RetrogeneDB ID:

retro_hsap_99

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:5:167956509..167957514(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000188573
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:FBL
Ensembl ID:ENSG00000105202
Aliases:FBL, FIB, FLRN, RNU3IP1
Description:fibrillarin [Source:HGNC Symbol;Acc:3599]


Retrocopy-Parental alignment summary:






>retro_hsap_99
ATGAAGTCGGCCGCGAGCTCGCGCGGGGGCGGTGGGGGCGGCCGCGGGGGCGGCGGCTGGGGCAGCTGGGGCGGGGGCCG
AGGCGGCGGCGGCGGCGCGGGCAAGGGCGGCGGGGGCGACGGCGGCGGCCAGGGGGGCAAGGGCGGCTTCGGGGCGCGGG
CGCGCGGCTTCGGCGGGGGCGGCCGGGGCCGGGGGCGCGGCGGCGGCGACGGCAAGGATCGCGGCGGCGGTGGACAGCGG
CGGGGCGGCGTGGCCAAGAGCAAGAGCCGCCGCAGGAAGGGCGCCATGGTGGTGTCGGTGGAGCCGCACCGGCACGAGGG
CGTCTTCATCTACCGCGGGGCGGAGGACGCGCTGGTCACGCTGAACATGGTGCCGGGCCAGTCTGTGTACGGCGAGAGGC
GCGTCACGGTGACCGAGGGCGGCGTGAAGCAGGAGTACCGCACGTGGAACCCGTTCCGCTCTAAGCTGGCCGCGGCCATC
CTGGGCGGGGTGGACCAGATCCACATCAAGCCCAAGTCCAAGGTGCTGTACCTGGGCGCCGCGTCGGGCACCACCGTCTC
CCATGTCTCCGACATCATTGGCCCAGACGGCCTGGTCTACGCCGTCGAGTTCTCCCACCGCGCCGGCCGCGATCTGGTCA
ACGTGGCCAAGAAGCGCACCAACATCATTCCGGTCCTGGAGGACGCGCGGCACCCGCTCAAGTACCGCATGCTCATCGGG
ATGGTGGACGTGATCTTCGCCGACGTGGCCCAGCCGGACCAGTCCCGCATCGTGGCCCTGAACGCCCACACCTTCCTGCG
CAATGGGGGCCACTTTCTCATCTCCATCAAGGCCAACTGCATCGACTCCACCGCATCCGCCGAGGCTGTGTTTGCTTCTG
AGGTGAGGAAGTTGCAGCAGGAGAACTTGAAGCCTCAAGAGCAGCTGACCCTGGAGCCCTATGAGCGGGACCACGCTGTG
GTGGTCGGGGTCTACCGACCTCTTCCCAAGAGCAGCAGCAAATAG

ORF - retro_hsap_99 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 77.74 %
Parental protein coverage: 96.57 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalGGGFGGRGGFGDRGGRGGRGGFGGGRGRGGGFRGRGRGGGGGGGGGGGGGRGGGGFHSGGNRGRGRGGKR
GGG..G.GG.GD.GG.GG.GGF.G.R.RG.G..GRGR....G.GGG.G..RGGGG...G...G......R
RetrocopyGGGGAGKGGGGDGGGQGGKGGF-GARARGFGGGGRGR----GRGGGDGKDRGGGGQRRG---GVAKSKSR
ParentalGNQSGKNVMVEPHRHEGVFICRGKEDALVTKNLVPGESVYGEKRVSISEGDDKIEYRAWNPFRSKLAAAI
.......V.VEPHRHEGVFI.RG.EDALVT.N.VPG.SVYGE.RV...EG..K.EYR.WNPFRSKLAAAI
RetrocopyRRKGAMVVSVEPHRHEGVFIYRGAEDALVTLNMVPGQSVYGERRVTVTEGGVKQEYRTWNPFRSKLAAAI
ParentalLGGVDQIHIKPGAKVLYLGAASGTTVSHVSDIVGPDGLVYAVEFSHRSGRDLINLAKKRTNIIPVIEDAR
LGGVDQIHIKP..KVLYLGAASGTTVSHVSDI.GPDGLVYAVEFSHR.GRDL.N.AKKRTNIIPV.EDAR
RetrocopyLGGVDQIHIKPKSKVLYLGAASGTTVSHVSDIIGPDGLVYAVEFSHRAGRDLVNVAKKRTNIIPVLEDAR
ParentalHPHKYRMLIAMVDVIFADVAQPDQTRIVALNAHTFLRNGGHFVISIKANCIDSTASAEAVFASEVKKMQQ
HP.KYRMLI.MVDVIFADVAQPDQ.RIVALNAHTFLRNGGHF.ISIKANCIDSTASAEAVFASEV.K.QQ
RetrocopyHPLKYRMLIGMVDVIFADVAQPDQSRIVALNAHTFLRNGGHFLISIKANCIDSTASAEAVFASEVRKLQQ
ParentalENMKPQEQLTLEPYERDHAVVVGVYRPPPK
EN.KPQEQLTLEPYERDHAVVVGVYRP.PK
RetrocopyENLKPQEQLTLEPYERDHAVVVGVYRPLPK

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

(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 106 .07 RPM
bodymap2_adrenal 0 .16 RPM 103 .72 RPM
bodymap2_brain 6 .19 RPM 20 .93 RPM
bodymap2_breast 0 .14 RPM 71 .52 RPM
bodymap2_colon 0 .73 RPM 89 .31 RPM
bodymap2_heart 0 .02 RPM 16 .65 RPM
bodymap2_kidney 0 .10 RPM 40 .91 RPM
bodymap2_liver 0 .00 RPM 25 .62 RPM
bodymap2_lung 0 .02 RPM 82 .74 RPM
bodymap2_lymph_node 0 .11 RPM 89 .82 RPM
bodymap2_ovary 0 .66 RPM 136 .92 RPM
bodymap2_prostate 0 .40 RPM 100 .61 RPM
bodymap2_skeletal_muscle 0 .18 RPM 64 .06 RPM
bodymap2_testis 3 .47 RPM 96 .68 RPM
bodymap2_thyroid 0 .00 RPM 62 .14 RPM
bodymap2_white_blood_cells 0 .00 RPM 103 .14 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_99 was not detected

EST - click to see more details

3 EST(s) were mapped to retro_hsap_99 retrocopy
EST ID Start End Identity Match Mis-match Score
BU069669 167956835 167957199 95.6 347 16 331
DB496895 167956581 167957064 99.6 481 2 479
Z20950 167956784 167956976 99 186 2 181

TSS - click to see more details



TSS No. TSS Name TSS expression level (Expr) in TPM range:
no expression 0 < Expr ≤ 1 1 < Expr ≤ 5 5 < Expr ≤ 10 Expr > 10
TSS #1 TSS_1518931106 libraries430 libraries209 libraries49 libraries35 libraries

The graphical summary, for retro_hsap_99 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1829 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Display detail expression values in each library
... or ...
Directly download all expression values

Lab - click to see more details

retro_hsap_99 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_99 has 5 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2208
Bos taurus retro_btau_108
Sus scrofa retro_sscr_39
Canis familiaris retro_cfam_1697
Equus caballus retro_ecab_308
Parental genes homology:
Parental genes homology involve 13 parental genes, and 22 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000025791 retrocopy
retro_btau_108,
Canis familiaris ENSCAFG000000054121 retrocopy
retro_cfam_1697,
Homo sapiens ENSG00000105202 1 retrocopy
retro_hsap_99 ,
Macropus eugenii ENSMEUG000000146841 retrocopy
retro_meug_1077,
Microcebus murinus ENSMICG000000076861 retrocopy
retro_mmur_1127,
Mus musculus ENSMUSG000000468654 retrocopies
retro_mmus_1141, retro_mmus_1585, retro_mmus_1609, retro_mmus_89,
Nomascus leucogenys ENSNLEG000000142341 retrocopy
retro_nleu_1947,
Otolemur garnettii ENSOGAG000000064632 retrocopies
retro_ogar_3102, retro_ogar_504,
Pan troglodytes ENSPTRG000000109822 retrocopies
retro_ptro_2208, retro_ptro_3074,
Pteropus vampyrus ENSPVAG000000108491 retrocopy
retro_pvam_231,
Rattus norvegicus ENSRNOG000000192294 retrocopies
retro_rnor_1082, retro_rnor_1780, retro_rnor_643, retro_rnor_75,
Sus scrofa ENSSSCG000000305101 retrocopy
retro_sscr_39,
Tupaia belangeri ENSTBEG000000077552 retrocopies
retro_tbel_3774, retro_tbel_3974,

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 Toscaniin Italia: Finnish inFinland: British in England and Scotland: Utah Residents (CEPH) with Northernand 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 = 0.4 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .03 RPM
CEU_NA11930 0 .13 RPM
CEU_NA12004 0 .04 RPM
CEU_NA12400 0 .11 RPM
CEU_NA12751 0 .10 RPM
CEU_NA12760 0 .40 RPM
CEU_NA12827 0 .05 RPM
CEU_NA12872 0 .05 RPM
CEU_NA12873 0 .00 RPM
FIN_HG00183 0 .11 RPM
FIN_HG00277 0 .04 RPM
FIN_HG00315 0 .19 RPM
FIN_HG00321 0 .03 RPM
FIN_HG00328 0 .05 RPM
FIN_HG00338 0 .06 RPM
FIN_HG00349 0 .11 RPM
FIN_HG00375 0 .07 RPM
FIN_HG00377 0 .00 RPM
FIN_HG00378 0 .00 RPM
GBR_HG00099 0 .06 RPM
GBR_HG00111 0 .06 RPM
GBR_HG00114 0 .05 RPM
GBR_HG00119 0 .07 RPM
GBR_HG00131 0 .00 RPM
GBR_HG00133 0 .00 RPM
GBR_HG00134 0 .02 RPM
GBR_HG00137 0 .03 RPM
GBR_HG00142 0 .06 RPM
GBR_HG00143 0 .06 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .05 RPM
TSI_NA20518 0 .06 RPM
TSI_NA20532 0 .14 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .06 RPM
TSI_NA20771 0 .11 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .12 RPM
YRI_NA18870 0 .10 RPM
YRI_NA18907 0 .03 RPM
YRI_NA18916 0 .08 RPM
YRI_NA19093 0 .00 RPM
YRI_NA19099 0 .00 RPM
YRI_NA19114 0 .00 RPM
YRI_NA19118 0 .02 RPM
YRI_NA19213 0 .02 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).





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