RetrogeneDB ID:

retro_hsap_600

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:10:81885696..81886070(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000230171
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL22
Ensembl ID:ENSG00000116251
Aliases:RPL22, EAP, HBP15, HBP15/L22, L22
Description:ribosomal protein L22 [Source:HGNC Symbol;Acc:10315]


Retrocopy-Parental alignment summary:






>retro_hsap_600
ATGGCTCCCGGGAAAAAGCTTGTGGTGAAGAGGGGCAAAAAAAAGAAGCAGGTTCTGAAGTTCAGTCTTGATTGCACCCA
CCCCGTAGAATATGGAATCATAGACGCTGCCAATTTTGAGCAGTTTCTGCAAGAGAGGATCAAAGTGAACTGAAAAGCTG
GGAAACTTGGCGGAGGGGTGGTGACCATCGAAAGGAGCAAGAGAAAGATCGCCATGATATCTGAGGTGACTTTTTCCAAA
AGGTATTTGAAATATTACACCAAAAAATATTCAAAGAAGAATAATCTATGTGATTGGTTTTCGTAGCTGCTAACAGCAAA
GAGAGTTATGGATTACATTATTTCTAAACTAATCAGGACGAGGAAGATGAGGAT

ORF - retro_hsap_600 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 77.78 %
Parental protein coverage: 97.66 %
Number of stop codons detected: 2
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMAPVKKLVVKGGKKKKQVLKFTLDCTHPVEDGIMDAANFEQFLQERIKVNGKAGNLGGGVVTIERSKSKI
MAP.KKLVVK.G...KQVLKF.LDCTHPVE.GI.DAANFEQFLQERIKVN.KAG.LGGGVVTIERSK.KI
RetrocopyMAPGKKLVVKRGXXXKQVLKFSLDCTHPVEYGIIDAANFEQFLQERIKVN*KAGKLGGGVVTIERSKRKI
ParentalTVTSEVPFSKRYLKYLTKKYLKKNNLRDWLR-VVANSKESYELRYFQINQDEEEEE
...SEV.FSKRYLKY.TKKY.KKNNL.DW...V.ANSKESY.L.YF..NQDEE.E.
RetrocopyAMISEVTFSKRYLKYYTKKYSKKNNLCDWFS<VAANSKESYGLHYF*TNQDEEDED

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






(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 206 .65 RPM
bodymap2_adrenal 0 .00 RPM 196 .92 RPM
bodymap2_brain 0 .02 RPM 89 .40 RPM
bodymap2_breast 0 .06 RPM 197 .41 RPM
bodymap2_colon 0 .00 RPM 279 .67 RPM
bodymap2_heart 0 .02 RPM 88 .35 RPM
bodymap2_kidney 0 .00 RPM 124 .17 RPM
bodymap2_liver 0 .00 RPM 77 .90 RPM
bodymap2_lung 0 .00 RPM 247 .10 RPM
bodymap2_lymph_node 0 .00 RPM 258 .85 RPM
bodymap2_ovary 0 .00 RPM 424 .80 RPM
bodymap2_prostate 0 .00 RPM 414 .95 RPM
bodymap2_skeletal_muscle 0 .00 RPM 144 .01 RPM
bodymap2_testis 0 .08 RPM 148 .81 RPM
bodymap2_thyroid 0 .00 RPM 215 .71 RPM
bodymap2_white_blood_cells 0 .00 RPM 289 .19 RPM
RNA Polymerase II actvity near the 5' end of retro_hsap_600 was not detected
No EST(s) were mapped for retro_hsap_600 retrocopy.
No TSS is located nearby retro_hsap_600 retrocopy 5' end.
retro_hsap_600 was not experimentally validated.


Parental genes homology:
Parental genes homology involve 22 parental genes, and 184 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000098647 retrocopies
Bos taurus ENSBTAG000000144234 retrocopies
Choloepus hoffmanni ENSCHOG000000074772 retrocopies
Callithrix jacchus ENSCJAG0000000013212 retrocopies
Dasypus novemcinctus ENSDNOG000000131668 retrocopies
Felis catus ENSFCAG000000063203 retrocopies
Homo sapiens ENSG00000116251 16 retrocopies
Homo sapiens ENSG000001635841 retrocopy
Gorilla gorilla ENSGGOG0000002773910 retrocopies
Loxodonta africana ENSLAFG000000063525 retrocopies
Macaca mulatta ENSMMUG0000001834712 retrocopies
Mustela putorius furoENSMPUG000000070876 retrocopies
Mus musculus ENSMUSG000000289365 retrocopies
Nomascus leucogenys ENSNLEG0000001033710 retrocopies
Otolemur garnettii ENSOGAG000000147767 retrocopies
Pongo abelii ENSPPYG0000000195111 retrocopies
Pan troglodytes ENSPTRG0000000007614 retrocopies
Rattus norvegicus ENSRNOG000000111045 retrocopies
Sus scrofa ENSSSCG000000033674 retrocopies
Tupaia belangeri ENSTBEG0000000917233 retrocopies
Tursiops truncatus ENSTTRG000000104888 retrocopies
Vicugna pacos ENSVPAG000000094661 retrocopy

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 ) Legend:


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


Indel association:

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




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