RetrogeneDB ID:

retro_hsap_1810

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:17:17286693..17287326(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000215030
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL13
Ensembl ID:ENSG00000167526
Aliases:RPL13, BBC1, D16S444E, D16S44E, L13
Description:ribosomal protein L13 [Source:HGNC Symbol;Acc:10303]


Retrocopy-Parental alignment summary:






>retro_hsap_1810
ATGACGCCCAGCCGGAATGGCATGGTCTTGAAGCCCCACTTCCACAAGGACTGGCAGCGGCGCGTGGCCACGTGGTTCAA
CCAGCCGGCCCGGAAGATCCGCAGACGTAAGGCCCGGCAAGCCAAGGCGCGCCGCATCGCCCCGCGCCCCGCGTCGGGGC
CCATCCGGCCCATCGTGTGCTGCCCCACGGTTCGGTACCACACGAAGGTGCGCGCCGGCCGCGGCTTCAATCTGGAGGAG
CTCAGGGTGGCCGGCATTCACAAGAAGGTGGCCCGGACCATCGGCATTTCTGTGGATCCGAGGAGGCGGAACAAGTCCAC
GGAGTCCCTGCAGGCGAACGTGCAGCGGCTGAAGGAGTACCGCTCCAAACTCATCCTCTTCCCCAGGAAGCCCTCGGCCC
CCAAGAAGGGAGACAGTTCTGCTGAAGAACTGAAACTGGCCACCCAGCTGACCGGACCGGTCATGCCCATCCGGAATGTC
TATAAGAAGGAGAAAGCTCGAGTGATCACTGAGGAAGAGAAGAATTTCAAAGCCTTCGCTAGTCTCCGTATGGCCCGTGC
CAACGCCCGGCTCTTCGGCATACGGGCAAAAAGAGCCAAGGAAGCCGCAGAACAGGATGTTGAAAAGAAAAAA

ORF - retro_hsap_1810 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 98.1 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMAPSRNGMVLKPHFHKDWQRRVATWFNQPARKIRRRKARQAKARRIAPRPASGPIRPIVRCPTVRYHTKV
M.PSRNGMVLKPHFHKDWQRRVATWFNQPARKIRRRKARQAKARRIAPRPASGPIRPIV.CPTVRYHTKV
RetrocopyMTPSRNGMVLKPHFHKDWQRRVATWFNQPARKIRRRKARQAKARRIAPRPASGPIRPIVCCPTVRYHTKV
ParentalRAGRGFSLEELRVAGIHKKVARTIGISVDPRRRNKSTESLQANVQRLKEYRSKLILFPRKPSAPKKGDSS
RAGRGF.LEELRVAGIHKKVARTIGISVDPRRRNKSTESLQANVQRLKEYRSKLILFPRKPSAPKKGDSS
RetrocopyRAGRGFNLEELRVAGIHKKVARTIGISVDPRRRNKSTESLQANVQRLKEYRSKLILFPRKPSAPKKGDSS
ParentalAEELKLATQLTGPVMPVRNVYKKEKARVITEEEKNFKAFASLRMARANARLFGIRAKRAKEAAEQDVEKK
AEELKLATQLTGPVMP.RNVYKKEKARVITEEEKNFKAFASLRMARANARLFGIRAKRAKEAAEQDVEKK
RetrocopyAEELKLATQLTGPVMPIRNVYKKEKARVITEEEKNFKAFASLRMARANARLFGIRAKRAKEAAEQDVEKK
ParentalK
K
RetrocopyK

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 10 .44 RPM 476 .99 RPM
bodymap2_adrenal 4 .18 RPM 586 .53 RPM
bodymap2_brain 0 .40 RPM 110 .54 RPM
bodymap2_breast 2 .02 RPM 300 .39 RPM
bodymap2_colon 2 .40 RPM 626 .85 RPM
bodymap2_heart 0 .87 RPM 135 .26 RPM
bodymap2_kidney 0 .77 RPM 213 .55 RPM
bodymap2_liver 0 .78 RPM 204 .96 RPM
bodymap2_lung 2 .87 RPM 687 .47 RPM
bodymap2_lymph_node 4 .42 RPM 880 .08 RPM
bodymap2_ovary 2 .29 RPM 665 .98 RPM
bodymap2_prostate 5 .47 RPM 974 .39 RPM
bodymap2_skeletal_muscle 4 .46 RPM 562 .00 RPM
bodymap2_testis 1 .45 RPM 347 .76 RPM
bodymap2_thyroid 5 .14 RPM 276 .73 RPM
bodymap2_white_blood_cells 4 .13 RPM 863 .96 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_1810 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_1810 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_55925331 libraries656 libraries751 libraries76 libraries15 libraries
TSS #2 TSS_559262 libraries0 libraries1 library3 libraries1823 libraries

The graphical summary, for retro_hsap_1810 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_1810 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1810 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_1175
Parental genes homology:
Parental genes homology involve 17 parental genes, and 121 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000170721 retrocopy
retro_acar_70,
Canis familiaris ENSCAFG000000198405 retrocopies
retro_cfam_1135, retro_cfam_1919, retro_cfam_2122, retro_cfam_565, retro_cfam_897,
Callithrix jacchus ENSCJAG000000096725 retrocopies
retro_cjac_2607, retro_cjac_2961, retro_cjac_4054, retro_cjac_663, retro_cjac_747,
Cavia porcellus ENSCPOG000000273484 retrocopies
retro_cpor_1014, retro_cpor_1192, retro_cpor_1242, retro_cpor_491,
Echinops telfairi ENSETEG000000150574 retrocopies
retro_etel_1240, retro_etel_1382, retro_etel_1606, retro_etel_703,
Felis catus ENSFCAG000000033384 retrocopies
retro_fcat_1946, retro_fcat_706, retro_fcat_852, retro_fcat_866,
Homo sapiens ENSG00000167526 12 retrocopies
retro_hsap_1377, retro_hsap_1810 , retro_hsap_2070, retro_hsap_2430, retro_hsap_2485, retro_hsap_2824, retro_hsap_3207, retro_hsap_3281, retro_hsap_3443, retro_hsap_4074, retro_hsap_478, retro_hsap_951,
Microcebus murinus ENSMICG000000081914 retrocopies
retro_mmur_249, retro_mmur_288, retro_mmur_779, retro_mmur_908,
Myotis lucifugus ENSMLUG000000109506 retrocopies
retro_mluc_1431, retro_mluc_1436, retro_mluc_1549, retro_mluc_2022, retro_mluc_891, retro_mluc_991,
Monodelphis domestica ENSMODG000000036634 retrocopies
retro_mdom_1001, retro_mdom_416, retro_mdom_439, retro_mdom_674,
Mus musculus ENSMUSG0000000074023 retrocopies
retro_mmus_1091, retro_mmus_1522, retro_mmus_1533, retro_mmus_1854, retro_mmus_2074, retro_mmus_2163, retro_mmus_2186, retro_mmus_2321, retro_mmus_2333, retro_mmus_2351, retro_mmus_25, retro_mmus_2668, retro_mmus_2718, retro_mmus_3097, retro_mmus_3274, retro_mmus_3453, retro_mmus_3489, retro_mmus_3500, retro_mmus_355, retro_mmus_3711, retro_mmus_692, retro_mmus_732, retro_mmus_863,
Nomascus leucogenys ENSNLEG0000001577413 retrocopies
retro_nleu_1156, retro_nleu_1202, retro_nleu_2299, retro_nleu_238, retro_nleu_2457, retro_nleu_2530, retro_nleu_2657, retro_nleu_273, retro_nleu_2732, retro_nleu_2885, retro_nleu_3016, retro_nleu_789, retro_nleu_892,
Ornithorhynchus anatinus ENSOANG000000067291 retrocopy
retro_oana_78,
Otolemur garnettii ENSOGAG000000264443 retrocopies
retro_ogar_1165, retro_ogar_1831, retro_ogar_1853,
Pan troglodytes ENSPTRG0000000848012 retrocopies
retro_ptro_1175, retro_ptro_1382, retro_ptro_1402, retro_ptro_1438, retro_ptro_1914, retro_ptro_2219, retro_ptro_2242, retro_ptro_2336, retro_ptro_2761, retro_ptro_359, retro_ptro_658, retro_ptro_946,
Pteropus vampyrus ENSPVAG000000151306 retrocopies
retro_pvam_1174, retro_pvam_1289, retro_pvam_1344, retro_pvam_228, retro_pvam_58, retro_pvam_616,
Rattus norvegicus ENSRNOG0000001533514 retrocopies
retro_rnor_1054, retro_rnor_1260, retro_rnor_158, retro_rnor_160, retro_rnor_1719, retro_rnor_1720, retro_rnor_1834, retro_rnor_1848, retro_rnor_2471, retro_rnor_2574, retro_rnor_2608, retro_rnor_2787, retro_rnor_2854, retro_rnor_682,

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 = 99.61 RPM Legend:


Library Retrogene expression
CEU_NA11831 7 .36 RPM
CEU_NA11843 11 .35 RPM
CEU_NA11930 9 .19 RPM
CEU_NA12004 6 .61 RPM
CEU_NA12400 8 .59 RPM
CEU_NA12751 5 .61 RPM
CEU_NA12760 11 .86 RPM
CEU_NA12827 61 .13 RPM
CEU_NA12872 6 .89 RPM
CEU_NA12873 7 .53 RPM
FIN_HG00183 7 .44 RPM
FIN_HG00277 11 .17 RPM
FIN_HG00315 6 .15 RPM
FIN_HG00321 4 .59 RPM
FIN_HG00328 4 .88 RPM
FIN_HG00338 8 .30 RPM
FIN_HG00349 8 .22 RPM
FIN_HG00375 6 .16 RPM
FIN_HG00377 5 .67 RPM
FIN_HG00378 5 .67 RPM
GBR_HG00099 7 .24 RPM
GBR_HG00111 85 .29 RPM
GBR_HG00114 86 .07 RPM
GBR_HG00119 50 .00 RPM
GBR_HG00131 28 .74 RPM
GBR_HG00133 50 .43 RPM
GBR_HG00134 91 .38 RPM
GBR_HG00137 10 .61 RPM
GBR_HG00142 65 .32 RPM
GBR_HG00143 64 .84 RPM
TSI_NA20512 99 .61 RPM
TSI_NA20513 62 .17 RPM
TSI_NA20518 7 .11 RPM
TSI_NA20532 10 .37 RPM
TSI_NA20538 10 .69 RPM
TSI_NA20756 36 .23 RPM
TSI_NA20765 4 .27 RPM
TSI_NA20771 7 .04 RPM
TSI_NA20786 4 .45 RPM
TSI_NA20798 5 .49 RPM
YRI_NA18870 7 .58 RPM
YRI_NA18907 66 .52 RPM
YRI_NA18916 5 .47 RPM
YRI_NA19093 6 .04 RPM
YRI_NA19099 5 .94 RPM
YRI_NA19114 70 .02 RPM
YRI_NA19118 9 .38 RPM
YRI_NA19213 3 .04 RPM
YRI_NA19214 48 .43 RPM
YRI_NA19223 6 .09 RPM

Indel association:

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



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