RetrogeneDB ID:

retro_hsap_267

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:1:173320834..173321146(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000232751
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL26
Ensembl ID:ENSG00000161970
Aliases:RPL26, DBA11, L26
Description:ribosomal protein L26 [Source:HGNC Symbol;Acc:10327]


Retrocopy-Parental alignment summary:






>retro_hsap_267
GTTCAATCCATGCCTAACCGAAAGGATAATGAAGTTCAGGTTGTACGAGTACGAGGACACTATAAAGGTCAGCAAATTGG
TACAGTAGTCCAGGTTTACAGGAAGAAATATGTCATCTACATTGAATGGGTGCAGCAGGAAAAGGCCAATGGCACAACTG
TCCATGTAGGCATTCACCCCAGCAAGGCGGTTATCACTAGGCTAAAACTGGACAAAGACCGCAAAAAGATCCCTGAACAG
AAAGCCAAATCTCACCAGGCAGGAAAGGAAAAGGGCAAATACAAGGAAGAAAAAATTGAGGAGATGCAGGAA

ORF - retro_hsap_267 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 85.58 %
Parental protein coverage: 70.34 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalVRSMPIRKDDEVQVVR--GHYKGQQIGKVVQVYRKKYVIYIERVQREKANGTTVHVGIHPSKVVITRLKL
V.SMP.RKD.EVQVVR..GHYKGQQIG.VVQVYRKKYVIYIE.VQ.EKANGTTVHVGIHPSK.VITRLKL
RetrocopyVQSMPNRKDNEVQVVRVRGHYKGQQIGTVVQVYRKKYVIYIEWVQQEKANGTTVHVGIHPSKAVITRLKL
ParentalDKDRKKILERKAKSRQVGKEKGKYKEETIEKMQE
DKDRKKI.E.KAKS.Q.GKEKGKYKEE.IE.MQE
RetrocopyDKDRKKIPEQKAKSHQAGKEKGKYKEEKIEEMQE

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 230 .25 RPM
bodymap2_adrenal 0 .04 RPM 312 .12 RPM
bodymap2_brain 0 .05 RPM 131 .90 RPM
bodymap2_breast 0 .00 RPM 213 .50 RPM
bodymap2_colon 0 .00 RPM 447 .49 RPM
bodymap2_heart 0 .00 RPM 108 .92 RPM
bodymap2_kidney 0 .15 RPM 180 .52 RPM
bodymap2_liver 0 .00 RPM 109 .88 RPM
bodymap2_lung 0 .00 RPM 352 .18 RPM
bodymap2_lymph_node 0 .00 RPM 392 .35 RPM
bodymap2_ovary 0 .02 RPM 384 .53 RPM
bodymap2_prostate 0 .00 RPM 473 .22 RPM
bodymap2_skeletal_muscle 0 .00 RPM 246 .63 RPM
bodymap2_testis 0 .00 RPM 253 .88 RPM
bodymap2_thyroid 0 .00 RPM 176 .26 RPM
bodymap2_white_blood_cells 0 .00 RPM 432 .25 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_267 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_267 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_267 retrocopy 5' end.

Lab - click to see more details

retro_hsap_267 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_267 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 26 parental genes, and 234 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000024537 retrocopies
retro_amel_1175, retro_amel_1535, retro_amel_1885, retro_amel_1934, retro_amel_360, retro_amel_499, retro_amel_900,
Bos taurus ENSBTAG000000123442 retrocopies
retro_btau_1090, retro_btau_230,
Choloepus hoffmanni ENSCHOG0000000470310 retrocopies
retro_chof_149, retro_chof_1893, retro_chof_2147, retro_chof_2276, retro_chof_2333, retro_chof_2383, retro_chof_244, retro_chof_312, retro_chof_816, retro_chof_942,
Callithrix jacchus ENSCJAG000000143728 retrocopies
retro_cjac_110, retro_cjac_119, retro_cjac_240, retro_cjac_250, retro_cjac_270, retro_cjac_297, retro_cjac_321, retro_cjac_362,
Cavia porcellus ENSCPOG0000000131510 retrocopies
retro_cpor_1009, retro_cpor_1161, retro_cpor_1346, retro_cpor_1421, retro_cpor_1503, retro_cpor_1526, retro_cpor_167, retro_cpor_522, retro_cpor_585, retro_cpor_858,
Dasypus novemcinctus ENSDNOG000000024703 retrocopies
retro_dnov_2054, retro_dnov_2174, retro_dnov_378,
Equus caballus ENSECAG000000157574 retrocopies
retro_ecab_429, retro_ecab_473, retro_ecab_515, retro_ecab_609,
Homo sapiens ENSG000000372412 retrocopies
retro_hsap_586, retro_hsap_837,
Homo sapiens ENSG00000161970 27 retrocopies
retro_hsap_1137, retro_hsap_1309, retro_hsap_1376, retro_hsap_1394, retro_hsap_191, retro_hsap_2108, retro_hsap_2165, retro_hsap_2253, retro_hsap_253, retro_hsap_267 , retro_hsap_2946, retro_hsap_3118, retro_hsap_3260, retro_hsap_3324, retro_hsap_3490, retro_hsap_3700, retro_hsap_3803, retro_hsap_3813, retro_hsap_3914, retro_hsap_4043, retro_hsap_4061, retro_hsap_4874, retro_hsap_4932, retro_hsap_642, retro_hsap_691, retro_hsap_915, retro_hsap_998,
Gorilla gorilla ENSGGOG000000239444 retrocopies
retro_ggor_2565, retro_ggor_270, retro_ggor_51, retro_ggor_974,
Macropus eugenii ENSMEUG000000098917 retrocopies
retro_meug_1239, retro_meug_1538, retro_meug_1607, retro_meug_1827, retro_meug_262, retro_meug_322, retro_meug_534,
Myotis lucifugus ENSMLUG000000021761 retrocopy
retro_mluc_232,
Macaca mulatta ENSMMUG0000000344822 retrocopies
retro_mmul_1117, retro_mmul_1361, retro_mmul_1398, retro_mmul_1497, retro_mmul_1710, retro_mmul_1773, retro_mmul_1899, retro_mmul_1986, retro_mmul_2052, retro_mmul_2163, retro_mmul_2332, retro_mmul_2344, retro_mmul_325, retro_mmul_360, retro_mmul_398, retro_mmul_405, retro_mmul_448, retro_mmul_548, retro_mmul_805, retro_mmul_903, retro_mmul_920, retro_mmul_992,
Monodelphis domestica ENSMODG000000062012 retrocopies
retro_mdom_36, retro_mdom_64,
Mustela putorius furoENSMPUG0000000798812 retrocopies
retro_mputfur_1003, retro_mputfur_1146, retro_mputfur_1385, retro_mputfur_1428, retro_mputfur_1595, retro_mputfur_251, retro_mputfur_365, retro_mputfur_395, retro_mputfur_488, retro_mputfur_522, retro_mputfur_643, retro_mputfur_685,
Nomascus leucogenys ENSNLEG000000099811 retrocopy
retro_nleu_76,
Otolemur garnettii ENSOGAG000000170703 retrocopies
retro_ogar_118, retro_ogar_255, retro_ogar_66,
Pan troglodytes ENSPTRG000000087423 retrocopies
retro_ptro_1546, retro_ptro_2510, retro_ptro_73,
Rattus norvegicus ENSRNOG000000042143 retrocopies
retro_rnor_213, retro_rnor_260, retro_rnor_273,
Sorex araneus ENSSARG0000000579813 retrocopies
retro_sara_172, retro_sara_208, retro_sara_228, retro_sara_273, retro_sara_319, retro_sara_334, retro_sara_393, retro_sara_527, retro_sara_578, retro_sara_627, retro_sara_641, retro_sara_656, retro_sara_740,
Sarcophilus harrisii ENSSHAG000000068901 retrocopy
retro_shar_458,
Sus scrofa ENSSSCG000000288509 retrocopies
retro_sscr_261, retro_sscr_363, retro_sscr_426, retro_sscr_427, retro_sscr_471, retro_sscr_485, retro_sscr_508, retro_sscr_609, retro_sscr_736,
Ictidomys tridecemlineatus ENSSTOG000000219236 retrocopies
retro_itri_1113, retro_itri_1145, retro_itri_1206, retro_itri_1262, retro_itri_1670, retro_itri_811,
Tupaia belangeri ENSTBEG0000000774953 retrocopies
retro_tbel_1053, retro_tbel_1088, retro_tbel_1103, retro_tbel_1140, retro_tbel_1366, retro_tbel_1389, retro_tbel_1390, retro_tbel_1391, retro_tbel_1433, retro_tbel_1497, retro_tbel_1512, retro_tbel_1767, retro_tbel_1793, retro_tbel_1928, retro_tbel_1930, retro_tbel_2005, retro_tbel_2033, retro_tbel_2053, retro_tbel_2057, retro_tbel_2099, retro_tbel_2105, retro_tbel_2332, retro_tbel_2416, retro_tbel_2465, retro_tbel_2500, retro_tbel_268, retro_tbel_2727, retro_tbel_2778, retro_tbel_2806, retro_tbel_2884, retro_tbel_3020, retro_tbel_3187, retro_tbel_3300, retro_tbel_3332, retro_tbel_3704, retro_tbel_3711, retro_tbel_3790, retro_tbel_3964, retro_tbel_404, retro_tbel_4162, retro_tbel_4200, retro_tbel_4381, retro_tbel_4416, retro_tbel_446, retro_tbel_4480, retro_tbel_470, retro_tbel_474, retro_tbel_495, retro_tbel_573, retro_tbel_863, retro_tbel_906, retro_tbel_964, retro_tbel_99,
Tarsius syrichta ENSTSYG0000000148317 retrocopies
retro_tsyr_1273, retro_tsyr_1274, retro_tsyr_1499, retro_tsyr_153, retro_tsyr_1705, retro_tsyr_1858, retro_tsyr_1869, retro_tsyr_2152, retro_tsyr_262, retro_tsyr_327, retro_tsyr_346, retro_tsyr_600, retro_tsyr_636, retro_tsyr_684, retro_tsyr_808, retro_tsyr_865, retro_tsyr_905,
Vicugna pacos ENSVPAG000000002794 retrocopies
retro_vpac_214, retro_vpac_255, retro_vpac_26, retro_vpac_357,

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 = 0.07 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .03 RPM
CEU_NA11930 0 .03 RPM
CEU_NA12004 0 .04 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 .03 RPM
FIN_HG00277 0 .00 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .00 RPM
FIN_HG00328 0 .00 RPM
FIN_HG00338 0 .02 RPM
FIN_HG00349 0 .00 RPM
FIN_HG00375 0 .02 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 .03 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 .03 RPM
TSI_NA20532 0 .03 RPM
TSI_NA20538 0 .05 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 .07 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 .02 RPM
YRI_NA19223 0 .00 RPM

Indel association:

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



Copyright © RetrogeneDB 2014-2017