RetrogeneDB ID:

retro_hsap_563

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:10:44126394..44126862(+)
Located in intron of:ENSG00000223910
Retrocopy
information
Ensembl ID:ENSG00000238263
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL21
Ensembl ID:ENSG00000122026
Aliases:RPL21, L21
Description:ribosomal protein L21 [Source:HGNC Symbol;Acc:10313]


Retrocopy-Parental alignment summary:






>retro_hsap_563
ATGACAAACACAAAGGGAAAGAGGAGAGGCTCCTGGTAGATGTCTTCTAGGCCTTTTAGGAAGCATGGAGTTGTTCCCTT
TGGTCACGTATATGTGAATCTATAAGAAAGATGATATTGTAGACATTAAAGGAGTGGGCACTGTTCAAGAAGGAATGCCC
CACAAGTGTTATCATGGCAGAACTGGAAGAGTCTACAGTGTTACGCAGCAGGCCGTCGGCATTGTTGTAAACACACAAGT
TAAGGGCAAGTTCTTGCCAAGAGAATTCATGTGGGTATTGAGCACTTTAAGCGCTCTGAGAGCTGAGCTAGCTTCCTGAA
ACTTGTGAAGGAAAATGATCAGAAAAAGAAGGAAGCCAAAGAGAAAGGTACCTGGATTCAGCAGAAGTGCCAGTCTGCTC
TGCCCAGAGAAGCGCACTGTGTGAGAACAAATGGGAAGGAGCTTGAGCTGCTGGAACCTCTTCCCTAT

ORF - retro_hsap_563 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 79.75 %
Parental protein coverage: 97.5 %
Number of stop codons detected: 3
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMTNTKGKRRGTRYMFSRPFRKHGVVP-LATYMRIYKKGDIVDIKGMGTVQKGMPHKCYHGKTGRVYNVTQ
MTNTKGKRRG...M.SRPFRKHGVVP.L.TYM.IYKK.DIVDIKG.GTVQ.GMPHKCYHG.TGRVY.VTQ
RetrocopyMTNTKGKRRGSW*MSSRPFRKHGVVP>LVTYM*IYKKDDIVDIKGVGTVQEGMPHKCYHGRTGRVYSVTQ
ParentalHAVGIVVNKQVKGK-ILAKRINVRIEHIKHSKSRDSFLKRVKENDQKKKEAKEKGTWVQLKRQPAPPREA
.AVGIVVN.QVKGK..LAKRI.V.IEH.K.S.S..SFLK.VKENDQKKKEAKEKGTW.Q.K.Q.A.PREA
RetrocopyQAVGIVVNTQVKGK<VLAKRIHVGIEHFKRSES*ASFLKLVKENDQKKKEAKEKGTWIQQKCQSALPREA
ParentalHFVRTNGKEPELLEPIPY
H.VRTNGKE.ELLEP.PY
RetrocopyHCVRTNGKELELLEPLPY

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 80 .68 RPM
bodymap2_adrenal 0 .12 RPM 121 .12 RPM
bodymap2_brain 0 .30 RPM 35 .89 RPM
bodymap2_breast 0 .00 RPM 60 .37 RPM
bodymap2_colon 0 .08 RPM 99 .58 RPM
bodymap2_heart 0 .00 RPM 111 .91 RPM
bodymap2_kidney 0 .00 RPM 84 .83 RPM
bodymap2_liver 0 .00 RPM 89 .65 RPM
bodymap2_lung 0 .11 RPM 422 .43 RPM
bodymap2_lymph_node 0 .00 RPM 336 .42 RPM
bodymap2_ovary 0 .04 RPM 157 .01 RPM
bodymap2_prostate 0 .00 RPM 418 .56 RPM
bodymap2_skeletal_muscle 0 .00 RPM 150 .89 RPM
bodymap2_testis 0 .00 RPM 54 .92 RPM
bodymap2_thyroid 0 .13 RPM 74 .87 RPM
bodymap2_white_blood_cells 0 .00 RPM 422 .68 RPM
RNA Polymerase II actvity near the 5' end of retro_hsap_563 was not detected
No EST(s) were mapped for retro_hsap_563 retrocopy.
No TSS is located nearby retro_hsap_563 retrocopy 5' end.
retro_hsap_563 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_563 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 10 parental genes, and 295 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000016485 retrocopies
Homo sapiens ENSG00000122026 105 retrocopies
retro_hsap_1007, retro_hsap_1011, retro_hsap_1019, retro_hsap_1032, retro_hsap_1040, retro_hsap_1099, retro_hsap_1107, retro_hsap_1213, retro_hsap_1218, retro_hsap_122, retro_hsap_1280, retro_hsap_1288, retro_hsap_1298, retro_hsap_1379, retro_hsap_1381, retro_hsap_1419, retro_hsap_143, retro_hsap_1430, retro_hsap_1446, retro_hsap_1453, retro_hsap_1505, retro_hsap_1576, retro_hsap_1578, retro_hsap_160, retro_hsap_1600, retro_hsap_1663, retro_hsap_1712, retro_hsap_1723, retro_hsap_1734, retro_hsap_1757, retro_hsap_1805, retro_hsap_1842, retro_hsap_1886, retro_hsap_1904, retro_hsap_1920, retro_hsap_2050, retro_hsap_2088, retro_hsap_2109, retro_hsap_2153, retro_hsap_2178, retro_hsap_2221, retro_hsap_2245, retro_hsap_2258, retro_hsap_2266, retro_hsap_2357, retro_hsap_2442, retro_hsap_252, retro_hsap_2625, retro_hsap_2635, retro_hsap_2655, retro_hsap_2716, retro_hsap_2855, retro_hsap_2876, retro_hsap_2916, retro_hsap_2937, retro_hsap_3037, retro_hsap_3039, retro_hsap_3091, retro_hsap_3094, retro_hsap_3119, retro_hsap_3160, retro_hsap_3185, retro_hsap_3264, retro_hsap_3304, retro_hsap_3375, retro_hsap_3429, retro_hsap_3435, retro_hsap_3521, retro_hsap_3555, retro_hsap_3558, retro_hsap_362, retro_hsap_3628, retro_hsap_3658, retro_hsap_3662, retro_hsap_367, retro_hsap_3688, retro_hsap_3694, retro_hsap_3705, retro_hsap_3747, retro_hsap_3764, retro_hsap_381, retro_hsap_3911, retro_hsap_3945, retro_hsap_3955, retro_hsap_4092, retro_hsap_4193, retro_hsap_424, retro_hsap_4276, retro_hsap_4283, retro_hsap_4286, retro_hsap_4302, retro_hsap_4713, retro_hsap_4733, retro_hsap_496, retro_hsap_503, retro_hsap_563 , retro_hsap_573, retro_hsap_582, retro_hsap_626, retro_hsap_654, retro_hsap_738, retro_hsap_752, retro_hsap_819, retro_hsap_900, retro_hsap_965,
Latimeria chalumnae ENSLACG000000126781 retrocopy
Loxodonta africana ENSLAFG0000000367711 retrocopies
Myotis lucifugus ENSMLUG0000001009346 retrocopies
Monodelphis domestica ENSMODG000000089231 retrocopy
Mus musculus ENSMUSG00000041453101 retrocopies
retro_mmus_1012, retro_mmus_1046, retro_mmus_1057, retro_mmus_1083, retro_mmus_1123, retro_mmus_1199, retro_mmus_1287, retro_mmus_1354, retro_mmus_1461, retro_mmus_1475, retro_mmus_1529, retro_mmus_1561, retro_mmus_1572, retro_mmus_1596, retro_mmus_1617, retro_mmus_1641, retro_mmus_1644, retro_mmus_17, retro_mmus_1714, retro_mmus_1739, retro_mmus_1762, retro_mmus_1797, retro_mmus_1848, retro_mmus_1860, retro_mmus_1862, retro_mmus_1875, retro_mmus_1897, retro_mmus_1915, retro_mmus_1931, retro_mmus_1936, retro_mmus_1994, retro_mmus_2042, retro_mmus_2049, retro_mmus_2101, retro_mmus_2130, retro_mmus_2176, retro_mmus_2179, retro_mmus_2185, retro_mmus_2214, retro_mmus_2233, retro_mmus_2237, retro_mmus_2238, retro_mmus_2279, retro_mmus_2309, retro_mmus_2312, retro_mmus_2335, retro_mmus_2344, retro_mmus_2395, retro_mmus_2447, retro_mmus_2517, retro_mmus_2567, retro_mmus_2585, retro_mmus_2598, retro_mmus_266, retro_mmus_2662, retro_mmus_2698, retro_mmus_2707, retro_mmus_2778, retro_mmus_2808, retro_mmus_2853, retro_mmus_2874, retro_mmus_2945, retro_mmus_2980, retro_mmus_3035, retro_mmus_3055, retro_mmus_3085, retro_mmus_3103, retro_mmus_3112, retro_mmus_3220, retro_mmus_3252, retro_mmus_3261, retro_mmus_3295, retro_mmus_3318, retro_mmus_3328, retro_mmus_333, retro_mmus_3341, retro_mmus_3446, retro_mmus_3545, retro_mmus_3581, retro_mmus_3712, retro_mmus_397, retro_mmus_400, retro_mmus_401, retro_mmus_598, retro_mmus_601, retro_mmus_606, retro_mmus_663, retro_mmus_734, retro_mmus_735, retro_mmus_758, retro_mmus_782, retro_mmus_806, retro_mmus_835, retro_mmus_862, retro_mmus_883, retro_mmus_918, retro_mmus_932, retro_mmus_940, retro_mmus_957, retro_mmus_993, retro_mmus_998,
Pan troglodytes ENSPTRG000000057281 retrocopy
Rattus norvegicus ENSRNOG0000000095713 retrocopies
Sarcophilus harrisii ENSSHAG0000000084511 retrocopies

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 = 0.04 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 .03 RPM
CEU_NA12873 0 .00 RPM
FIN_HG00183 0 .00 RPM
FIN_HG00277 0 .04 RPM
FIN_HG00315 0 .03 RPM
FIN_HG00321 0 .03 RPM
FIN_HG00328 0 .00 RPM
FIN_HG00338 0 .02 RPM
FIN_HG00349 0 .03 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 .00 RPM
GBR_HG00134 0 .00 RPM
GBR_HG00137 0 .00 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 .03 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .02 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 .03 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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