RetrogeneDB ID:

retro_hsap_1635

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:16:48634085..48634557(+)
Located in intron of:ENSG00000102921
Retrocopy
information
Ensembl ID:ENSG00000260033
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RSL24D1
Ensembl ID:ENSG00000137876
Aliases:None
Description:ribosomal L24 domain containing 1 [Source:HGNC Symbol;Acc:18479]


Retrocopy-Parental alignment summary:






>retro_hsap_1635
AAGTGTTATTTCTGTTTGGGCCCATCTACCCTGGCCACGGCATGATGTTCATCCGCAACGACTGAAAGGTGTTCAGATTT
TGTAAATCTAAATGTCATAAAAACTTTAAAAAGAAGCACAATCCTTGCAAAGTTAGGTGGACCAAAGCATTCCGGAAAGC
AGGTGGCAAAGAGCTTACACTGGATAATTCATTTGAATATGAAAAACATAGAAATGAAACCATCAAATACCAGTGAGAGC
TATGGAATAAAACTACTGAAGCAATGAAGACAGTTGAAGAGATCAAACAGAAACGCCAAGCTAAATTTATAATGAACAGA
TTGAAGAAAAATAAGAGCTACAGAAAGTTCAGGATATCAAACAGGTCAAGCAAAACATCCATCTTATCTGAGTTCCTCTT
GCAGGCAAAGGGAAGCAGTTGGAAGAGAAAACAGTACAGCAGTTACAAGAGAATGTGGACATGGAAGATGCT

ORF - retro_hsap_1635 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 86.88 %
Parental protein coverage: 96.93 %
Number of stop codons detected: 3
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalKCYFCSGP-IYPGHGMMFVRNDCKVFRFCKSKCHKNFKKKRNPRKVRWTKAFRKAAGKELTVDNSFEFEK
KCYFC.GP.IYPGHGMMF.RND.KVFRFCKSKCHKNFKKK.NP.KVRWTKAFRKA.GKELT.DNSFE.EK
RetrocopyKCYFCLGP<IYPGHGMMFIRND*KVFRFCKSKCHKNFKKKHNPCKVRWTKAFRKAGGKELTLDNSFEYEK
ParentalRRNEPIKYQRELWNKTIDAMKRVEEIKQKRQAKFIMNRLKKNK-ELQKVQDIKEVKQNIHLIRAPLAGKG
.RNE.IKYQ.ELWNKT..AMK.VEEIKQKRQAKFIMNRLKKNK.ELQKVQDIK.VKQNIHLI..PLAGKG
RetrocopyHRNETIKYQ*ELWNKTTEAMKTVEEIKQKRQAKFIMNRLKKNK<ELQKVQDIKQVKQNIHLI*VPLAGKG
ParentalKQLEEKMVQQLQEDVDMEDA
KQLEEK.VQQLQE.VDMEDA
RetrocopyKQLEEKTVQQLQENVDMEDA

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 84 .38 RPM
bodymap2_adrenal 0 .10 RPM 100 .71 RPM
bodymap2_brain 0 .02 RPM 97 .58 RPM
bodymap2_breast 0 .04 RPM 89 .90 RPM
bodymap2_colon 0 .02 RPM 204 .32 RPM
bodymap2_heart 0 .17 RPM 49 .05 RPM
bodymap2_kidney 0 .06 RPM 74 .84 RPM
bodymap2_liver 0 .00 RPM 36 .42 RPM
bodymap2_lung 0 .00 RPM 159 .14 RPM
bodymap2_lymph_node 0 .00 RPM 91 .24 RPM
bodymap2_ovary 0 .00 RPM 199 .23 RPM
bodymap2_prostate 0 .00 RPM 236 .44 RPM
bodymap2_skeletal_muscle 0 .00 RPM 76 .08 RPM
bodymap2_testis 0 .00 RPM 147 .26 RPM
bodymap2_thyroid 0 .00 RPM 138 .01 RPM
bodymap2_white_blood_cells 0 .00 RPM 121 .36 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_1635 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_1635 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_1635 retrocopy 5' end.

Lab - click to see more details

retro_hsap_1635 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1635 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_1103
Gorilla gorilla retro_ggor_1235
Pongo abelii retro_pabe_1350
Macaca mulatta retro_mmul_1560
Parental genes homology:
Parental genes homology involve 29 parental genes, and 171 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000013421 retrocopy
retro_btau_1304,
Canis familiaris ENSCAFG000000159041 retrocopy
retro_cfam_1744,
Choloepus hoffmanni ENSCHOG000000117999 retrocopies
retro_chof_112, retro_chof_1237, retro_chof_1314, retro_chof_1357, retro_chof_1938, retro_chof_243, retro_chof_67, retro_chof_809, retro_chof_896,
Callithrix jacchus ENSCJAG000000007952 retrocopies
retro_cjac_109, retro_cjac_7,
Dasypus novemcinctus ENSDNOG000000108122 retrocopies
retro_dnov_858, retro_dnov_954,
Equus caballus ENSECAG000000188611 retrocopy
retro_ecab_30,
Erinaceus europaeus ENSEEUG000000067551 retrocopy
retro_eeur_50,
Felis catus ENSFCAG000000192721 retrocopy
retro_fcat_851,
Homo sapiens ENSG00000137876 17 retrocopies
retro_hsap_1049, retro_hsap_1125, retro_hsap_1355, retro_hsap_1635 , retro_hsap_1829, retro_hsap_1887, retro_hsap_1941, retro_hsap_1963, retro_hsap_2268, retro_hsap_2467, retro_hsap_3378, retro_hsap_338, retro_hsap_3566, retro_hsap_3861, retro_hsap_4015, retro_hsap_4101, retro_hsap_894,
Gorilla gorilla ENSGGOG0000000519515 retrocopies
retro_ggor_1055, retro_ggor_1081, retro_ggor_1151, retro_ggor_1194, retro_ggor_1235, retro_ggor_1412, retro_ggor_1536, retro_ggor_1688, retro_ggor_2286, retro_ggor_2406, retro_ggor_2600, retro_ggor_2697, retro_ggor_2754, retro_ggor_359, retro_ggor_879,
Microcebus murinus ENSMICG000000026213 retrocopies
retro_mmur_1378, retro_mmur_306, retro_mmur_952,
Myotis lucifugus ENSMLUG000000119764 retrocopies
retro_mluc_1415, retro_mluc_1512, retro_mluc_2173, retro_mluc_2320,
Macaca mulatta ENSMMUG0000002069316 retrocopies
retro_mmul_1030, retro_mmul_1107, retro_mmul_1257, retro_mmul_1363, retro_mmul_1406, retro_mmul_1560, retro_mmul_1824, retro_mmul_1907, retro_mmul_2105, retro_mmul_2364, retro_mmul_322, retro_mmul_424, retro_mmul_582, retro_mmul_599, retro_mmul_817, retro_mmul_872,
Monodelphis domestica ENSMODG000000079661 retrocopy
retro_mdom_825,
Mustela putorius furoENSMPUG000000022281 retrocopy
retro_mputfur_514,
Mus musculus ENSMUSG000000322151 retrocopy
retro_mmus_1695,
Nomascus leucogenys ENSNLEG0000000657816 retrocopies
retro_nleu_1289, retro_nleu_1321, retro_nleu_1392, retro_nleu_1468, retro_nleu_1779, retro_nleu_1809, retro_nleu_185, retro_nleu_2309, retro_nleu_2449, retro_nleu_2606, retro_nleu_2874, retro_nleu_2974, retro_nleu_386, retro_nleu_570, retro_nleu_919, retro_nleu_967,
Oryctolagus cuniculus ENSOCUG000000074472 retrocopies
retro_ocun_1108, retro_ocun_1899,
Otolemur garnettii ENSOGAG0000001040015 retrocopies
retro_ogar_1135, retro_ogar_1320, retro_ogar_1433, retro_ogar_1539, retro_ogar_1876, retro_ogar_1947, retro_ogar_2088, retro_ogar_2171, retro_ogar_2579, retro_ogar_3029, retro_ogar_3154, retro_ogar_3174, retro_ogar_3239, retro_ogar_3445, retro_ogar_619,
Ochotona princeps ENSOPRG000000131154 retrocopies
retro_opri_1047, retro_opri_1226, retro_opri_66, retro_opri_777,
Pongo abelii ENSPPYG0000000649519 retrocopies
retro_pabe_1123, retro_pabe_1350, retro_pabe_1499, retro_pabe_1568, retro_pabe_1602, retro_pabe_1614, retro_pabe_1623, retro_pabe_1726, retro_pabe_1819, retro_pabe_1873, retro_pabe_1949, retro_pabe_2774, retro_pabe_2939, retro_pabe_3046, retro_pabe_3297, retro_pabe_3359, retro_pabe_771, retro_pabe_875, retro_pabe_930,
Pan troglodytes ENSPTRG0000000709416 retrocopies
retro_ptro_1103, retro_ptro_1164, retro_ptro_1268, retro_ptro_1296, retro_ptro_1311, retro_ptro_1426, retro_ptro_1607, retro_ptro_2422, retro_ptro_2631, retro_ptro_270, retro_ptro_2725, retro_ptro_2783, retro_ptro_617, retro_ptro_679, retro_ptro_715, retro_ptro_929,
Pteropus vampyrus ENSPVAG000000040933 retrocopies
retro_pvam_331, retro_pvam_619, retro_pvam_671,
Rattus norvegicus ENSRNOG000000076302 retrocopies
retro_rnor_1945, retro_rnor_506,
Sarcophilus harrisii ENSSHAG000000114941 retrocopy
retro_shar_465,
Sus scrofa ENSSSCG000000249831 retrocopy
retro_sscr_916,
Ictidomys tridecemlineatus ENSSTOG000000094086 retrocopies
retro_itri_100, retro_itri_1246, retro_itri_1388, retro_itri_1605, retro_itri_1699, retro_itri_1767,
Tupaia belangeri ENSTBEG000000107509 retrocopies
retro_tbel_1552, retro_tbel_2292, retro_tbel_3033, retro_tbel_4025, retro_tbel_4076, retro_tbel_4138, retro_tbel_4462, retro_tbel_4711, retro_tbel_720,
Tarsius syrichta ENSTSYG000000012711 retrocopy
retro_tsyr_677,

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 = 0.1 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .06 RPM
CEU_NA11930 0 .00 RPM
CEU_NA12004 0 .08 RPM
CEU_NA12400 0 .04 RPM
CEU_NA12751 0 .02 RPM
CEU_NA12760 0 .04 RPM
CEU_NA12827 0 .00 RPM
CEU_NA12872 0 .00 RPM
CEU_NA12873 0 .06 RPM
FIN_HG00183 0 .03 RPM
FIN_HG00277 0 .04 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .00 RPM
FIN_HG00328 0 .05 RPM
FIN_HG00338 0 .00 RPM
FIN_HG00349 0 .00 RPM
FIN_HG00375 0 .00 RPM
FIN_HG00377 0 .00 RPM
FIN_HG00378 0 .04 RPM
GBR_HG00099 0 .06 RPM
GBR_HG00111 0 .00 RPM
GBR_HG00114 0 .03 RPM
GBR_HG00119 0 .05 RPM
GBR_HG00131 0 .06 RPM
GBR_HG00133 0 .02 RPM
GBR_HG00134 0 .00 RPM
GBR_HG00137 0 .03 RPM
GBR_HG00142 0 .00 RPM
GBR_HG00143 0 .10 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .02 RPM
TSI_NA20518 0 .03 RPM
TSI_NA20532 0 .00 RPM
TSI_NA20538 0 .05 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .02 RPM
TSI_NA20771 0 .03 RPM
TSI_NA20786 0 .05 RPM
TSI_NA20798 0 .00 RPM
YRI_NA18870 0 .07 RPM
YRI_NA18907 0 .00 RPM
YRI_NA18916 0 .04 RPM
YRI_NA19093 0 .05 RPM
YRI_NA19099 0 .03 RPM
YRI_NA19114 0 .00 RPM
YRI_NA19118 0 .02 RPM
YRI_NA19213 0 .05 RPM
YRI_NA19214 0 .02 RPM
YRI_NA19223 0 .06 RPM

Indel association:

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



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