RetrogeneDB ID:

retro_hsap_1937

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:18:36914838..36915636(-)
Located in intron of:ENSG00000267374
Retrocopy
information
Ensembl ID:ENSG00000175886
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL7A
Ensembl ID:ENSG00000260501
Aliases:None
Description:ribosomal protein L7a [Source:HGNC Symbol;Acc:10364]


Retrocopy-Parental alignment summary:






>retro_hsap_1937
ATGCCGAAAGGAAAGAAGGCCAAGGGAAAGAAGGTGGCTCCGGCCCCTGCTGTCGTGAAGAAGCAGGAGGCTAAGAAAGT
GGTGAATCCCCTGCTTGAGAAAAGGCCTAAGAATTTTGGCATTGGACAGGACATCCAGCCCAAAAGAGACCTCACCCGCT
TTGTGAAATGGCCCCGCTATATCAGGTTGCAGCGGCAGAGAGCCATCCTCTATAAGCGGCTGAAAGTGCCTCCTGCGATT
AACCAGTTCACCCAGGCCCTGGACCGCCAAACAGCTACTCAGCTGCTTAAGCTGGCCCACAAATACAGACCAGAGACAAA
GCAAGAGAAGAAGCAGAGACTGCTGGCCCGGGAGGAGAAGAAAGCTGCTGGCAAAGGGGACGTCCCCACGAAAAGACCAC
CTGTCCTTCGAGCAGGAGTTAATACCGTCACCACCTTGGTGGAGAACAAGAAAGCTCAGCTGGTGGTAATTGCACATGAC
GTGGATCCCATCGAGCTGGTTGTCTTCTTGGCTGCCCTGTGTCGTAAAATGGGGGTCCCTTACTGCATTATCAAGGGGAA
GGCAAGACTGGGACGTCTAGTCCACAGGAAGACCTGCACCACTGTCGCCTTCACACAGGTGAACTCGGAAGACAAAGGCA
CTTTGGCTAAGCTGATGGAAGCTATCAGGACCAATTACAATGACAGATACGATGAGATCCGCCGTCACTGGGGCGGCAAC
GTCCTGGGTCCTAAGTCTGTGGCTCGTATCGCCAAGCTCGAAAAGGCAAAGGCTAAAGACCTTGCCACTAAACTGGGT

ORF - retro_hsap_1937 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 97.74 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMPKGKKAKGKKVAPAPAVVKKQEAKKVVNPLFEKRPKNFGIGQDIQPKRDLTRFVKWPRYIRLQRQRAIL
MPKGKKAKGKKVAPAPAVVKKQEAKKVVNPL.EKRPKNFGIGQDIQPKRDLTRFVKWPRYIRLQRQRAIL
RetrocopyMPKGKKAKGKKVAPAPAVVKKQEAKKVVNPLLEKRPKNFGIGQDIQPKRDLTRFVKWPRYIRLQRQRAIL
ParentalYKRLKVPPAINQFTQALDRQTATQLLKLAHKYRPETKQEKKQRLLARAEKKAAGKGDVPTKRPPVLRAGV
YKRLKVPPAINQFTQALDRQTATQLLKLAHKYRPETKQEKKQRLLAR.EKKAAGKGDVPTKRPPVLRAGV
RetrocopyYKRLKVPPAINQFTQALDRQTATQLLKLAHKYRPETKQEKKQRLLAREEKKAAGKGDVPTKRPPVLRAGV
ParentalNTVTTLVENKKAQLVVIAHDVDPIELVVFLPALCRKMGVPYCIIKGKARLGRLVHRKTCTTVAFTQVNSE
NTVTTLVENKKAQLVVIAHDVDPIELVVFL.ALCRKMGVPYCIIKGKARLGRLVHRKTCTTVAFTQVNSE
RetrocopyNTVTTLVENKKAQLVVIAHDVDPIELVVFLAALCRKMGVPYCIIKGKARLGRLVHRKTCTTVAFTQVNSE
ParentalDKGALAKLVEAIRTNYNDRYDEIRRHWGGNVLGPKSVARIAKLEKAKAKELATKLG
DKG.LAKL.EAIRTNYNDRYDEIRRHWGGNVLGPKSVARIAKLEKAKAK.LATKLG
RetrocopyDKGTLAKLMEAIRTNYNDRYDEIRRHWGGNVLGPKSVARIAKLEKAKAKDLATKLG

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 .30 RPM 0 .00 RPM
bodymap2_adrenal 0 .43 RPM 0 .00 RPM
bodymap2_brain 0 .07 RPM 0 .00 RPM
bodymap2_breast 0 .12 RPM 0 .00 RPM
bodymap2_colon 0 .35 RPM 0 .00 RPM
bodymap2_heart 0 .02 RPM 0 .00 RPM
bodymap2_kidney 0 .14 RPM 0 .00 RPM
bodymap2_liver 0 .00 RPM 0 .00 RPM
bodymap2_lung 0 .19 RPM 0 .00 RPM
bodymap2_lymph_node 0 .09 RPM 0 .00 RPM
bodymap2_ovary 0 .40 RPM 0 .00 RPM
bodymap2_prostate 0 .16 RPM 0 .00 RPM
bodymap2_skeletal_muscle 0 .15 RPM 0 .00 RPM
bodymap2_testis 0 .17 RPM 0 .00 RPM
bodymap2_thyroid 0 .41 RPM 0 .00 RPM
bodymap2_white_blood_cells 0 .10 RPM 0 .00 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_1937 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_1937 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_67075191 libraries284 libraries1145 libraries181 libraries28 libraries

The graphical summary, for retro_hsap_1937 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_1937 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1937 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Gorilla gorilla retro_ggor_1409
Parental genes homology:
Parental genes homology involve 1 parental gene, and 36 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG00000260501 36 retrocopies
retro_hsap_1031, retro_hsap_1103, retro_hsap_1157, retro_hsap_1327, retro_hsap_1340, retro_hsap_1402, retro_hsap_1435, retro_hsap_1565, retro_hsap_1656, retro_hsap_1936, retro_hsap_1937 , retro_hsap_2016, retro_hsap_2172, retro_hsap_218, retro_hsap_2476, retro_hsap_261, retro_hsap_2697, retro_hsap_2806, retro_hsap_2893, retro_hsap_2931, retro_hsap_297, retro_hsap_3060, retro_hsap_3572, retro_hsap_3603, retro_hsap_3749, retro_hsap_3766, retro_hsap_377, retro_hsap_3873, retro_hsap_3877, retro_hsap_4135, retro_hsap_4141, retro_hsap_612, retro_hsap_660, retro_hsap_750, retro_hsap_767, retro_hsap_771,

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 = 0.81 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .19 RPM
CEU_NA11843 0 .68 RPM
CEU_NA11930 0 .36 RPM
CEU_NA12004 0 .38 RPM
CEU_NA12400 0 .49 RPM
CEU_NA12751 0 .56 RPM
CEU_NA12760 0 .72 RPM
CEU_NA12827 0 .24 RPM
CEU_NA12872 0 .44 RPM
CEU_NA12873 0 .61 RPM
FIN_HG00183 0 .47 RPM
FIN_HG00277 0 .41 RPM
FIN_HG00315 0 .47 RPM
FIN_HG00321 0 .36 RPM
FIN_HG00328 0 .38 RPM
FIN_HG00338 0 .51 RPM
FIN_HG00349 0 .40 RPM
FIN_HG00375 0 .22 RPM
FIN_HG00377 0 .71 RPM
FIN_HG00378 0 .45 RPM
GBR_HG00099 0 .29 RPM
GBR_HG00111 0 .45 RPM
GBR_HG00114 0 .39 RPM
GBR_HG00119 0 .34 RPM
GBR_HG00131 0 .69 RPM
GBR_HG00133 0 .36 RPM
GBR_HG00134 0 .70 RPM
GBR_HG00137 0 .58 RPM
GBR_HG00142 0 .36 RPM
GBR_HG00143 0 .22 RPM
TSI_NA20512 0 .76 RPM
TSI_NA20513 0 .12 RPM
TSI_NA20518 0 .31 RPM
TSI_NA20532 0 .27 RPM
TSI_NA20538 0 .32 RPM
TSI_NA20756 0 .64 RPM
TSI_NA20765 0 .31 RPM
TSI_NA20771 0 .57 RPM
TSI_NA20786 0 .68 RPM
TSI_NA20798 0 .62 RPM
YRI_NA18870 0 .81 RPM
YRI_NA18907 0 .42 RPM
YRI_NA18916 0 .51 RPM
YRI_NA19093 0 .26 RPM
YRI_NA19099 0 .77 RPM
YRI_NA19114 0 .68 RPM
YRI_NA19118 0 .39 RPM
YRI_NA19213 0 .31 RPM
YRI_NA19214 0 .25 RPM
YRI_NA19223 0 .14 RPM

Indel association:

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



Copyright © RetrogeneDB 2014-2017