RetrogeneDB ID:

retro_hsap_3542

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:6:163784229..163784503(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000217514
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL37A
Ensembl ID:ENSG00000197756
Aliases:None
Description:ribosomal protein L37a [Source:HGNC Symbol;Acc:10348]


Retrocopy-Parental alignment summary:






>retro_hsap_3542
ATGGTTGAATGCACCAAGAGAGTTGGAATCGTTGATAAATACGGAACCCGCTAGAGTGCCTCCCTCTGGAAAACGGTGAA
GAAAATCAAAATCAGCCAGCACGTCAAGTATACTTGCTCTTTCCATGATAAAATTGAGGTGAAGAGATGAGCTGTGGGGA
TCTGCACTGTGGTTGCTGCATGAAGACAGTAGCTGGCAGTGCCTGGACCTCTAACACCACTTCTGCTCTCACAAGAAAGT
CCACCATCAGACAACTAAAGGATTAAAAGACCAG

ORF - retro_hsap_3542 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 70.21 %
Parental protein coverage: 100. %
Number of stop codons detected: 2
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMAKRTKKVGIVGKYGTRYGASLRKMVKKIEISQHAKYTCSFCGKTKMKRRAVGI-WHCGSCMKTVAGGAW
M...TK.VGIV.KYGTR..ASL.K.VKKI.ISQH.KYTCSF..K...KR.AVGI..HCG.CMKTVAG.AW
RetrocopyMVECTKRVGIVDKYGTR*SASLWKTVKKIKISQHVKYTCSFHDKIEVKR*AVGI<LHCGCCMKTVAGSAW
ParentalTYNTTSAVTVKSAIRRLKE-LKDQ
T.NTTSA.T.KS.IR.LK..LKDQ
RetrocopyTSNTTSALTRKSTIRQLKD<LKDQ

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 446 .28 RPM
bodymap2_adrenal 0 .00 RPM 532 .92 RPM
bodymap2_brain 0 .00 RPM 150 .06 RPM
bodymap2_breast 0 .00 RPM 359 .89 RPM
bodymap2_colon 0 .00 RPM 548 .85 RPM
bodymap2_heart 0 .00 RPM 183 .71 RPM
bodymap2_kidney 0 .00 RPM 239 .25 RPM
bodymap2_liver 0 .00 RPM 207 .77 RPM
bodymap2_lung 0 .00 RPM 468 .39 RPM
bodymap2_lymph_node 0 .00 RPM 598 .08 RPM
bodymap2_ovary 0 .00 RPM 602 .34 RPM
bodymap2_prostate 0 .00 RPM 811 .13 RPM
bodymap2_skeletal_muscle 0 .00 RPM 726 .73 RPM
bodymap2_testis 0 .00 RPM 359 .26 RPM
bodymap2_thyroid 0 .00 RPM 295 .56 RPM
bodymap2_white_blood_cells 0 .00 RPM 620 .54 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3542 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3542 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_3542 retrocopy 5' end.

Lab - click to see more details

retro_hsap_3542 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3542 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2408
Gorilla gorilla retro_ggor_2393
Macaca mulatta retro_mmul_1811
Parental genes homology:
Parental genes homology involve 17 parental genes, and 243 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000038469 retrocopies
retro_btau_1039, retro_btau_1070, retro_btau_1083, retro_btau_1240, retro_btau_1269, retro_btau_1366, retro_btau_1531, retro_btau_382, retro_btau_437,
Choloepus hoffmanni ENSCHOG0000000400014 retrocopies
retro_chof_1281, retro_chof_1338, retro_chof_1734, retro_chof_1744, retro_chof_1839, retro_chof_1866, retro_chof_1885, retro_chof_2338, retro_chof_2566, retro_chof_2645, retro_chof_298, retro_chof_731, retro_chof_814, retro_chof_885,
Felis catus ENSFCAG0000002701021 retrocopies
retro_fcat_1001, retro_fcat_1070, retro_fcat_1099, retro_fcat_1221, retro_fcat_1343, retro_fcat_1364, retro_fcat_1403, retro_fcat_149, retro_fcat_1644, retro_fcat_1662, retro_fcat_1704, retro_fcat_1738, retro_fcat_1756, retro_fcat_1850, retro_fcat_1918, retro_fcat_1940, retro_fcat_2018, retro_fcat_271, retro_fcat_595, retro_fcat_612, retro_fcat_633,
Homo sapiens ENSG00000197756 6 retrocopies
retro_hsap_1086, retro_hsap_2482, retro_hsap_3542 , retro_hsap_3773, retro_hsap_764, retro_hsap_926,
Gorilla gorilla ENSGGOG000000148275 retrocopies
retro_ggor_1546, retro_ggor_2393, retro_ggor_2538, retro_ggor_2636, retro_ggor_633,
Latimeria chalumnae ENSLACG000000115781 retrocopy
retro_lcha_71,
Monodelphis domestica ENSMODG000000254859 retrocopies
retro_mdom_1106, retro_mdom_1555, retro_mdom_1848, retro_mdom_1934, retro_mdom_350, retro_mdom_521, retro_mdom_771, retro_mdom_805, retro_mdom_975,
Mus musculus ENSMUSG0000004633018 retrocopies
retro_mmus_1036, retro_mmus_1764, retro_mmus_1979, retro_mmus_1993, retro_mmus_2070, retro_mmus_2114, retro_mmus_2594, retro_mmus_2768, retro_mmus_3010, retro_mmus_3130, retro_mmus_322, retro_mmus_3367, retro_mmus_350, retro_mmus_508, retro_mmus_577, retro_mmus_589, retro_mmus_699, retro_mmus_830,
Nomascus leucogenys ENSNLEG000000072768 retrocopies
retro_nleu_129, retro_nleu_1621, retro_nleu_1926, retro_nleu_2271, retro_nleu_2623, retro_nleu_271, retro_nleu_396, retro_nleu_406,
Ochotona princeps ENSOPRG0000000443610 retrocopies
retro_opri_1043, retro_opri_1060, retro_opri_1188, retro_opri_260, retro_opri_318, retro_opri_430, retro_opri_471, retro_opri_864, retro_opri_870, retro_opri_994,
Petromyzon marinus ENSPMAG000000000011 retrocopy
retro_pmar_11,
Pongo abelii ENSPPYG000000258781 retrocopy
retro_pabe_62,
Pan troglodytes ENSPTRG000000290296 retrocopies
retro_ptro_1436, retro_ptro_2408, retro_ptro_2558, retro_ptro_535, retro_ptro_642, retro_ptro_738,
Sarcophilus harrisii ENSSHAG0000001341710 retrocopies
retro_shar_133, retro_shar_197, retro_shar_246, retro_shar_322, retro_shar_339, retro_shar_460, retro_shar_466, retro_shar_605, retro_shar_611, retro_shar_642,
Tupaia belangeri ENSTBEG00000007409108 retrocopies
retro_tbel_1089, retro_tbel_1095, retro_tbel_1113, retro_tbel_1168, retro_tbel_1198, retro_tbel_1204, retro_tbel_1218, retro_tbel_1244, retro_tbel_1345, retro_tbel_1352, retro_tbel_141, retro_tbel_1434, retro_tbel_1466, retro_tbel_1471, retro_tbel_148, retro_tbel_1489, retro_tbel_1502, retro_tbel_151, retro_tbel_1534, retro_tbel_1683, retro_tbel_1714, retro_tbel_1807, retro_tbel_1835, retro_tbel_1838, retro_tbel_1922, retro_tbel_194, retro_tbel_1973, retro_tbel_1992, retro_tbel_1995, retro_tbel_2002, retro_tbel_2044, retro_tbel_2083, retro_tbel_209, retro_tbel_2101, retro_tbel_2178, retro_tbel_2190, retro_tbel_223, retro_tbel_2381, retro_tbel_2631, retro_tbel_2699, retro_tbel_2705, retro_tbel_2725, retro_tbel_2780, retro_tbel_2813, retro_tbel_2844, retro_tbel_285, retro_tbel_286, retro_tbel_2985, retro_tbel_3022, retro_tbel_3048, retro_tbel_3108, retro_tbel_3118, retro_tbel_3211, retro_tbel_3490, retro_tbel_350, retro_tbel_3565, retro_tbel_3593, retro_tbel_3632, retro_tbel_3641, retro_tbel_3651, retro_tbel_3757, retro_tbel_3784, retro_tbel_3837, retro_tbel_3901, retro_tbel_3910, retro_tbel_3912, retro_tbel_3916, retro_tbel_3919, retro_tbel_3955, retro_tbel_3969, retro_tbel_3970, retro_tbel_4055, retro_tbel_4098, retro_tbel_4099, retro_tbel_4117, retro_tbel_412, retro_tbel_4148, retro_tbel_4188, retro_tbel_420, retro_tbel_4244, retro_tbel_4382, retro_tbel_4452, retro_tbel_4522, retro_tbel_4524, retro_tbel_458, retro_tbel_4586, retro_tbel_4588, retro_tbel_4613, retro_tbel_4703, retro_tbel_472, retro_tbel_500, retro_tbel_566, retro_tbel_574, retro_tbel_583, retro_tbel_590, retro_tbel_594, retro_tbel_595, retro_tbel_622, retro_tbel_648, retro_tbel_681, retro_tbel_739, retro_tbel_767, retro_tbel_790, retro_tbel_834, retro_tbel_870, retro_tbel_893, retro_tbel_907, retro_tbel_998,
Tarsius syrichta ENSTSYG0000000425811 retrocopies
retro_tsyr_1122, retro_tsyr_1704, retro_tsyr_1707, retro_tsyr_1831, retro_tsyr_1999, retro_tsyr_213, retro_tsyr_278, retro_tsyr_316, retro_tsyr_321, retro_tsyr_800, retro_tsyr_815,
Vicugna pacos ENSVPAG000000025295 retrocopies
retro_vpac_208, retro_vpac_240, retro_vpac_271, retro_vpac_307, retro_vpac_479,

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 ) 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 .00 RPM
CEU_NA12873 0 .00 RPM
FIN_HG00183 0 .00 RPM
FIN_HG00277 0 .00 RPM
FIN_HG00315 0 .00 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 .00 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 .00 RPM

Indel association:

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



Copyright © RetrogeneDB 2014-2017