RetrogeneDB ID:

retro_hsap_288

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:1:200832935..200833271(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000231333
Aliases:RPL34P6, RPL34_4_146
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL34
Ensembl ID:ENSG00000109475
Aliases:RPL34, L34
Description:ribosomal protein L34 [Source:HGNC Symbol;Acc:10340]


Retrocopy-Parental alignment summary:






>retro_hsap_288
ATGGTCCAGCATTTGACATACTGTCATAGGCTTTCCTACAATACAGCCTCTAACAAAACTACGCGAACCCCTGGTAATAG
AATTGTTTACCTTTATACCAAGAAGGTTGGGAAAGCATCAAAATCTGCGTGTGGCGTGTGCCCAGGCAGACTTTGAAGGG
TTTGTGCTGTAAGACCTAAAGTTCTTATGAGGTTGTCCAAAACAAAGAAACATGTCAGCAGGGCCTATGTTGGTTCCATG
TGTGCTAAATGTGTTTGTGACAGGATCAAGCGTGCTTTCCTTATCAAGGAGCAGAAAATTGTTGTGAAAGTGTTGAAGGC
ACAAGCAGAGTCAGAA

ORF - retro_hsap_288 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 86.84 %
Parental protein coverage: 97.44 %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMVQRLTYRRRLSYNTASNKTRLSRTPGNRIVYLYTKKVGKAPKSACGVCPGRLRGVRAVRPKVLMRLSKT
MVQ.LTY..RLSYNTASNKT...RTPGNRIVYLYTKKVGKA.KSACGVCPGRL..V.AVRPKVLMRLSKT
RetrocopyMVQHLTYCHRLSYNTASNKT--TRTPGNRIVYLYTKKVGKASKSACGVCPGRL*RVCAVRPKVLMRLSKT
ParentalKKHVSRAYGGSMCAKCVRDRIKRAFLIEEQKIVVKVLKAQAQSQ
KKHVSRAY.GSMCAKCV.DRIKRAFLI.EQKIVVKVLKAQA.S.
RetrocopyKKHVSRAYVGSMCAKCVCDRIKRAFLIKEQKIVVKVLKAQAESE

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 419 .31 RPM
bodymap2_adrenal 0 .04 RPM 769 .57 RPM
bodymap2_brain 0 .00 RPM 183 .84 RPM
bodymap2_breast 0 .04 RPM 451 .46 RPM
bodymap2_colon 0 .21 RPM 750 .27 RPM
bodymap2_heart 0 .00 RPM 148 .09 RPM
bodymap2_kidney 0 .04 RPM 272 .59 RPM
bodymap2_liver 0 .02 RPM 186 .14 RPM
bodymap2_lung 0 .02 RPM 692 .23 RPM
bodymap2_lymph_node 0 .18 RPM 808 .72 RPM
bodymap2_ovary 0 .02 RPM 610 .59 RPM
bodymap2_prostate 0 .00 RPM 887 .12 RPM
bodymap2_skeletal_muscle 0 .00 RPM 251 .28 RPM
bodymap2_testis 0 .06 RPM 477 .68 RPM
bodymap2_thyroid 0 .00 RPM 340 .56 RPM
bodymap2_white_blood_cells 0 .00 RPM 928 .04 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_288 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_288 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_87638842 libraries803 libraries181 libraries3 libraries0 libraries

The graphical summary, for retro_hsap_288 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_288 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_288 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Gorilla gorilla retro_ggor_327
Pongo abelii retro_pabe_385
Parental genes homology:
Parental genes homology involve 15 parental genes, and 182 retrocopies.

Species Parental gene accession Retrocopies number
Dasypus novemcinctus ENSDNOG0000001117926 retrocopies
retro_dnov_1172, retro_dnov_1775, retro_dnov_2020, retro_dnov_2025, retro_dnov_2079, retro_dnov_2127, retro_dnov_2137, retro_dnov_2275, retro_dnov_2385, retro_dnov_2501, retro_dnov_252, retro_dnov_262, retro_dnov_2627, retro_dnov_2651, retro_dnov_325, retro_dnov_339, retro_dnov_430, retro_dnov_553, retro_dnov_565, retro_dnov_59, retro_dnov_606, retro_dnov_635, retro_dnov_658, retro_dnov_862, retro_dnov_88, retro_dnov_978,
Homo sapiens ENSG00000109475 33 retrocopies
retro_hsap_1245, retro_hsap_126, retro_hsap_1265, retro_hsap_1417, retro_hsap_1636, retro_hsap_1735, retro_hsap_1756, retro_hsap_1921, retro_hsap_1987, retro_hsap_2041, retro_hsap_2145, retro_hsap_232, retro_hsap_2570, retro_hsap_258, retro_hsap_2624, retro_hsap_2695, retro_hsap_288 , retro_hsap_2997, retro_hsap_3090, retro_hsap_3463, retro_hsap_3550, retro_hsap_3689, retro_hsap_4055, retro_hsap_4091, retro_hsap_4314, retro_hsap_520, retro_hsap_720, retro_hsap_769, retro_hsap_830, retro_hsap_853, retro_hsap_927, retro_hsap_941, retro_hsap_977,
Gadus morhua ENSGMOG000000099821 retrocopy
retro_gmor_31,
Loxodonta africana ENSLAFG000000326156 retrocopies
retro_lafr_1039, retro_lafr_1232, retro_lafr_182, retro_lafr_298, retro_lafr_306, retro_lafr_733,
Macropus eugenii ENSMEUG000000093613 retrocopies
retro_meug_1012, retro_meug_1754, retro_meug_1775,
Myotis lucifugus ENSMLUG000000004644 retrocopies
retro_mluc_125, retro_mluc_1372, retro_mluc_1427, retro_mluc_1847,
Monodelphis domestica ENSMODG000000206013 retrocopies
retro_mdom_1690, retro_mdom_774, retro_mdom_836,
Pelodiscus sinensis ENSPSIG000000032951 retrocopy
retro_psin_60,
Rattus norvegicus ENSRNOG0000001638736 retrocopies
retro_rnor_1031, retro_rnor_1083, retro_rnor_1101, retro_rnor_1172, retro_rnor_1376, retro_rnor_1550, retro_rnor_1575, retro_rnor_1630, retro_rnor_1694, retro_rnor_1695, retro_rnor_1696, retro_rnor_1775, retro_rnor_1803, retro_rnor_1844, retro_rnor_1857, retro_rnor_2029, retro_rnor_2090, retro_rnor_2095, retro_rnor_2139, retro_rnor_2230, retro_rnor_2565, retro_rnor_2578, retro_rnor_2597, retro_rnor_2621, retro_rnor_2651, retro_rnor_2794, retro_rnor_282, retro_rnor_367, retro_rnor_500, retro_rnor_575, retro_rnor_605, retro_rnor_617, retro_rnor_672, retro_rnor_848, retro_rnor_866, retro_rnor_869,
Sarcophilus harrisii ENSSHAG000000013571 retrocopy
retro_shar_799,
Sarcophilus harrisii ENSSHAG000000020523 retrocopies
retro_shar_131, retro_shar_324, retro_shar_419,
Tupaia belangeri ENSTBEG0000000357424 retrocopies
retro_tbel_1109, retro_tbel_1298, retro_tbel_1337, retro_tbel_1532, retro_tbel_1781, retro_tbel_1857, retro_tbel_1941, retro_tbel_213, retro_tbel_2162, retro_tbel_2165, retro_tbel_2372, retro_tbel_2391, retro_tbel_2601, retro_tbel_279, retro_tbel_335, retro_tbel_3606, retro_tbel_3984, retro_tbel_4059, retro_tbel_4398, retro_tbel_657, retro_tbel_74, retro_tbel_901, retro_tbel_974, retro_tbel_983,
Tarsius syrichta ENSTSYG0000000178134 retrocopies
retro_tsyr_1071, retro_tsyr_1087, retro_tsyr_1141, retro_tsyr_1249, retro_tsyr_1253, retro_tsyr_1292, retro_tsyr_1328, retro_tsyr_1375, retro_tsyr_140, retro_tsyr_1414, retro_tsyr_1425, retro_tsyr_1514, retro_tsyr_1573, retro_tsyr_164, retro_tsyr_1702, retro_tsyr_1849, retro_tsyr_2033, retro_tsyr_2035, retro_tsyr_2094, retro_tsyr_211, retro_tsyr_2172, retro_tsyr_220, retro_tsyr_221, retro_tsyr_254, retro_tsyr_300, retro_tsyr_375, retro_tsyr_49, retro_tsyr_59, retro_tsyr_597, retro_tsyr_678, retro_tsyr_812, retro_tsyr_853, retro_tsyr_872, retro_tsyr_897,
Tursiops truncatus ENSTTRG000000034436 retrocopies
retro_ttru_1667, retro_ttru_1831, retro_ttru_355, retro_ttru_710, retro_ttru_717, retro_ttru_821,
Xenopus tropicalis ENSXETG000000210951 retrocopy
retro_xtro_5,

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 = 0.18 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .06 RPM
CEU_NA11930 0 .03 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .04 RPM
CEU_NA12751 0 .02 RPM
CEU_NA12760 0 .00 RPM
CEU_NA12827 0 .05 RPM
CEU_NA12872 0 .03 RPM
CEU_NA12873 0 .03 RPM
FIN_HG00183 0 .14 RPM
FIN_HG00277 0 .04 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .03 RPM
FIN_HG00328 0 .00 RPM
FIN_HG00338 0 .02 RPM
FIN_HG00349 0 .09 RPM
FIN_HG00375 0 .05 RPM
FIN_HG00377 0 .00 RPM
FIN_HG00378 0 .04 RPM
GBR_HG00099 0 .00 RPM
GBR_HG00111 0 .00 RPM
GBR_HG00114 0 .08 RPM
GBR_HG00119 0 .07 RPM
GBR_HG00131 0 .06 RPM
GBR_HG00133 0 .00 RPM
GBR_HG00134 0 .02 RPM
GBR_HG00137 0 .05 RPM
GBR_HG00142 0 .03 RPM
GBR_HG00143 0 .03 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .12 RPM
TSI_NA20518 0 .00 RPM
TSI_NA20532 0 .03 RPM
TSI_NA20538 0 .18 RPM
TSI_NA20756 0 .06 RPM
TSI_NA20765 0 .02 RPM
TSI_NA20771 0 .00 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .09 RPM
YRI_NA18870 0 .03 RPM
YRI_NA18907 0 .00 RPM
YRI_NA18916 0 .02 RPM
YRI_NA19093 0 .00 RPM
YRI_NA19099 0 .03 RPM
YRI_NA19114 0 .03 RPM
YRI_NA19118 0 .02 RPM
YRI_NA19213 0 .02 RPM
YRI_NA19214 0 .02 RPM
YRI_NA19223 0 .02 RPM

Indel association:

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



Copyright © RetrogeneDB 2014-2017