RetrogeneDB ID:

retro_hsap_852

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:11:16996242..16996590(-)
Located in intron of:ENSG00000166689
Retrocopy
information
Ensembl ID:ENSG00000244398
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL36A
Ensembl ID:ENSG00000269315
Aliases:None
Description:ribosomal protein L36a [Source:HGNC Symbol;Acc:10359]


Retrocopy-Parental alignment summary:






>retro_hsap_852
TCTTTCCGCGCCGATAGCGCTCACGCAAGCATGGTTAACGTCCCTAAAACCCGCCGGACTTTCTGTAAGAAGTGTGGCAA
GCACCAACCCCATAAAGTGACACAGTACAAGAAGGGCAAGGATTCTCTGTACGCCCAGGGAAAGCGGCGTTATGACAGGA
AGCAGAGTGGCTATGGTGGGCAAACTAAGCCGATTTTCCGGAAAAAGGCTAAAACTACAAAGAAGATTGTGCTAAGGCTT
GAGTGCGTTGAGCCCAACTGCAGATCTAAGAGAATGCTGGCTATTAAAAGATGCAAGCATTTTGAACTGGGAGGAGATAA
GAAGAGAAAGGGCCAAGTGATCCAGTTC

ORF - retro_hsap_852 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 100. %
Parental protein coverage: 81.69 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalSFRADSAHASMVNVPKTRRTFCKKCGKHQPHKVTQYKKGKDSLYAQGKRRYDRKQSGYGGQTKPIFRKKA
SFRADSAHASMVNVPKTRRTFCKKCGKHQPHKVTQYKKGKDSLYAQGKRRYDRKQSGYGGQTKPIFRKKA
RetrocopySFRADSAHASMVNVPKTRRTFCKKCGKHQPHKVTQYKKGKDSLYAQGKRRYDRKQSGYGGQTKPIFRKKA
ParentalKTTKKIVLRLECVEPNCRSKRMLAIKRCKHFELGGDKKRKGQVIQF
KTTKKIVLRLECVEPNCRSKRMLAIKRCKHFELGGDKKRKGQVIQF
RetrocopyKTTKKIVLRLECVEPNCRSKRMLAIKRCKHFELGGDKKRKGQVIQF

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 2 .72 RPM 0 .00 RPM
bodymap2_adrenal 2 .95 RPM 0 .00 RPM
bodymap2_brain 0 .61 RPM 0 .00 RPM
bodymap2_breast 1 .17 RPM 0 .00 RPM
bodymap2_colon 2 .71 RPM 0 .00 RPM
bodymap2_heart 0 .57 RPM 0 .00 RPM
bodymap2_kidney 1 .18 RPM 0 .00 RPM
bodymap2_liver 0 .34 RPM 0 .00 RPM
bodymap2_lung 1 .72 RPM 0 .00 RPM
bodymap2_lymph_node 2 .19 RPM 0 .00 RPM
bodymap2_ovary 3 .01 RPM 0 .00 RPM
bodymap2_prostate 3 .83 RPM 0 .00 RPM
bodymap2_skeletal_muscle 2 .04 RPM 0 .00 RPM
bodymap2_testis 1 .15 RPM 0 .00 RPM
bodymap2_thyroid 0 .64 RPM 0 .00 RPM
bodymap2_white_blood_cells 2 .11 RPM 0 .00 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_852 was not detected

EST - click to see more details

6 EST(s) were mapped to retro_hsap_852 retrocopy
EST ID Start End Identity Match Mis-match Score
BG943625 100645811 100646811 100 398 0 396
BU963265 100645976 100646809 100 231 0 229
DA558358 100645972 100647146 100 572 0 570
DA839483 100645998 100647163 100 563 0 561
DB130228 100646002 100647173 100 569 0 567
DT215156 100645972 100647239 100 664 0 661

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_1222418 libraries0 libraries16 libraries69 libraries1726 libraries

The graphical summary, for retro_hsap_852 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_852 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_852 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 1 parental gene, and 16 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG00000269315 16 retrocopies
retro_hsap_1374, retro_hsap_1420, retro_hsap_1776, retro_hsap_182, retro_hsap_1851, retro_hsap_1915, retro_hsap_196, retro_hsap_1982, retro_hsap_2083, retro_hsap_3150, retro_hsap_3702, retro_hsap_3919, retro_hsap_423, retro_hsap_744, retro_hsap_852 , retro_hsap_858,

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 = 19.36 RPM Legend:


Library Retrogene expression
CEU_NA11831 11 .81 RPM
CEU_NA11843 15 .87 RPM
CEU_NA11930 19 .36 RPM
CEU_NA12004 7 .56 RPM
CEU_NA12400 11 .08 RPM
CEU_NA12751 7 .12 RPM
CEU_NA12760 15 .63 RPM
CEU_NA12827 14 .01 RPM
CEU_NA12872 6 .83 RPM
CEU_NA12873 12 .32 RPM
FIN_HG00183 9 .69 RPM
FIN_HG00277 12 .09 RPM
FIN_HG00315 7 .09 RPM
FIN_HG00321 6 .83 RPM
FIN_HG00328 6 .08 RPM
FIN_HG00338 8 .39 RPM
FIN_HG00349 11 .92 RPM
FIN_HG00375 9 .46 RPM
FIN_HG00377 6 .71 RPM
FIN_HG00378 7 .31 RPM
GBR_HG00099 9 .13 RPM
GBR_HG00111 8 .77 RPM
GBR_HG00114 7 .81 RPM
GBR_HG00119 7 .97 RPM
GBR_HG00131 5 .69 RPM
GBR_HG00133 8 .37 RPM
GBR_HG00134 6 .73 RPM
GBR_HG00137 9 .92 RPM
GBR_HG00142 8 .89 RPM
GBR_HG00143 9 .03 RPM
TSI_NA20512 11 .05 RPM
TSI_NA20513 6 .17 RPM
TSI_NA20518 14 .63 RPM
TSI_NA20532 11 .19 RPM
TSI_NA20538 9 .90 RPM
TSI_NA20756 12 .10 RPM
TSI_NA20765 5 .01 RPM
TSI_NA20771 10 .18 RPM
TSI_NA20786 4 .79 RPM
TSI_NA20798 7 .11 RPM
YRI_NA18870 10 .70 RPM
YRI_NA18907 6 .59 RPM
YRI_NA18916 6 .78 RPM
YRI_NA19093 6 .61 RPM
YRI_NA19099 6 .20 RPM
YRI_NA19114 5 .95 RPM
YRI_NA19118 10 .90 RPM
YRI_NA19213 4 .62 RPM
YRI_NA19214 4 .11 RPM
YRI_NA19223 7 .50 RPM

Indel association:

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





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