
GBR_HG00134
FIN_HG00378
FIN_HG00338
FIN_HG00349
FIN_HG00375
FIN_HG00315
FIN_HG00277
FIN_HG00328
FIN_HG00321
FIN_HG00377
FIN_HG00183
TSI_NA20756
TSI_NA20538
TSI_NA20798
TSI_NA20532
TSI_NA20765
TSI_NA20518
TSI_NA20513
TSI_NA20512
TSI_NA20771
TSI_NA20786
YRI_NA19114
YRI_NA19099
YRI_NA18870
YRI_NA18907
YRI_NA19223
YRI_NA19214
YRI_NA18916
YRI_NA19093
YRI_NA19118
YRI_NA19213
Toscani in Italia:
Finnish in Finland:
British in England and Scotland:
Utah Residents (CEPH) with Northern and Western European Ancestry:
Yoruba in Ibadan, Nigeria:
CEU_NA12760
CEU_NA12827
CEU_NA12872
CEU_NA12751
CEU_NA12873
CEU_NA12400
CEU_NA11930
CEU_NA12004
CEU_NA11831
CEU_NA11843
No expression ( = 0 RPM )
> 0 RPM
= 0.03 RPM
Legend:
Show / hide detail expression values
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 .00 RPM
CEU_NA12760
0 .00 RPM
CEU_NA12827
0 .00 RPM
CEU_NA12872
0 .00 RPM
CEU_NA12873
0 .00 RPM
FIN_HG00183
0 .00 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 .00 RPM
FIN_HG00375
0 .00 RPM
FIN_HG00377
0 .00 RPM
FIN_HG00378
0 .00 RPM
GBR_HG00099
0 .00 RPM
GBR_HG00111
0 .00 RPM
GBR_HG00114
0 .00 RPM
GBR_HG00119
0 .00 RPM
GBR_HG00131
0 .00 RPM
GBR_HG00133
0 .02 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 .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 .00 RPM
YRI_NA19118
0 .00 RPM
YRI_NA19213
0 .00 RPM
YRI_NA19214
0 .00 RPM
YRI_NA19223
0 .00 RPM
Hide detail expression values Indel association: No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (
PubMed ).