RetrogeneDB ID:

retro_hsap_120

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:1:20852515..20853174(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000215520
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RPS4X
Ensembl ID:ENSG00000198034
Aliases:None
Description:ribosomal protein S4, X-linked [Source:HGNC Symbol;Acc:10424]


Retrocopy-Parental alignment summary:






>retro_hsap_120
AGCAGCTCAAAGCAATGGATGCTGGAGACACTGACTGGTGTGTCTGCTCCTCATCCATCCACCAGTCCCCACAAGCTGAG
AGTATGTCTCCTCCTCATCATTTTTCCTAAGAAACAGAATTAAGTATGCCCTGATCAGAGATGAACTAAAGATTTGGATG
CTGCGGCTCATTAAGATTGACGACAAGGTCCAAACTGATAGAACCTACCCTGCTGGATTCAAAGATGTCATCATCATTGA
CAAGACCAGAGAGAATGTCCGTCTGACCTGTAACATCAGGGTCACTTTGCCATTCACCGTATTACAGCTGAGGAGGCCAA
GTACAAATTGTGCAAAGTGAGAAAAATCTTGCGGCTACAAAAGGAATCCCTCATCTGGTAACCAATGATGCTGGCACCAT
CCGCTACCCTGGTCCCCTCATCAAGGTGAATGACATCATTCAGATTGATTTGGATACTGGCAAGAGTACCGATGTCATCA
AGTTTGATACTGGTAACCTGTGGATGGTGACTGGAGGTGCGAACCTGGGAAGAATTGGTGTGATTACCAACAGAGAGAGG
CACCCTGGATCTTTTGATGTGGTTCATGTGAAAGATGCCAACAGCAACAGCTTTGCCACCTGGCTTTCCAGCATTTTTGT
TATTGGCAAGGGCAACAAA

ORF - retro_hsap_120 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 77.23 %
Parental protein coverage: 84.03 %
Number of stop codons detected: 0
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalAAPKHWMLDKLTGVFAPRPSTGPHKLRECLPLIIF-LRNRLKYALTGDEVKKICMQRFIKIDGKVRTDIT
...K.WML..LTGV.AP.PST.PHKLR.CL.LIIF.LRNR.KYAL..DE.K.I.M.R.IKID.KV.TD.T
RetrocopySSSKQWMLETLTGVSAPHPSTSPHKLRVCLLLIIF>LRNRIKYALIRDELK-IWMLRLIKIDDKVQTDRT
ParentalYPAGFMDVISIDKTGENFRLIYDTK-GRFAVHRITPEEAKYKLCKVRKIF-VGTKGIPHLVTHDARTIRY
YPAGF.DVI.IDKT.EN.RL......G.FA.HRIT.EEAKYKLCKVRKI....TKGIPHLVT.DA.TIRY
RetrocopyYPAGFKDVIIIDKTRENVRLTCNIR<GHFAIHRITAEEAKYKLCKVRKIL<AATKGIPHLVTNDAGTIRY
ParentalPDPLIKVNDTIQIDLETGKITDFIKFDTGNLCMVTGGANLGRIGVITNRERHPGSFDVVHVKDANGNSFA
P.PLIKVND.IQIDL.TGK.TD.IKFDTGNL.MVTGGANLGRIGVITNRERHPGSFDVVHVKDAN.NSFA
RetrocopyPGPLIKVNDIIQIDLDTGKSTDVIKFDTGNLWMVTGGANLGRIGVITNRERHPGSFDVVHVKDANSNSFA
ParentalTRLSNIFVIGKGNK
T.LS.IFVIGKGNK
RetrocopyTWLSSIFVIGKGNK

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 1077 .78 RPM
bodymap2_adrenal 0 .00 RPM 994 .39 RPM
bodymap2_brain 0 .00 RPM 249 .47 RPM
bodymap2_breast 0 .00 RPM 912 .87 RPM
bodymap2_colon 0 .00 RPM 1472 .93 RPM
bodymap2_heart 0 .00 RPM 215 .90 RPM
bodymap2_kidney 0 .00 RPM 575 .10 RPM
bodymap2_liver 0 .00 RPM 226 .26 RPM
bodymap2_lung 0 .00 RPM 826 .90 RPM
bodymap2_lymph_node 0 .00 RPM 1412 .13 RPM
bodymap2_ovary 0 .02 RPM 2009 .69 RPM
bodymap2_prostate 0 .00 RPM 1321 .94 RPM
bodymap2_skeletal_muscle 0 .00 RPM 719 .78 RPM
bodymap2_testis 0 .02 RPM 641 .02 RPM
bodymap2_thyroid 0 .00 RPM 887 .86 RPM
bodymap2_white_blood_cells 0 .00 RPM 1229 .94 RPM
RNA Polymerase II actvity near the 5' end of retro_hsap_120 was not detected
No EST(s) were mapped for retro_hsap_120 retrocopy.
No TSS is located nearby retro_hsap_120 retrocopy 5' end.
retro_hsap_120 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_120 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_131
Gorilla gorilla retro_ggor_223
Pongo abelii retro_pabe_493

Parental genes homology:
Parental genes homology involve 22 parental genes, and 210 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000146011 retrocopy
Bos taurus ENSBTAG000000188005 retrocopies
Canis familiaris ENSCAFG000000171512 retrocopies
Callithrix jacchus ENSCJAG000000041922 retrocopies
Cavia porcellus ENSCPOG000000063373 retrocopies
Equus caballus ENSECAG000000108526 retrocopies
Homo sapiens ENSG000001298241 retrocopy
Homo sapiens ENSG00000198034 19 retrocopies
Macropus eugenii ENSMEUG0000000796916 retrocopies
Meleagris gallopavo ENSMGAG000000096711 retrocopy
Microcebus murinus ENSMICG0000001660658 retrocopies
Monodelphis domestica ENSMODG000000110701 retrocopy
Mustela putorius furoENSMPUG0000000529411 retrocopies
Mus musculus ENSMUSG0000003132013 retrocopies
Nomascus leucogenys ENSNLEG0000001812125 retrocopies
Otolemur garnettii ENSOGAG000000118082 retrocopies
Pongo abelii ENSPPYG0000002046224 retrocopies
Pan troglodytes ENSPTRG000000220259 retrocopies
Pan troglodytes ENSPTRG000000224701 retrocopy
Rattus norvegicus ENSRNOG000000032011 retrocopy
Sus scrofa ENSSSCG000000124055 retrocopies
Vicugna pacos ENSVPAG000000109524 retrocopies

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 = 0.04 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 .04 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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