RetrogeneDB ID:

retro_hsap_1551

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:15:35590450..35591621(-)
Located in intron of:ENSG00000134146
Retrocopy
information
Ensembl ID:ENSG00000259585
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RBM17
Ensembl ID:ENSG00000134453
Aliases:RBM17, SPF45
Description:RNA binding motif protein 17 [Source:HGNC Symbol;Acc:16944]


Retrocopy-Parental alignment summary:






>retro_hsap_1551
GAAACCAGTGACTCAAAAACAGAAGGCTGGTCCAAAAACTTCAAACTTCTACAGTCTCAGCTTCAGGTGAAGAAGGCAGC
TCTCACTCAGGCAAAGAGCCAAAGGACGAAACAAGGTACAGTTCTTGCCCCAGTCATTGACCTACAACGAGGTGGCTCCT
CAGATGACCGGGCAAATTGTGGACACACCACCGCATGTGCCAGCTGGGCTGAAGGATCCTGTTCCCAGTGGGTTTTCTGC
AGGGGAAGTTCTGATTCCCTTAGCTGACGAATATGATCCTATGTTTCCTAACGATTGTAAGAAAGTAGTGAAACGCCAGA
GAGGAAGGACAAAGACAGCGGGAGCTGGAAAGACAGAAGAAATAGAAGAAAGAGAAGAAAGGCATAAATACAGACATGAT
GCACGTGAGTTTTCAAGGAGTTCAGATCCGGATTCTGATGAAGATGAAGATTAGGAGCGAGAGAAGAGGAAAACAAGTAT
GGGCGGAGCTGCCATTGCCTCACCCACTTCTCTGGCAGTAAAAGACAGTTACCCCGAGATTTTCCTTATGAAGAGGACTC
AAGACCTCGATCACAGTCTTCCAAAACTGCCATTCCTCCCCCAGTGTACGAGGAACAAGACAGACCGAGATCTCCAACCC
GGCCCAGCGCAACTCCTTCCTCGCTAACTTGGGGGGCACGGTGGCGCACAAGATCATACAGAAGTACGGCTTCCGGGAGG
GCCAGGGTCTGGGGAAGCATGAGCAGGGGCTGAGCACCGCCTTTTCGGTGGAGAAGACCAGCAAGCTTGGTGGCAAGATC
ATCGTGGGTGACGCCACGGAGAAAGATGCATCCAAGAAGTCAGATTCAAATCCACTGACTGAAATACTTAAGTGTCTTAA
TAAAGTGGTCCTACTAAGGAACATGGTTGGTGCGGGAAAGGTGGATGAAGACTTGGAAGTTAAAACCAAGGAAGAACGTG
AAAAATATCTCAAAGTTGGGGAAAGTGTGTTGTTTGAAATTCTGGTGCCCCTGATGATGAAGCAGTACGGATATTTTTAG
AATTTGAGAGAGTTAAATCAGCAATTCAAGCGGTTATTGACTCGAATGGGAGGTATTTTGGTGGACAGGTGGCAAATGCA
TGTTTCTACAATTTGGAAAAATTCAGTATCTTGGATTTGGCAGAACAAGTT

ORF - retro_hsap_1551 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 77.33 %
Parental protein coverage: 97.76 %
Number of stop codons detected: 1
Number of frameshifts detected 5


Retrocopy - Parental Gene Alignment:

ParentalETSDSKTEGWSKNFKLLQSQLQVKKAALTQAKSQRTKQSTVLAPVIDLKRGGSSDDR-QIVDTPPHVAAG
ETSDSKTEGWSKNFKLLQSQLQVKKAALTQAKSQRTKQ.TVLAPVIDL.RGGSSDDR.QIVDTPPHV.AG
RetrocopyETSDSKTEGWSKNFKLLQSQLQVKKAALTQAKSQRTKQGTVLAPVIDLQRGGSSDDR>QIVDTPPHVPAG
ParentalLKDPVPSGFSAGEVLIPLADEYDPMFPNDYEKVVKRQREERQRQRELERQKEIEEREKRRKDRHEASGFA
LKDPVPSGFSAGEVLIPLADEYDPMFPND..K.V......R...................K.RH.A..F.
RetrocopyLKDPVPSGFSAGEVLIPLADEYDPMFPNDCKK-VVKRQRGRTKTAGAXXXXXXXXXXXXHKYRHDAREFS
ParentalRRPDPDSDEDEDYERERRKRSMGGAAIAPP-TSLVEKDKELPRDFPYEEDSRPRSQSSKAAIPPPVYEEQ
R..DPDSDEDED.ERE.......G.A.....T........LPRDFPYEEDSRPRSQSSK.AIPPPVYEEQ
RetrocopyRSSDPDSDEDED*ERE-KRKTSMGGAAIAS<THFSGSKRQLPRDFPYEEDSRPRSQSSKTAIPPPVYEEQ
ParentalDRPRSPT-GPS-NSFLANMGGTVAHKIMQKYGFREGQGLGKHEQGLSTALSVEKTSKRGGKIIVGDATEK
DRPRSPT.GP..NSFLAN.GGTVAHKI.QKYGFREGQGLGKHEQGLSTA.SVEKTSK.GGKIIVGDATEK
RetrocopyDRPRSPT>GPA>NSFLANLGGTVAHKIIQKYGFREGQGLGKHEQGLSTAFSVEKTSKLGGKIIVGDATEK
ParentalDASKKSDSNPLTEILKCPTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEI-PGAPDDEAVR
DASKKSDSNPLTEILKC..KVVLLRNMVGAG.VDEDLEV.TKEE.EKY.KVG..V.FEI..GAPDDEAVR
RetrocopyDASKKSDSNPLTEILKCLNKVVLLRNMVGAGKVDEDLEVKTKEEREKYLKVGESVLFEI<SGAPDDEAVR
ParentalIFLEFERVESAIKAVVDLNGRYFGGRVVKACFYNLDKFRVLDLAEQV
IFLEFERV.SAI.AV.D.NGRYFGG.V..ACFYNL.KF..LDLAEQV
RetrocopyIFLEFERVKSAIQAVIDSNGRYFGGQVANACFYNLEKFSILDLAEQV

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 73 .79 RPM
bodymap2_adrenal 0 .20 RPM 128 .57 RPM
bodymap2_brain 0 .19 RPM 77 .96 RPM
bodymap2_breast 0 .04 RPM 76 .25 RPM
bodymap2_colon 0 .00 RPM 90 .92 RPM
bodymap2_heart 0 .02 RPM 45 .97 RPM
bodymap2_kidney 0 .06 RPM 65 .89 RPM
bodymap2_liver 0 .00 RPM 23 .45 RPM
bodymap2_lung 0 .00 RPM 119 .53 RPM
bodymap2_lymph_node 0 .00 RPM 96 .45 RPM
bodymap2_ovary 0 .06 RPM 102 .80 RPM
bodymap2_prostate 0 .00 RPM 76 .50 RPM
bodymap2_skeletal_muscle 0 .00 RPM 62 .98 RPM
bodymap2_testis 2 .22 RPM 96 .83 RPM
bodymap2_thyroid 0 .00 RPM 102 .69 RPM
bodymap2_white_blood_cells 0 .00 RPM 64 .69 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_1551 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_1551 retrocopy.

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_429681534 libraries232 libraries46 libraries13 libraries4 libraries

The graphical summary, for retro_hsap_1551 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_1551 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1551 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_1044
Pongo abelii retro_pabe_1284
Parental genes homology:
Parental genes homology involve 14 parental genes, and 16 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000219512 retrocopies
retro_btau_1057, retro_btau_530,
Canis familiaris ENSCAFG000000052061 retrocopy
retro_cfam_844,
Callithrix jacchus ENSCJAG000000205731 retrocopy
retro_cjac_432,
Equus caballus ENSECAG000000089391 retrocopy
retro_ecab_547,
Erinaceus europaeus ENSEEUG000000130771 retrocopy
retro_eeur_390,
Homo sapiens ENSG00000134453 1 retrocopy
retro_hsap_1551 ,
Macropus eugenii ENSMEUG000000113471 retrocopy
retro_meug_438,
Macaca mulatta ENSMMUG000000151522 retrocopies
retro_mmul_1209, retro_mmul_771,
Mus musculus ENSMUSG000000371971 retrocopy
retro_mmus_2855,
Otolemur garnettii ENSOGAG000000156871 retrocopy
retro_ogar_1119,
Pongo abelii ENSPPYG000000020671 retrocopy
retro_pabe_1284,
Pan troglodytes ENSPTRG000000022651 retrocopy
retro_ptro_1044,
Ictidomys tridecemlineatus ENSSTOG000000135911 retrocopy
retro_itri_1376,
Tursiops truncatus ENSTTRG000000013441 retrocopy
retro_ttru_1758,

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 = 0.06 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .02 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .03 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .05 RPM
CEU_NA12760 0 .04 RPM
CEU_NA12827 0 .05 RPM
CEU_NA12872 0 .00 RPM
CEU_NA12873 0 .00 RPM
FIN_HG00183 0 .03 RPM
FIN_HG00277 0 .00 RPM
FIN_HG00315 0 .06 RPM
FIN_HG00321 0 .03 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 .02 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 .00 RPM
GBR_HG00143 0 .03 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .02 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 .03 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .00 RPM
YRI_NA18870 0 .00 RPM
YRI_NA18907 0 .00 RPM
YRI_NA18916 0 .02 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 .02 RPM
YRI_NA19223 0 .04 RPM

Indel association:

No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (PubMed).





Copyright © RetrogeneDB 2014-2017