RetrogeneDB ID:

retro_hsap_2651

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:3:57168163..57168748(+)
Located in intron of:ENSG00000144730
Retrocopy
information
Ensembl ID:ENSG00000229863
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL19
Ensembl ID:ENSG00000108298
Aliases:RPL19, L19
Description:ribosomal protein L19 [Source:HGNC Symbol;Acc:10312]


Retrocopy-Parental alignment summary:






>retro_hsap_2651
ATGAGTATGCTCAGGTTTCAGATGAGGCTCGCCTTTAGTGTCCTCTGCTGTGGCAAGAAGAAGGTCTGGTTGGACCCCAA
TAAGACCAATGAAATCGCCAATGCCAACTTCCATCAGCAGATCCAGAAGCTGATCAAAGATGGGCTGATCATCTACAAAC
CTGTGACTTTCCATTCCCGGGCTTGATGCCGGGAAAACACCTTGGCCCGCTGGAAGGGCAGGCACATGGGCATAAGTAAG
CGAAAGGGTACAGCCAATGCCCAAATGCCAGGGAACGTAACTTGGATGAGGAGAATGCGGATTCTGTGCTGGCTGCTGAG
AAGATACTGTGAATCTAAGAAGATTGATCACCACACATATCACAGCCTGTACCTGAAGGTGAAGGGGAATGTGTTCAAAA
ACAAGTGGATTCTCATGGAACACATCCTCAAGCTGAAGGCAGACAAGGCCCACAAGAAGCTGCAGGCTGACCAGGCTAAG
GCCCGCAGGTCTAAGACCAAGGAAGCACGCAAGCACCATGAAGACCGCCTACAGGCCAAGGAGGAGATCATCAAGACTTT
GTCTAAGGAGGAAGAGACCGAGAAG

ORF - retro_hsap_2651 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 83.67 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMSMLRLQKRLASSVLRCGKKKVWLDPNETNEIANANSRQQIRKLIKDGLIIRKPVTVHSRARCRKNTLAR
MSMLR.Q.RLA.SVL.CGKKKVWLDPN.TNEIANAN..QQI.KLIKDGLII.KPVT.HSRA.CR.NTLAR
RetrocopyMSMLRFQMRLAFSVLCCGKKKVWLDPNKTNEIANANFHQQIQKLIKDGLIIYKPVTFHSRA*CRENTLAR
ParentalRKGRHMGIGKRKGTANARMPEKVTWMRRMRILRRLLRRYRESKKIDRHMYHSLYLKVKGNVFKNKRILME
.KGRHMGI.KRKGTANA.MP..VTWMRRMRIL..LLRRY.ESKKID.H.YHSLYLKVKGNVFKNK.ILME
RetrocopyWKGRHMGISKRKGTANAQMPGNVTWMRRMRILCWLLRRYCESKKIDHHTYHSLYLKVKGNVFKNKWILME
ParentalHIHKLKADKARKKLLADQAEARRSKTKEARKRREERLQAKKEEIIKTLSKEEETKK
HI.KLKADKA.KKL.ADQA.ARRSKTKEARK..E.RLQA.KEEIIKTLSKEEET.K
RetrocopyHILKLKADKAHKKLQADQAKARRSKTKEARKHHEDRLQA-KEEIIKTLSKEEETEK

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 516 .45 RPM
bodymap2_adrenal 0 .02 RPM 693 .61 RPM
bodymap2_brain 0 .00 RPM 128 .03 RPM
bodymap2_breast 0 .00 RPM 337 .42 RPM
bodymap2_colon 0 .00 RPM 559 .54 RPM
bodymap2_heart 0 .00 RPM 177 .80 RPM
bodymap2_kidney 0 .00 RPM 314 .43 RPM
bodymap2_liver 0 .00 RPM 244 .38 RPM
bodymap2_lung 0 .00 RPM 650 .91 RPM
bodymap2_lymph_node 0 .00 RPM 827 .28 RPM
bodymap2_ovary 0 .00 RPM 567 .84 RPM
bodymap2_prostate 0 .02 RPM 843 .80 RPM
bodymap2_skeletal_muscle 0 .00 RPM 579 .48 RPM
bodymap2_testis 0 .00 RPM 375 .55 RPM
bodymap2_thyroid 0 .00 RPM 358 .00 RPM
bodymap2_white_blood_cells 0 .00 RPM 888 .83 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_2651 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_2651 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_13654945 libraries13 libraries374 libraries604 libraries793 libraries

The graphical summary, for retro_hsap_2651 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_2651 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2651 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_1786
Pongo abelii retro_pabe_2320
Parental genes homology:
Parental genes homology involve 14 parental genes, and 163 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000041215 retrocopies
retro_amel_1195, retro_amel_1663, retro_amel_451, retro_amel_531, retro_amel_889,
Callithrix jacchus ENSCJAG000000085204 retrocopies
retro_cjac_131, retro_cjac_220, retro_cjac_32, retro_cjac_64,
Dasypus novemcinctus ENSDNOG000000197427 retrocopies
retro_dnov_1478, retro_dnov_1897, retro_dnov_2, retro_dnov_2170, retro_dnov_2431, retro_dnov_691, retro_dnov_720,
Dipodomys ordii ENSDORG000000043301 retrocopy
retro_dord_105,
Equus caballus ENSECAG000000250806 retrocopies
retro_ecab_104, retro_ecab_319, retro_ecab_351, retro_ecab_456, retro_ecab_497, retro_ecab_905,
Homo sapiens ENSG00000108298 21 retrocopies
retro_hsap_1085, retro_hsap_1802, retro_hsap_2072, retro_hsap_2157, retro_hsap_2209, retro_hsap_2406, retro_hsap_2651 , retro_hsap_2679, retro_hsap_2850, retro_hsap_3012, retro_hsap_3155, retro_hsap_3274, retro_hsap_3401, retro_hsap_3885, retro_hsap_3933, retro_hsap_399, retro_hsap_3991, retro_hsap_4219, retro_hsap_4680, retro_hsap_4774, retro_hsap_739,
Macaca mulatta ENSMMUG000000042352 retrocopies
retro_mmul_283, retro_mmul_63,
Mus musculus ENSMUSG0000001740425 retrocopies
retro_mmus_1174, retro_mmus_1235, retro_mmus_1248, retro_mmus_1273, retro_mmus_1323, retro_mmus_1397, retro_mmus_1591, retro_mmus_1614, retro_mmus_1699, retro_mmus_1700, retro_mmus_1877, retro_mmus_1885, retro_mmus_1964, retro_mmus_2301, retro_mmus_2688, retro_mmus_2749, retro_mmus_2967, retro_mmus_3110, retro_mmus_3187, retro_mmus_3310, retro_mmus_341, retro_mmus_3413, retro_mmus_507, retro_mmus_571, retro_mmus_600,
Nomascus leucogenys ENSNLEG0000000074819 retrocopies
retro_nleu_1182, retro_nleu_1570, retro_nleu_1602, retro_nleu_1620, retro_nleu_1889, retro_nleu_2171, retro_nleu_2236, retro_nleu_2284, retro_nleu_2335, retro_nleu_2430, retro_nleu_2446, retro_nleu_2538, retro_nleu_2695, retro_nleu_2702, retro_nleu_2735, retro_nleu_3116, retro_nleu_479, retro_nleu_540, retro_nleu_656,
Pongo abelii ENSPPYG0000000849220 retrocopies
retro_pabe_1546, retro_pabe_1687, retro_pabe_1709, retro_pabe_1815, retro_pabe_2177, retro_pabe_2300, retro_pabe_2320, retro_pabe_2496, retro_pabe_2625, retro_pabe_2799, retro_pabe_2800, retro_pabe_3166, retro_pabe_3278, retro_pabe_3299, retro_pabe_3513, retro_pabe_3635, retro_pabe_3829, retro_pabe_4, retro_pabe_973, retro_pabe_980,
Pteropus vampyrus ENSPVAG000000084989 retrocopies
retro_pvam_1191, retro_pvam_1332, retro_pvam_183, retro_pvam_244, retro_pvam_468, retro_pvam_792, retro_pvam_914, retro_pvam_918, retro_pvam_950,
Rattus norvegicus ENSRNOG0000000474137 retrocopies
retro_rnor_1029, retro_rnor_1039, retro_rnor_1295, retro_rnor_1338, retro_rnor_1405, retro_rnor_1440, retro_rnor_1449, retro_rnor_1478, retro_rnor_1512, retro_rnor_1525, retro_rnor_1558, retro_rnor_1577, retro_rnor_1765, retro_rnor_1766, retro_rnor_1795, retro_rnor_1814, retro_rnor_1860, retro_rnor_1885, retro_rnor_1905, retro_rnor_1907, retro_rnor_1970, retro_rnor_1981, retro_rnor_208, retro_rnor_2169, retro_rnor_2522, retro_rnor_2536, retro_rnor_2708, retro_rnor_2773, retro_rnor_2783, retro_rnor_2921, retro_rnor_2943, retro_rnor_326, retro_rnor_426, retro_rnor_434, retro_rnor_464, retro_rnor_465, retro_rnor_829,
Sarcophilus harrisii ENSSHAG000000164824 retrocopies
retro_shar_159, retro_shar_287, retro_shar_317, retro_shar_415,
Sus scrofa ENSSSCG000000175093 retrocopies
retro_sscr_1108, retro_sscr_398, retro_sscr_913,

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 = 0.03 RPM Legend:


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 .03 RPM
GBR_HG00142 0 .00 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

Indel association:

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



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