RetrogeneDB ID:

retro_hsap_1060

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:12:118683888..118684767(+)
Located in intron of:ENSG00000135090
Retrocopy
information
Ensembl ID:ENSG00000240342
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_1060
ATGGCGGATGACGCCGGTGCAGCGGGGGGGCACGGAGGCCCTGGTGGCCCTGGGATGGGGAACCGCGGTGGCTTCCGCGG
AGGTTTCGGCAGTGGCATCCGGGGCCGGGGTCGCGGCCGTGGACGGGGCCGGGGCCGAGGCCGCGGAGCTCGCGGAGGCA
AGGCCGAGGATAAGGAGTGGATGCCCGTCACCAAGTTGGGCCGCTTGGTCAAGGACATGAAGATCAAGTCCCTGGAGGAG
ATCTATCTCTTCTCCCTGCCCATTAAGGAATCAGAGATCATTGATTTCTTCCTGGGGGCCTCTCTCAAGGATGAGGTTTT
GAAGATTATGCCAGTGCAGAAGCAGACCCGTGCCAGCCAGCGCACCAGGTTCAAGGCGTTTGTTGCTATCGGGGACTACA
ATGGCCACGTCGGTCTGGGTGTTAAGTGCTCCAAGGAGGTGGCCACCGCCATCCGTGGGGCCATCATCCTGGCCAAGCTC
TCCATTGTCCCCGTGCGCAGAGGCTACTGGGGGAACAAGATCGGCAAGCCCCACACTGTCCCTTGCAAGGTGACAGGCCG
CTGCGGCTCTGTGCTGGTGCGCCTCATCCCTGCACCCAGGGGCACTGGCATCGTCTCCGCACCTGTGCCTAAGAAGCTGC
TCATGATGGCTGGTATCGATGACTGCTACACCTCAGCCCGGGGCTGCACTGCCACCCTGGGCAACTTCGCCAAGGCCACC
TTTGATGCCATTTCTAAGACCTACAGCTACCTGACCCCCGACCTCTGGAAGGAGACTGTATTTACCAAGTCTCCCTATCA
GGAATTCACTGACCACCTCGTTAAGACCCACACCAGAGTCTCCGTGCAGCGGACTCAGGATCCAGCTGTGGCTACAACA

ORF - retro_hsap_1060 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 93.17 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMADDAGAAGGPGGPGGPGMGNRGGFRGGFGSGIRGRGRGRGRGRGRGRGARGGKAEDKEWMPVTKLGRLV
MADDAGAAGG.GGPGGPGMGNRGGFRGGFGSG.................ARGGKAEDKEWMPVTKLGRLV
RetrocopyMADDAGAAGGHGGPGGPGMGNRGGFRGGFGSGXXXXXXXXXXXXXXXXXARGGKAEDKEWMPVTKLGRLV
ParentalKDMKIKSLEEIYLFSLPIKESEIIDFFLGASLKDEVLKIMPVQKQTRAGQRTRFKAFVAIGDYNGHVGLG
KDMKIKSLEEIYLFSLPIKESEIIDFFLGASLKDEVLKIMPVQKQTRA.QRTRFKAFVAIGDYNGHVGLG
RetrocopyKDMKIKSLEEIYLFSLPIKESEIIDFFLGASLKDEVLKIMPVQKQTRASQRTRFKAFVAIGDYNGHVGLG
ParentalVKCSKEVATAIRGAIILAKLSIVPVRRGYWGNKIGKPHTVPCKVTGRCGSVLVRLIPAPRGTGIVSAPVP
VKCSKEVATAIRGAIILAKLSIVPVRRGYWGNKIGKPHTVPCKVTGRCGSVLVRLIPAPRGTGIVSAPVP
RetrocopyVKCSKEVATAIRGAIILAKLSIVPVRRGYWGNKIGKPHTVPCKVTGRCGSVLVRLIPAPRGTGIVSAPVP
ParentalKKLLMMAGIDDCYTSARGCTATLGNFAKATFDAISKTYSYLTPDLWKETVFTKSPYQEFTDHLVKTHTRV
KKLLMMAGIDDCYTSARGCTATLGNFAKATFDAISKTYSYLTPDLWKETVFTKSPYQEFTDHLVKTHTRV
RetrocopyKKLLMMAGIDDCYTSARGCTATLGNFAKATFDAISKTYSYLTPDLWKETVFTKSPYQEFTDHLVKTHTRV
ParentalSVQRTQAPAVATT
SVQRTQ.PAVATT
RetrocopySVQRTQDPAVATT

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 12 .74 RPM 496 .47 RPM
bodymap2_adrenal 54 .65 RPM 505 .10 RPM
bodymap2_brain 1 .71 RPM 53 .79 RPM
bodymap2_breast 5 .04 RPM 261 .89 RPM
bodymap2_colon 21 .75 RPM 444 .16 RPM
bodymap2_heart 3 .32 RPM 116 .21 RPM
bodymap2_kidney 5 .73 RPM 179 .65 RPM
bodymap2_liver 7 .27 RPM 249 .89 RPM
bodymap2_lung 8 .33 RPM 464 .79 RPM
bodymap2_lymph_node 15 .24 RPM 651 .42 RPM
bodymap2_ovary 13 .80 RPM 445 .62 RPM
bodymap2_prostate 25 .32 RPM 603 .00 RPM
bodymap2_skeletal_muscle 20 .42 RPM 731 .68 RPM
bodymap2_testis 7 .05 RPM 238 .89 RPM
bodymap2_thyroid 0 .98 RPM 257 .52 RPM
bodymap2_white_blood_cells 48 .81 RPM 782 .33 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_1060 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_1060 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_21715192 libraries271 libraries777 libraries332 libraries257 libraries

The graphical summary, for retro_hsap_1060 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_1060 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1060 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Gorilla gorilla retro_ggor_129
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 = 476.11 RPM Legend:


Library Retrogene expression
CEU_NA11831 319 .66 RPM
CEU_NA11843 476 .11 RPM
CEU_NA11930 295 .43 RPM
CEU_NA12004 179 .29 RPM
CEU_NA12400 251 .07 RPM
CEU_NA12751 206 .58 RPM
CEU_NA12760 424 .69 RPM
CEU_NA12827 186 .74 RPM
CEU_NA12872 190 .15 RPM
CEU_NA12873 417 .73 RPM
FIN_HG00183 343 .67 RPM
FIN_HG00277 324 .59 RPM
FIN_HG00315 173 .58 RPM
FIN_HG00321 333 .60 RPM
FIN_HG00328 169 .58 RPM
FIN_HG00338 435 .60 RPM
FIN_HG00349 182 .22 RPM
FIN_HG00375 314 .97 RPM
FIN_HG00377 301 .96 RPM
FIN_HG00378 323 .99 RPM
GBR_HG00099 150 .71 RPM
GBR_HG00111 162 .49 RPM
GBR_HG00114 350 .83 RPM
GBR_HG00119 166 .53 RPM
GBR_HG00131 265 .68 RPM
GBR_HG00133 174 .86 RPM
GBR_HG00134 339 .97 RPM
GBR_HG00137 351 .07 RPM
GBR_HG00142 144 .15 RPM
GBR_HG00143 140 .27 RPM
TSI_NA20512 398 .06 RPM
TSI_NA20513 263 .68 RPM
TSI_NA20518 338 .40 RPM
TSI_NA20532 3 .91 RPM
TSI_NA20538 308 .05 RPM
TSI_NA20756 209 .88 RPM
TSI_NA20765 260 .25 RPM
TSI_NA20771 377 .37 RPM
TSI_NA20786 365 .67 RPM
TSI_NA20798 346 .05 RPM
YRI_NA18870 338 .65 RPM
YRI_NA18907 311 .52 RPM
YRI_NA18916 364 .28 RPM
YRI_NA19093 399 .75 RPM
YRI_NA19099 321 .89 RPM
YRI_NA19114 449 .48 RPM
YRI_NA19118 362 .97 RPM
YRI_NA19213 195 .83 RPM
YRI_NA19214 331 .09 RPM
YRI_NA19223 251 .69 RPM

Indel association:

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



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