RetrogeneDB ID:

retro_hsap_2030

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:19:12754091..12754733(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000178464
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL10
Ensembl ID:ENSG00000147403
Aliases:RPL10, AUTSX5, DXS648, DXS648E, L10, NOV, QM
Description:ribosomal protein L10 [Source:HGNC Symbol;Acc:10298]


Retrocopy-Parental alignment summary:






>retro_hsap_2030
ATGGGCCGCCGCCCCGCCCGTTGTTACCGGTATTGTAAGAACAAGCCGTACCCAAAGTCTCGCTTCTGCCGAGGTGTCCC
TGATGCCAAGATTCGCATTTTTGACCTGGGGCGGAAAAAGGCAAAAGTGGATGAGTTTCCGCTCTGTGGCCACATGGTGT
CAGATGAATATGAGCAGCTGTCCTCTGAAGCCCTGGAGGCTGCCCGAATTTGTGCCAATAAGTACATGGTAAAAAGTTGT
GGCAAAGATGGCTTCCATATCCGGGTGCGGCTCCACCCCTTCCACGTCATCCGCATCAACAAGATGTCGTCCTGTGCTGG
GGCTGACAGGCTCCAAACAGGAATGCGAGGTGCCTTTGGAAAGCCCCAGGGCACTGTGGCCAGGGTTCACATTGGCCAAG
TTATCATGTCCATCCGCACCAAGCTGCAGAACAAGGAGCGTGTGATTGAGGCCCTGCGCAGGGCCAAGTTCAAGTTTCCT
GGCCGCCAGAAGATCCACATCTCAAAGAAGTGGGGCTTCACCAAGTTCAATGCTGATGAATTTGAAGACATGGTGGCTGA
AAAGCGGCTCATCCCAGATGGCTGTGGGGTCAAGTATATCCCCAATCGTGGCCCTCTGGACAAGTGGTGGGCCCTGCACT
CA

ORF - retro_hsap_2030 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 98.6 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMGRRPARCYRYCKNKPYPKSRFCRGVPDAKIRIFDLGRKKAKVDEFPLCGHMVSDEYEQLSSEALEAARI
MGRRPARCYRYCKNKPYPKSRFCRGVPDAKIRIFDLGRKKAKVDEFPLCGHMVSDEYEQLSSEALEAARI
RetrocopyMGRRPARCYRYCKNKPYPKSRFCRGVPDAKIRIFDLGRKKAKVDEFPLCGHMVSDEYEQLSSEALEAARI
ParentalCANKYMVKSCGKDGFHIRVRLHPFHVIRINKMLSCAGADRLQTGMRGAFGKPQGTVARVHIGQVIMSIRT
CANKYMVKSCGKDGFHIRVRLHPFHVIRINKM.SCAGADRLQTGMRGAFGKPQGTVARVHIGQVIMSIRT
RetrocopyCANKYMVKSCGKDGFHIRVRLHPFHVIRINKMSSCAGADRLQTGMRGAFGKPQGTVARVHIGQVIMSIRT
ParentalKLQNKEHVIEALRRAKFKFPGRQKIHISKKWGFTKFNADEFEDMVAEKRLIPDGCGVKYIPNRGPLDKWR
KLQNKE.VIEALRRAKFKFPGRQKIHISKKWGFTKFNADEFEDMVAEKRLIPDGCGVKYIPNRGPLDKW.
RetrocopyKLQNKERVIEALRRAKFKFPGRQKIHISKKWGFTKFNADEFEDMVAEKRLIPDGCGVKYIPNRGPLDKWW
ParentalALHS
ALHS
RetrocopyALHS

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 3 .98 RPM 465 .66 RPM
bodymap2_adrenal 5 .81 RPM 522 .26 RPM
bodymap2_brain 0 .68 RPM 102 .06 RPM
bodymap2_breast 2 .45 RPM 310 .82 RPM
bodymap2_colon 6 .86 RPM 703 .36 RPM
bodymap2_heart 0 .52 RPM 249 .13 RPM
bodymap2_kidney 1 .80 RPM 366 .37 RPM
bodymap2_liver 0 .46 RPM 302 .00 RPM
bodymap2_lung 1 .83 RPM 1014 .17 RPM
bodymap2_lymph_node 2 .50 RPM 1033 .94 RPM
bodymap2_ovary 7 .48 RPM 739 .54 RPM
bodymap2_prostate 4 .23 RPM 1347 .95 RPM
bodymap2_skeletal_muscle 2 .29 RPM 691 .03 RPM
bodymap2_testis 2 .49 RPM 282 .25 RPM
bodymap2_thyroid 2 .35 RPM 300 .94 RPM
bodymap2_white_blood_cells 2 .40 RPM 1398 .58 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_2030 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_2030 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_7007355 libraries2 libraries118 libraries246 libraries1408 libraries

The graphical summary, for retro_hsap_2030 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_2030 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2030 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 7 parental genes, and 19 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000074542 retrocopies
retro_btau_140, retro_btau_99,
Homo sapiens ENSG00000147403 3 retrocopies
retro_hsap_2030 , retro_hsap_3265, retro_hsap_3437,
Macropus eugenii ENSMEUG000000131633 retrocopies
retro_meug_1839, retro_meug_5, retro_meug_547,
Myotis lucifugus ENSMLUG000000143373 retrocopies
retro_mluc_1592, retro_mluc_191, retro_mluc_275,
Monodelphis domestica ENSMODG000000087312 retrocopies
retro_mdom_177, retro_mdom_829,
Mus musculus ENSMUSG000000086821 retrocopy
retro_mmus_71,
Pongo abelii ENSPPYG000000208745 retrocopies
retro_pabe_173, retro_pabe_1854, retro_pabe_2036, retro_pabe_2843, retro_pabe_2955,

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 = 7.41 RPM Legend:


Library Retrogene expression
CEU_NA11831 4 .56 RPM
CEU_NA11843 4 .04 RPM
CEU_NA11930 5 .77 RPM
CEU_NA12004 2 .17 RPM
CEU_NA12400 4 .14 RPM
CEU_NA12751 2 .96 RPM
CEU_NA12760 7 .41 RPM
CEU_NA12827 4 .20 RPM
CEU_NA12872 3 .57 RPM
CEU_NA12873 2 .90 RPM
FIN_HG00183 5 .02 RPM
FIN_HG00277 2 .85 RPM
FIN_HG00315 3 .17 RPM
FIN_HG00321 3 .48 RPM
FIN_HG00328 2 .44 RPM
FIN_HG00338 3 .30 RPM
FIN_HG00349 5 .12 RPM
FIN_HG00375 4 .03 RPM
FIN_HG00377 4 .11 RPM
FIN_HG00378 3 .00 RPM
GBR_HG00099 3 .81 RPM
GBR_HG00111 3 .33 RPM
GBR_HG00114 2 .79 RPM
GBR_HG00119 2 .87 RPM
GBR_HG00131 3 .16 RPM
GBR_HG00133 3 .40 RPM
GBR_HG00134 2 .84 RPM
GBR_HG00137 4 .12 RPM
GBR_HG00142 3 .08 RPM
GBR_HG00143 2 .49 RPM
TSI_NA20512 2 .60 RPM
TSI_NA20513 2 .39 RPM
TSI_NA20518 4 .30 RPM
TSI_NA20532 3 .13 RPM
TSI_NA20538 4 .01 RPM
TSI_NA20756 4 .45 RPM
TSI_NA20765 2 .71 RPM
TSI_NA20771 5 .45 RPM
TSI_NA20786 2 .88 RPM
TSI_NA20798 3 .40 RPM
YRI_NA18870 6 .87 RPM
YRI_NA18907 3 .19 RPM
YRI_NA18916 2 .76 RPM
YRI_NA19093 2 .76 RPM
YRI_NA19099 3 .75 RPM
YRI_NA19114 3 .25 RPM
YRI_NA19118 3 .34 RPM
YRI_NA19213 2 .27 RPM
YRI_NA19214 2 .12 RPM
YRI_NA19223 2 .33 RPM

Indel association:

The presence of retro_hsap_2030 across human populations is associated with 1 indel. The percentage values indicate the frequencies of retro_hsap_2030 presence in various populations. Based on Kabza et al. 2015 (PubMed).


# Indel coordinates AFR, African AMR, Ad Mixed American EUR, European EAS, East Asian
ASW YRI LWK MXL PUR CLM CEU IBS GBR FIN TSI JPT CHB CHS
1. 19:12753336..12754500 97.54 100 98.45 83.33 88.18 87.5 90.59 92.86 91.01 89.25 94.39 95.51 92.78 91

Indel #1, located at the genomic coordinates 19:12753336..12754500.

image/svg+xml Mexican Ancestryfrom Los Angeles USA MXL 83.33 % Puerto Ricansfrom Puerto Rico PUR 88.18 % Colombians fromMedellin, Colombia CLM 87.5 % Americans of AfricanAncestry in SW USA ASW 97.54 % Yoruba in Ibadan,Nigeria YRI 100 % Luhya in Webuye,Kenya LWK 98.45 % Utah Residents (CEPH)with Northern andWestern European Ancestry CEU 90.59 % Iberian Populationin Spain IBS 92.86 % British in Englandand Scotland GBR 91.01 % Finnish in Finland FIN 89.25 % Toscani in Italia TSI 94.39 % Han Chinese in Bejing,China CHB 92.78 % Japanese in Tokyo,Japan 95.51 % Southern Han Chinese CHS 91 % JPT EUROPE AMERICAS AFRICA EAST ASIA




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