RetrogeneDB ID:

retro_hsap_837

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:11:2356544..2356979(-)
Located in intron of:ENSG00000238184
Retrocopy
information
Ensembl ID:ENSG00000236264
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL26L1
Ensembl ID:ENSG00000037241
Aliases:RPL26L1, RPL26P1
Description:ribosomal protein L26-like 1 [Source:HGNC Symbol;Acc:17050]


Retrocopy-Parental alignment summary:






>retro_hsap_837
ATGAAGTTCAATCCCTTCGTTACCTCGGACCGCAGTAAAAACCGCAAACGTTACTTCAATGCCCCCTCACACGTGCGCAG
GAAGATCATGTCATCCCCGCTCTCCAAGGAGCTGCGGCAGAAGTACAATGTCCGCTCCATGCCCATCCGCAAGGACGACG
AGGTCCAGGTAGTTCGAGGACACTACAAAGGTCAGCAAATTGGCAAGGTAATCCAGGTGTACAGAAAGAAATATGTCATC
TACATCGAGCGGGTGCAGCGTGAGAAGGCCAACGGCACGACTGTCCACGTGGGCATTCACCCAAGCAAGGTGGTTATCAC
CAGGCTAAAACTGGACAAGGATCGGAAAAAAATTCTTGAACGCAAAGCCAAGTCTCAACAAGTTGGAAAAGAGAAAGGCA
AATATAAAGAAGAACTTATTGAGAAAATGCAGGAA

ORF - retro_hsap_837 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 97.93 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMKFNPFVTSDRSKNRKRHFNAPSHVRRKIMSSPLSKELRQKYNVRSMPIRKDDEVQVVRGHYKGQQIGKV
MKFNPFVTSDRSKNRKR.FNAPSHVRRKIMSSPLSKELRQKYNVRSMPIRKDDEVQVVRGHYKGQQIGKV
RetrocopyMKFNPFVTSDRSKNRKRYFNAPSHVRRKIMSSPLSKELRQKYNVRSMPIRKDDEVQVVRGHYKGQQIGKV
ParentalVQVYRKKYVIYIERVQREKANGTTVHVGIHPSKVVITRLKLDKDRKKILERKAKSRQVGKEKGKYKEELI
.QVYRKKYVIYIERVQREKANGTTVHVGIHPSKVVITRLKLDKDRKKILERKAKS.QVGKEKGKYKEELI
RetrocopyIQVYRKKYVIYIERVQREKANGTTVHVGIHPSKVVITRLKLDKDRKKILERKAKSQQVGKEKGKYKEELI
ParentalEKMQE
EKMQE
RetrocopyEKMQE

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 .20 RPM 4 .75 RPM
bodymap2_adrenal 0 .10 RPM 9 .03 RPM
bodymap2_brain 0 .12 RPM 5 .72 RPM
bodymap2_breast 0 .08 RPM 6 .21 RPM
bodymap2_colon 0 .10 RPM 4 .47 RPM
bodymap2_heart 0 .00 RPM 6 .61 RPM
bodymap2_kidney 0 .02 RPM 11 .29 RPM
bodymap2_liver 0 .02 RPM 12 .13 RPM
bodymap2_lung 0 .19 RPM 5 .92 RPM
bodymap2_lymph_node 0 .13 RPM 6 .49 RPM
bodymap2_ovary 0 .02 RPM 7 .98 RPM
bodymap2_prostate 0 .12 RPM 9 .92 RPM
bodymap2_skeletal_muscle 0 .02 RPM 8 .46 RPM
bodymap2_testis 0 .09 RPM 28 .94 RPM
bodymap2_thyroid 0 .24 RPM 7 .53 RPM
bodymap2_white_blood_cells 0 .16 RPM 9 .98 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_837 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_837 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_1311227 libraries0 libraries53 libraries156 libraries1593 libraries

The graphical summary, for retro_hsap_837 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_837 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_837 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 13 parental genes, and 112 retrocopies.

Species Parental gene accession Retrocopies number
Dasypus novemcinctus ENSDNOG0000000228935 retrocopies
retro_dnov_1106, retro_dnov_1147, retro_dnov_1171, retro_dnov_1258, retro_dnov_1304, retro_dnov_1319, retro_dnov_1344, retro_dnov_1381, retro_dnov_1501, retro_dnov_1676, retro_dnov_1819, retro_dnov_1959, retro_dnov_2039, retro_dnov_2041, retro_dnov_2061, retro_dnov_2078, retro_dnov_2103, retro_dnov_2116, retro_dnov_2121, retro_dnov_2287, retro_dnov_2297, retro_dnov_2438, retro_dnov_2545, retro_dnov_2580, retro_dnov_2632, retro_dnov_300, retro_dnov_306, retro_dnov_467, retro_dnov_646, retro_dnov_666, retro_dnov_681, retro_dnov_760, retro_dnov_850, retro_dnov_970, retro_dnov_985,
Felis catus ENSFCAG000000269491 retrocopy
retro_fcat_524,
Homo sapiens ENSG00000037241 2 retrocopies
retro_hsap_586, retro_hsap_837 ,
Homo sapiens ENSG0000016197027 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,
Latimeria chalumnae ENSLACG000000075992 retrocopies
retro_lcha_5, retro_lcha_8,
Microcebus murinus ENSMICG0000001131210 retrocopies
retro_mmur_1020, retro_mmur_1144, retro_mmur_313, retro_mmur_327, retro_mmur_346, retro_mmur_412, retro_mmur_471, retro_mmur_623, retro_mmur_72, retro_mmur_75,
Macaca mulatta ENSMMUG000000030701 retrocopy
retro_mmul_676,
Oryctolagus cuniculus ENSOCUG000000061724 retrocopies
retro_ocun_1015, retro_ocun_1224, retro_ocun_354, retro_ocun_845,
Procavia capensis ENSPCAG0000000224610 retrocopies
retro_pcap_137, retro_pcap_157, retro_pcap_188, retro_pcap_204, retro_pcap_337, retro_pcap_404, retro_pcap_419, retro_pcap_42, retro_pcap_422, retro_pcap_448,
Pteropus vampyrus ENSPVAG000000032538 retrocopies
retro_pvam_1062, retro_pvam_1208, retro_pvam_122, retro_pvam_353, retro_pvam_688, retro_pvam_71, retro_pvam_769, retro_pvam_877,
Sus scrofa ENSSSCG000000169893 retrocopies
retro_sscr_1104, retro_sscr_462, retro_sscr_685,
Ictidomys tridecemlineatus ENSSTOG000000268761 retrocopy
retro_itri_1141,
Tursiops truncatus ENSTTRG000000106248 retrocopies
retro_ttru_1070, retro_ttru_1124, retro_ttru_1694, retro_ttru_1818, retro_ttru_364, retro_ttru_386, retro_ttru_474, retro_ttru_646,

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 = 2.52 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .04 RPM
CEU_NA11843 0 .06 RPM
CEU_NA11930 0 .23 RPM
CEU_NA12004 0 .08 RPM
CEU_NA12400 0 .07 RPM
CEU_NA12751 0 .05 RPM
CEU_NA12760 0 .09 RPM
CEU_NA12827 0 .14 RPM
CEU_NA12872 0 .08 RPM
CEU_NA12873 0 .00 RPM
FIN_HG00183 0 .05 RPM
FIN_HG00277 2 .18 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .06 RPM
FIN_HG00328 0 .02 RPM
FIN_HG00338 0 .13 RPM
FIN_HG00349 0 .00 RPM
FIN_HG00375 0 .02 RPM
FIN_HG00377 0 .08 RPM
FIN_HG00378 0 .13 RPM
GBR_HG00099 0 .09 RPM
GBR_HG00111 0 .04 RPM
GBR_HG00114 0 .08 RPM
GBR_HG00119 0 .02 RPM
GBR_HG00131 0 .09 RPM
GBR_HG00133 0 .05 RPM
GBR_HG00134 0 .04 RPM
GBR_HG00137 0 .11 RPM
GBR_HG00142 0 .06 RPM
GBR_HG00143 2 .52 RPM
TSI_NA20512 0 .06 RPM
TSI_NA20513 0 .10 RPM
TSI_NA20518 0 .11 RPM
TSI_NA20532 0 .03 RPM
TSI_NA20538 0 .23 RPM
TSI_NA20756 0 .15 RPM
TSI_NA20765 0 .06 RPM
TSI_NA20771 0 .20 RPM
TSI_NA20786 0 .03 RPM
TSI_NA20798 0 .03 RPM
YRI_NA18870 0 .00 RPM
YRI_NA18907 0 .07 RPM
YRI_NA18916 0 .04 RPM
YRI_NA19093 0 .05 RPM
YRI_NA19099 0 .08 RPM
YRI_NA19114 0 .08 RPM
YRI_NA19118 0 .02 RPM
YRI_NA19213 0 .10 RPM
YRI_NA19214 0 .05 RPM
YRI_NA19223 0 .10 RPM

Indel association:

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



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