RetrogeneDB ID:

retro_hsap_2315

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:2:130697475..130697749(-)
Located in intron of:ENSG00000237574
Retrocopy
information
Ensembl ID:ENSG00000234559
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL22
Ensembl ID:ENSG00000116251
Aliases:RPL22, EAP, HBP15, HBP15/L22, L22
Description:ribosomal protein L22 [Source:HGNC Symbol;Acc:10315]


Retrocopy-Parental alignment summary:






>retro_hsap_2315
AAGCAGGTTCTGAAGTTCACTCTAGATTGCAGCCACCCCGTGGAAGACGGAATCATGGACGCTGCCAATTTTGAACAGCC
TTTCCGAGAGAGGATCAAAGTGAACTGAAAAGCTGGGAAACCTGGTGGAGGGGTGGTGACCATCGAAAGGAGCAAGAGCA
AGATCACCATGACATCTGAGGTGCCTTTTTCCAAAAGATATTTGAAATATCACACCAAAAAATTTTGAAGAAGAATAATC
TATGTGATTGGTTTGTGTAGCTGCTAACAGCAGA

ORF - retro_hsap_2315 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 81.91 %
Parental protein coverage: 71.88 %
Number of stop codons detected: 1
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalKQVLKFTLDCTHPVEDGIMDAANFEQFLQERIKVNGKAGNLGGGVVTIERSKSKITVTSEVPFSKRYLKY
KQVLKFTLDC.HPVEDGIMDAANFEQ...ERIKVN.KAG..GGGVVTIERSKSKIT.TSEVPFSKRYLKY
RetrocopyKQVLKFTLDCSHPVEDGIMDAANFEQPFRERIKVN*KAGKPGGGVVTIERSKSKITMTSEVPFSKRYLKY
ParentalLTKKY-LKKNNLRDW-LRVVANSK
.TKK..LKKNNL.DW...V.ANS.
RetrocopyHTKKF<LKKNNLCDW<VCVAANSR

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 206 .65 RPM
bodymap2_adrenal 0 .00 RPM 196 .92 RPM
bodymap2_brain 0 .00 RPM 89 .40 RPM
bodymap2_breast 0 .00 RPM 197 .41 RPM
bodymap2_colon 0 .00 RPM 279 .67 RPM
bodymap2_heart 0 .00 RPM 88 .35 RPM
bodymap2_kidney 0 .00 RPM 124 .17 RPM
bodymap2_liver 0 .00 RPM 77 .90 RPM
bodymap2_lung 0 .00 RPM 247 .10 RPM
bodymap2_lymph_node 0 .00 RPM 258 .85 RPM
bodymap2_ovary 0 .00 RPM 424 .80 RPM
bodymap2_prostate 0 .00 RPM 414 .95 RPM
bodymap2_skeletal_muscle 0 .00 RPM 144 .01 RPM
bodymap2_testis 0 .00 RPM 148 .81 RPM
bodymap2_thyroid 0 .00 RPM 215 .71 RPM
bodymap2_white_blood_cells 0 .00 RPM 289 .19 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_2315 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_2315 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_1121561263 libraries469 libraries57 libraries14 libraries26 libraries

The graphical summary, for retro_hsap_2315 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_2315 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2315 has 9 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_600
Gorilla gorilla retro_ggor_531
Pan troglodytes retro_ptro_502
Pongo abelii retro_pabe_590
Gorilla gorilla retro_ggor_1757
Pan troglodytes retro_ptro_1690
Homo sapiens retro_hsap_1299
Pan troglodytes retro_ptro_950
Macaca mulatta retro_mmul_1047
Parental genes homology:
Parental genes homology involve 22 parental genes, and 184 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000098647 retrocopies
retro_amel_1219, retro_amel_1247, retro_amel_1775, retro_amel_1793, retro_amel_369, retro_amel_830, retro_amel_870,
Bos taurus ENSBTAG000000144234 retrocopies
retro_btau_1491, retro_btau_566, retro_btau_694, retro_btau_892,
Choloepus hoffmanni ENSCHOG000000074772 retrocopies
retro_chof_1785, retro_chof_2537,
Callithrix jacchus ENSCJAG0000000013212 retrocopies
retro_cjac_1032, retro_cjac_1055, retro_cjac_1257, retro_cjac_1301, retro_cjac_2352, retro_cjac_2436, retro_cjac_2874, retro_cjac_2954, retro_cjac_3925, retro_cjac_472, retro_cjac_611, retro_cjac_867,
Dasypus novemcinctus ENSDNOG000000131668 retrocopies
retro_dnov_1282, retro_dnov_1523, retro_dnov_2043, retro_dnov_2126, retro_dnov_38, retro_dnov_382, retro_dnov_425, retro_dnov_567,
Felis catus ENSFCAG000000063203 retrocopies
retro_fcat_1591, retro_fcat_1656, retro_fcat_1715,
Homo sapiens ENSG00000116251 16 retrocopies
retro_hsap_1162, retro_hsap_1299, retro_hsap_1445, retro_hsap_1720, retro_hsap_2136, retro_hsap_2138, retro_hsap_2142, retro_hsap_2306, retro_hsap_2315 , retro_hsap_349, retro_hsap_3814, retro_hsap_485, retro_hsap_4865, retro_hsap_4909, retro_hsap_600, retro_hsap_726,
Homo sapiens ENSG000001635841 retrocopy
retro_hsap_2929,
Gorilla gorilla ENSGGOG0000002773910 retrocopies
retro_ggor_1111, retro_ggor_1652, retro_ggor_1655, retro_ggor_1708, retro_ggor_1757, retro_ggor_2268, retro_ggor_2567, retro_ggor_37, retro_ggor_531, retro_ggor_613,
Loxodonta africana ENSLAFG000000063525 retrocopies
retro_lafr_1100, retro_lafr_380, retro_lafr_649, retro_lafr_981, retro_lafr_993,
Macaca mulatta ENSMMUG0000001834712 retrocopies
retro_mmul_1004, retro_mmul_1044, retro_mmul_1047, retro_mmul_1512, retro_mmul_2209, retro_mmul_2264, retro_mmul_2467, retro_mmul_2601, retro_mmul_271, retro_mmul_445, retro_mmul_469, retro_mmul_80,
Mustela putorius furoENSMPUG000000070876 retrocopies
retro_mputfur_1074, retro_mputfur_1277, retro_mputfur_134, retro_mputfur_1433, retro_mputfur_578, retro_mputfur_873,
Mus musculus ENSMUSG000000289365 retrocopies
retro_mmus_1883, retro_mmus_1906, retro_mmus_2123, retro_mmus_2459, retro_mmus_3171,
Nomascus leucogenys ENSNLEG0000001033710 retrocopies
retro_nleu_1309, retro_nleu_2354, retro_nleu_2367, retro_nleu_2509, retro_nleu_2747, retro_nleu_2772, retro_nleu_2783, retro_nleu_2881, retro_nleu_2946, retro_nleu_3003,
Otolemur garnettii ENSOGAG000000147767 retrocopies
retro_ogar_1116, retro_ogar_1415, retro_ogar_1418, retro_ogar_2188, retro_ogar_2979, retro_ogar_399, retro_ogar_917,
Pongo abelii ENSPPYG0000000195111 retrocopies
retro_pabe_1196, retro_pabe_1213, retro_pabe_1435, retro_pabe_166, retro_pabe_248, retro_pabe_3114, retro_pabe_349, retro_pabe_3782, retro_pabe_3817, retro_pabe_590, retro_pabe_966,
Pan troglodytes ENSPTRG0000000007614 retrocopies
retro_ptro_1562, retro_ptro_1563, retro_ptro_1630, retro_ptro_1690, retro_ptro_2596, retro_ptro_275, retro_ptro_3056, retro_ptro_3240, retro_ptro_365, retro_ptro_502, retro_ptro_517, retro_ptro_795, retro_ptro_950, retro_ptro_984,
Rattus norvegicus ENSRNOG000000111045 retrocopies
retro_rnor_1315, retro_rnor_1687, retro_rnor_2089, retro_rnor_2149, retro_rnor_439,
Sus scrofa ENSSSCG000000033674 retrocopies
retro_sscr_257, retro_sscr_276, retro_sscr_497, retro_sscr_509,
Tupaia belangeri ENSTBEG0000000917233 retrocopies
retro_tbel_1047, retro_tbel_1181, retro_tbel_1263, retro_tbel_1422, retro_tbel_1773, retro_tbel_1951, retro_tbel_2121, retro_tbel_2182, retro_tbel_2231, retro_tbel_2429, retro_tbel_2452, retro_tbel_2801, retro_tbel_2923, retro_tbel_3090, retro_tbel_3160, retro_tbel_3265, retro_tbel_3362, retro_tbel_3482, retro_tbel_3719, retro_tbel_3885, retro_tbel_3960, retro_tbel_397, retro_tbel_4199, retro_tbel_4225, retro_tbel_4386, retro_tbel_4437, retro_tbel_4607, retro_tbel_504, retro_tbel_582, retro_tbel_659, retro_tbel_680, retro_tbel_755, retro_tbel_920,
Tursiops truncatus ENSTTRG000000104888 retrocopies
retro_ttru_1268, retro_ttru_147, retro_ttru_1519, retro_ttru_1564, retro_ttru_1739, retro_ttru_413, retro_ttru_714, retro_ttru_871,
Vicugna pacos ENSVPAG000000094661 retrocopy
retro_vpac_330,

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 .03 RPM
CEU_NA12873 0 .00 RPM
FIN_HG00183 0 .00 RPM
FIN_HG00277 0 .00 RPM
FIN_HG00315 0 .03 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 .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 .02 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 .02 RPM

Indel association:

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



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