RetrogeneDB ID:

retro_hsap_1752

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:17:35814698..35815035(+)
Located in intron of:ENSG00000108264
Retrocopy
information
Ensembl ID:ENSG00000267562
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL24
Ensembl ID:ENSG00000114391
Aliases:RPL24, HEL-S-310, L24
Description:ribosomal protein L24 [Source:HGNC Symbol;Acc:10325]


Retrocopy-Parental alignment summary:






>retro_hsap_1752
GCATTCCTTTCTAAGGAATCCTTAGCAAATAAACTGGTCCTCTACAGAAGAAAGCATAAAAAAGGGACACTTGGAAGAAA
TTCAAAAGAAAAGAACCTGCTGAGCAGTCAAATTCCAGAAGGCCATTACTGGTGCATCTCTTGCTAATATAGTGGCCAAG
AGGAATGAGAAACATGAAGTTAAAAAGGCTCAATGAAAACAAGCTAGCAGGGCTGCTAAGGAAGCAAAAAAGGCTAAGCT
AGCATCTGAAAAGACCGCAATGGCTGCTGCTAAGGCAGCATCTACACAAAAGATGGTGAAGCCTGTGAAAGTGTCAGCTC
CCCGAGGTGGTTCAAAA

ORF - retro_hsap_1752 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 72.27 %
Parental protein coverage: 75.16 %
Number of stop codons detected: 2
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalAFLSKRNPRQINWTVLYRRKHKKG-QSEEIQKKRTRRAVKFQRAITGASLADIMAKRNQKPEVRKAQREQ
AFLSK......N..VLYRRKHKKG...EEIQKKRT..AVKFQ.AITGASLA.I.AKRN.K.EV.KAQ..Q
RetrocopyAFLSKES--LANKLVLYRRKHKKG>HLEEIQKKRTC*AVKFQKAITGASLANIVAKRNEKHEVKKAQ*KQ
ParentalAIRAAKEAKKAKQASKKTAMAAAKAPTKAAPKQKIVKPVKVSAPRVGGK
A.RAAKEAKKAK.AS.KTAMAAAKA....A..QK.VKPVKVSAPR.G.K
RetrocopyASRAAKEAKKAKLASEKTAMAAAKA----ASTQKMVKPVKVSAPRGGSK

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 341 .30 RPM
bodymap2_adrenal 0 .39 RPM 408 .71 RPM
bodymap2_brain 0 .00 RPM 165 .67 RPM
bodymap2_breast 0 .19 RPM 275 .51 RPM
bodymap2_colon 0 .00 RPM 476 .15 RPM
bodymap2_heart 0 .00 RPM 145 .77 RPM
bodymap2_kidney 0 .00 RPM 194 .71 RPM
bodymap2_liver 0 .15 RPM 148 .52 RPM
bodymap2_lung 0 .00 RPM 506 .66 RPM
bodymap2_lymph_node 0 .11 RPM 378 .56 RPM
bodymap2_ovary 0 .13 RPM 616 .67 RPM
bodymap2_prostate 0 .00 RPM 602 .13 RPM
bodymap2_skeletal_muscle 0 .09 RPM 255 .01 RPM
bodymap2_testis 0 .06 RPM 306 .44 RPM
bodymap2_thyroid 0 .17 RPM 410 .22 RPM
bodymap2_white_blood_cells 0 .00 RPM 390 .61 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_1752 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_1752 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_1752 retrocopy 5' end.

Lab - click to see more details

retro_hsap_1752 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1752 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Gorilla gorilla retro_ggor_2252
Pongo abelii retro_pabe_1450
Macaca mulatta retro_mmul_1234
Parental genes homology:
Parental genes homology involve 25 parental genes, and 162 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000134611 retrocopy
retro_btau_1143,
Callithrix jacchus ENSCJAG000000004963 retrocopies
retro_cjac_2544, retro_cjac_2941, retro_cjac_327,
Cavia porcellus ENSCPOG000000199415 retrocopies
retro_cpor_1020, retro_cpor_461, retro_cpor_474, retro_cpor_904, retro_cpor_947,
Dasypus novemcinctus ENSDNOG000000031949 retrocopies
retro_dnov_1209, retro_dnov_1259, retro_dnov_1449, retro_dnov_1643, retro_dnov_2191, retro_dnov_2407, retro_dnov_2537, retro_dnov_523, retro_dnov_657,
Erinaceus europaeus ENSEEUG000000093203 retrocopies
retro_eeur_505, retro_eeur_534, retro_eeur_621,
Felis catus ENSFCAG000000033271 retrocopy
retro_fcat_31,
Homo sapiens ENSG00000114391 8 retrocopies
retro_hsap_1437, retro_hsap_1752 , retro_hsap_2418, retro_hsap_2614, retro_hsap_2743, retro_hsap_281, retro_hsap_3583, retro_hsap_4179,
Gorilla gorilla ENSGGOG000000116098 retrocopies
retro_ggor_1106, retro_ggor_1504, retro_ggor_1831, retro_ggor_1909, retro_ggor_2252, retro_ggor_2417, retro_ggor_2803, retro_ggor_324,
Macropus eugenii ENSMEUG000000091777 retrocopies
retro_meug_1769, retro_meug_371, retro_meug_385, retro_meug_449, retro_meug_730, retro_meug_759, retro_meug_963,
Myotis lucifugus ENSMLUG000000170054 retrocopies
retro_mluc_1990, retro_mluc_2185, retro_mluc_35, retro_mluc_393,
Macaca mulatta ENSMMUG000000150599 retrocopies
retro_mmul_1234, retro_mmul_1711, retro_mmul_1803, retro_mmul_2263, retro_mmul_2521, retro_mmul_37, retro_mmul_560, retro_mmul_609, retro_mmul_823,
Monodelphis domestica ENSMODG000000019163 retrocopies
retro_mdom_675, retro_mdom_854, retro_mdom_974,
Nomascus leucogenys ENSNLEG000000032766 retrocopies
retro_nleu_1413, retro_nleu_1790, retro_nleu_1894, retro_nleu_2031, retro_nleu_2815, retro_nleu_2937,
Oryctolagus cuniculus ENSOCUG000000007918 retrocopies
retro_ocun_1401, retro_ocun_190, retro_ocun_303, retro_ocun_323, retro_ocun_420, retro_ocun_480, retro_ocun_526, retro_ocun_531,
Ochotona princeps ENSOPRG000000042556 retrocopies
retro_opri_1100, retro_opri_1109, retro_opri_1131, retro_opri_900, retro_opri_918, retro_opri_95,
Procavia capensis ENSPCAG000000059181 retrocopy
retro_pcap_192,
Pongo abelii ENSPPYG000000135886 retrocopies
retro_pabe_1191, retro_pabe_1450, retro_pabe_1782, retro_pabe_2277, retro_pabe_2343, retro_pabe_3419,
Pan troglodytes ENSPTRG000000151762 retrocopies
retro_ptro_1214, retro_ptro_85,
Pteropus vampyrus ENSPVAG000000098893 retrocopies
retro_pvam_1317, retro_pvam_743, retro_pvam_831,
Rattus norvegicus ENSRNOG0000000161125 retrocopies
retro_rnor_1244, retro_rnor_1245, retro_rnor_1247, retro_rnor_1248, retro_rnor_1250, retro_rnor_1251, retro_rnor_1252, retro_rnor_1253, retro_rnor_1452, retro_rnor_1643, retro_rnor_1699, retro_rnor_1850, retro_rnor_1851, retro_rnor_1985, retro_rnor_2026, retro_rnor_2134, retro_rnor_2148, retro_rnor_2205, retro_rnor_2214, retro_rnor_2294, retro_rnor_2709, retro_rnor_435, retro_rnor_751, retro_rnor_964, retro_rnor_993,
Sorex araneus ENSSARG000000076156 retrocopies
retro_sara_198, retro_sara_204, retro_sara_330, retro_sara_535, retro_sara_574, retro_sara_711,
Sarcophilus harrisii ENSSHAG000000082262 retrocopies
retro_shar_171, retro_shar_264,
Ictidomys tridecemlineatus ENSSTOG000000146542 retrocopies
retro_itri_442, retro_itri_69,
Tupaia belangeri ENSTBEG0000001204430 retrocopies
retro_tbel_1349, retro_tbel_1429, retro_tbel_1676, retro_tbel_2076, retro_tbel_2248, retro_tbel_2553, retro_tbel_2836, retro_tbel_2853, retro_tbel_2931, retro_tbel_3363, retro_tbel_3507, retro_tbel_3544, retro_tbel_3552, retro_tbel_3557, retro_tbel_3634, retro_tbel_3636, retro_tbel_3664, retro_tbel_4105, retro_tbel_4114, retro_tbel_4139, retro_tbel_4236, retro_tbel_4237, retro_tbel_431, retro_tbel_4677, retro_tbel_569, retro_tbel_607, retro_tbel_678, retro_tbel_700, retro_tbel_73, retro_tbel_779,
Tarsius syrichta ENSTSYG000000023144 retrocopies
retro_tsyr_266, retro_tsyr_285, retro_tsyr_401, retro_tsyr_460,

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 = 0.2 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .04 RPM
CEU_NA11843 0 .03 RPM
CEU_NA11930 0 .16 RPM
CEU_NA12004 0 .04 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .07 RPM
CEU_NA12760 0 .00 RPM
CEU_NA12827 0 .00 RPM
CEU_NA12872 0 .00 RPM
CEU_NA12873 0 .00 RPM
FIN_HG00183 0 .11 RPM
FIN_HG00277 0 .00 RPM
FIN_HG00315 0 .03 RPM
FIN_HG00321 0 .09 RPM
FIN_HG00328 0 .07 RPM
FIN_HG00338 0 .04 RPM
FIN_HG00349 0 .00 RPM
FIN_HG00375 0 .05 RPM
FIN_HG00377 0 .00 RPM
FIN_HG00378 0 .00 RPM
GBR_HG00099 0 .03 RPM
GBR_HG00111 0 .06 RPM
GBR_HG00114 0 .00 RPM
GBR_HG00119 0 .05 RPM
GBR_HG00131 0 .06 RPM
GBR_HG00133 0 .02 RPM
GBR_HG00134 0 .02 RPM
GBR_HG00137 0 .00 RPM
GBR_HG00142 0 .08 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .03 RPM
TSI_NA20513 0 .00 RPM
TSI_NA20518 0 .03 RPM
TSI_NA20532 0 .20 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .08 RPM
TSI_NA20771 0 .00 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .06 RPM
YRI_NA18870 0 .10 RPM
YRI_NA18907 0 .00 RPM
YRI_NA18916 0 .02 RPM
YRI_NA19093 0 .03 RPM
YRI_NA19099 0 .05 RPM
YRI_NA19114 0 .00 RPM
YRI_NA19118 0 .02 RPM
YRI_NA19213 0 .05 RPM
YRI_NA19214 0 .00 RPM
YRI_NA19223 0 .04 RPM

Indel association:

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





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