RetrogeneDB ID:

retro_hsap_1830

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:17:34930300..34931032(-)
Located in intron of:ENSG00000005955
Retrocopy
information
Ensembl ID:ENSG00000236002
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RPS2
Ensembl ID:ENSG00000140988
Aliases:RPS2, LLREP3, S2
Description:ribosomal protein S2 [Source:HGNC Symbol;Acc:10404]


Retrocopy-Parental alignment summary:






>retro_hsap_1830
GCTCATGGAGGCAAGGCCGAGGATAAAGAGTGGATGCCTATCACCAAGCTGGGCCGCCTGGTCAAGCACATGAAGATCAA
GTCCCTGGAGGAGATGTATGTCTTCTCCCTGCCCATGAAGGAATCTGAGATCACTAACTTTTTCCTGGGGGCCTCTCTCA
AGGACGAGGTTTTGAAGATTATGCCAGTGCAGAAGCAGACCCGTGCCGGCCAGCGCACCAGGTTCAAGATGTTTGTTGCC
ATCGTGGACTACAATGGCCACATCGGTCTGGGTGTTAAGTGCTCCAAGGAGGTGGCCACTGCCATCCACGGGGCCATCAT
CCTGGCCAAGCTCTCTATTGTCCCTGTGCACAGAGGCTACTGGGGGAACAAGATCAGCAAGCCCCACACCATCCCTTGCA
AGCCGACAGGCCACCACGGCTCTGTGCTGGTGCGCCTCATCCCTACGCCCAGAGGCACTGGCATCGTCTCAGTGCCTGTA
CCCAAGAAGCTGCTTATGATGGCTGGTATTGATGACTGCTACACCTTAGCCAGGGGCTACACTGCCGCCCTGGGTAACTA
TACCAAGGACACCTTTGATGCCATCTCTAAGACCTACAGCTACCTGACCCCCGACCTCTGGAAGGAGACTGTATTCATCA
AGTCTTCCTGTCAGGAATTCACTGACCATCTCGTCAAGACCCACACCAGAGTCTCCATGCAGAGGACCCAGGCTCCAGCT
GTGGCTACAACA

ORF - retro_hsap_1830 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 87.7 %
Parental protein coverage: 83.28 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalARGGKAEDKEWMPVTKLGRLVKDMKIKSLEEIYLFSLPIKESEIIDFFLGASLKDEVLKIMPVQKQTRAG
A.GGKAEDKEWMP.TKLGRLVK.MKIKSLEE.Y.FSLP.KESEI..FFLGASLKDEVLKIMPVQKQTRAG
RetrocopyAHGGKAEDKEWMPITKLGRLVKHMKIKSLEEMYVFSLPMKESEITNFFLGASLKDEVLKIMPVQKQTRAG
ParentalQRTRFKAFVAIGDYNGHVGLGVKCSKEVATAIRGAIILAKLSIVPVRRGYWGNKIGKPHTVPCKVTGRCG
QRTRFK.FVAI.DYNGH.GLGVKCSKEVATAI.GAIILAKLSIVPV.RGYWGNKI.KPHT.PCK.TG..G
RetrocopyQRTRFKMFVAIVDYNGHIGLGVKCSKEVATAIHGAIILAKLSIVPVHRGYWGNKISKPHTIPCKPTGHHG
ParentalSVLVRLIPAPRGTGIVSAPVPKKLLMMAGIDDCYTSARGCTATLGNFAKATFDAISKTYSYLTPDLWKET
SVLVRLIP.PRGTGIVS.PVPKKLLMMAGIDDCYT.ARG.TA.LGN..K.TFDAISKTYSYLTPDLWKET
RetrocopySVLVRLIPTPRGTGIVSVPVPKKLLMMAGIDDCYTLARGYTAALGNYTKDTFDAISKTYSYLTPDLWKET
ParentalVFTKSPYQEFTDHLVKTHTRVSVQRTQAPAVATT
VF.KS..QEFTDHLVKTHTRVS.QRTQAPAVATT
RetrocopyVFIKSSCQEFTDHLVKTHTRVSMQRTQAPAVATT

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 .16 RPM 496 .47 RPM
bodymap2_adrenal 0 .45 RPM 505 .10 RPM
bodymap2_brain 0 .12 RPM 53 .79 RPM
bodymap2_breast 0 .16 RPM 261 .89 RPM
bodymap2_colon 0 .00 RPM 444 .16 RPM
bodymap2_heart 0 .11 RPM 116 .21 RPM
bodymap2_kidney 0 .08 RPM 179 .65 RPM
bodymap2_liver 0 .15 RPM 249 .89 RPM
bodymap2_lung 0 .21 RPM 464 .79 RPM
bodymap2_lymph_node 0 .53 RPM 651 .42 RPM
bodymap2_ovary 0 .29 RPM 445 .62 RPM
bodymap2_prostate 0 .00 RPM 603 .00 RPM
bodymap2_skeletal_muscle 0 .07 RPM 731 .68 RPM
bodymap2_testis 0 .04 RPM 238 .89 RPM
bodymap2_thyroid 0 .06 RPM 257 .52 RPM
bodymap2_white_blood_cells 0 .02 RPM 782 .33 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_1830 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_1830 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_1830 retrocopy 5' end.

Lab - click to see more details

retro_hsap_1830 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1830 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 6 parental genes, and 79 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000025491 retrocopy
retro_acar_57,
Felis catus ENSFCAG000000291916 retrocopies
retro_fcat_1245, retro_fcat_1328, retro_fcat_1606, retro_fcat_1610, retro_fcat_1737, retro_fcat_517,
Homo sapiens ENSG00000140988 47 retrocopies
retro_hsap_1060, retro_hsap_136, retro_hsap_140, retro_hsap_141, retro_hsap_1443, retro_hsap_1444, retro_hsap_1457, retro_hsap_1463, retro_hsap_148, retro_hsap_1648, retro_hsap_1688, retro_hsap_1722, retro_hsap_1812, retro_hsap_1830 , retro_hsap_1831, retro_hsap_1838, retro_hsap_1845, retro_hsap_1897, retro_hsap_1953, retro_hsap_1965, retro_hsap_1971, retro_hsap_2124, retro_hsap_2198, retro_hsap_2424, retro_hsap_244, retro_hsap_2483, retro_hsap_2486, retro_hsap_250, retro_hsap_282, retro_hsap_2871, retro_hsap_3035, retro_hsap_3097, retro_hsap_3106, retro_hsap_3182, retro_hsap_3211, retro_hsap_3369, retro_hsap_3464, retro_hsap_3584, retro_hsap_3779, retro_hsap_385, retro_hsap_4094, retro_hsap_4290, retro_hsap_435, retro_hsap_4811, retro_hsap_754, retro_hsap_761, retro_hsap_970,
Monodelphis domestica ENSMODG000000160771 retrocopy
retro_mdom_536,
Otolemur garnettii ENSOGAG0000001009819 retrocopies
retro_ogar_1051, retro_ogar_1120, retro_ogar_1205, retro_ogar_1557, retro_ogar_1821, retro_ogar_1835, retro_ogar_1837, retro_ogar_1851, retro_ogar_2101, retro_ogar_2164, retro_ogar_2313, retro_ogar_2648, retro_ogar_2817, retro_ogar_2842, retro_ogar_2965, retro_ogar_3109, retro_ogar_3177, retro_ogar_3180, retro_ogar_794,
Sarcophilus harrisii ENSSHAG000000152135 retrocopies
retro_shar_186, retro_shar_288, retro_shar_456, retro_shar_525, retro_shar_783,

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 = 0.39 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .11 RPM
CEU_NA11843 0 .11 RPM
CEU_NA11930 0 .36 RPM
CEU_NA12004 0 .04 RPM
CEU_NA12400 0 .11 RPM
CEU_NA12751 0 .17 RPM
CEU_NA12760 0 .22 RPM
CEU_NA12827 0 .24 RPM
CEU_NA12872 0 .19 RPM
CEU_NA12873 0 .32 RPM
FIN_HG00183 0 .14 RPM
FIN_HG00277 0 .15 RPM
FIN_HG00315 0 .08 RPM
FIN_HG00321 0 .12 RPM
FIN_HG00328 0 .14 RPM
FIN_HG00338 0 .13 RPM
FIN_HG00349 0 .06 RPM
FIN_HG00375 0 .20 RPM
FIN_HG00377 0 .08 RPM
FIN_HG00378 0 .04 RPM
GBR_HG00099 0 .15 RPM
GBR_HG00111 0 .06 RPM
GBR_HG00114 0 .26 RPM
GBR_HG00119 0 .36 RPM
GBR_HG00131 0 .32 RPM
GBR_HG00133 0 .17 RPM
GBR_HG00134 0 .35 RPM
GBR_HG00137 0 .22 RPM
GBR_HG00142 0 .39 RPM
GBR_HG00143 0 .19 RPM
TSI_NA20512 0 .06 RPM
TSI_NA20513 0 .34 RPM
TSI_NA20518 0 .08 RPM
TSI_NA20532 0 .27 RPM
TSI_NA20538 0 .37 RPM
TSI_NA20756 0 .17 RPM
TSI_NA20765 0 .27 RPM
TSI_NA20771 0 .14 RPM
TSI_NA20786 0 .03 RPM
TSI_NA20798 0 .19 RPM
YRI_NA18870 0 .24 RPM
YRI_NA18907 0 .10 RPM
YRI_NA18916 0 .08 RPM
YRI_NA19093 0 .21 RPM
YRI_NA19099 0 .05 RPM
YRI_NA19114 0 .05 RPM
YRI_NA19118 0 .17 RPM
YRI_NA19213 0 .17 RPM
YRI_NA19214 0 .15 RPM
YRI_NA19223 0 .36 RPM

Indel association:

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





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