RetrogeneDB ID:

retro_hsap_4235

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:9:19200579..19201044(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000232176
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RPS6
Ensembl ID:ENSG00000137154
Aliases:RPS6, S6
Description:ribosomal protein S6 [Source:HGNC Symbol;Acc:10429]


Retrocopy-Parental alignment summary:






>retro_hsap_4235
ATGAAGCTGAACATCTCCTTCCCAGCCACTGGCTGCCAGAAACTCATTGAAATGGATGATGAATGCAAACTTCGTACTTT
TTATGAGAAACGTACGGCCACAAAAGTTGCTGCTGACACACTGGGTGAAGAATGGAAGGGTTATGTGGTCCGAATCAGTG
GTGGGAACGACAAATAAGGTTTCCCCATGAAGCAGGGTGTCTTGACCCATGGCCATGTCCACCTGCTACTGAGTAAGGGG
CATTCCTGTTACAGACCAAGGAGAACTGGAGAAAGGAAGGGAAAATCAGTTCATGGTTGCATTGTGGTTGCCAATCTGAG
CATTCTCAACTTGGTTATTGTAAAAAAAGGAGAGAAGGATATTCCTGGACTGACTGATACTATGGTGCCTCATCACCTGG
GACCCAAAAGAGCTAGCAGAATCCATAAACTTTTCAATCTCTCTAAAGAAAGCCCTTAAAGAAGG

ORF - retro_hsap_4235 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 87.1 %
Parental protein coverage: 62.25 %
Number of stop codons detected: 2
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalMKLNISFPATGCQKLIEVDDERKLRTFYEKRMATEVAADALGEEWKGYVVRISGGNDKQGFPMKQGVLTH
MKLNISFPATGCQKLIE.DDE.KLRTFYEKR.AT.VAAD.LGEEWKGYVVRISGGNDK.GFPMKQGVLTH
RetrocopyMKLNISFPATGCQKLIEMDDECKLRTFYEKRTATKVAADTLGEEWKGYVVRISGGNDK*GFPMKQGVLTH
ParentalGRVRLLLSKGHSCYRPRRTGERKRKSVRGCIVDANLSVLNLVIVKKGEKDIPGLTDTTVPRRLGPKRASR
G.V.LLLSKGHSCYRPRRTGERK.KSV.GCIV.ANLS.LNLVIVKKGEKDIPGLTDT.VP..LGPKRASR
RetrocopyGHVHLLLSKGHSCYRPRRTGERKGKSVHGCIVVANLSILNLVIVKKGEKDIPGLTDTMVPHHLGPKRASR
ParentalIRKLFNLSKEDDVRQ
I.KLFNLSKE...R.
RetrocopyIHKLFNLSKESP*RR

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 .28 RPM 1049 .46 RPM
bodymap2_adrenal 1 .58 RPM 1614 .86 RPM
bodymap2_brain 0 .40 RPM 360 .09 RPM
bodymap2_breast 0 .45 RPM 775 .53 RPM
bodymap2_colon 1 .14 RPM 1858 .77 RPM
bodymap2_heart 0 .15 RPM 309 .57 RPM
bodymap2_kidney 0 .54 RPM 734 .45 RPM
bodymap2_liver 0 .36 RPM 424 .99 RPM
bodymap2_lung 1 .05 RPM 1344 .15 RPM
bodymap2_lymph_node 1 .32 RPM 1605 .87 RPM
bodymap2_ovary 1 .29 RPM 1927 .03 RPM
bodymap2_prostate 1 .23 RPM 1953 .08 RPM
bodymap2_skeletal_muscle 0 .47 RPM 449 .82 RPM
bodymap2_testis 0 .57 RPM 1017 .90 RPM
bodymap2_thyroid 0 .79 RPM 1022 .65 RPM
bodymap2_white_blood_cells 0 .93 RPM 1936 .41 RPM

ChIP-Seq - click to see more details

RNA Polymerase II activity near the 5' end of retro_hsap_4235 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_4235 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_4235 retrocopy 5' end.

Lab - click to see more details

retro_hsap_4235 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_4235 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2878
Parental genes homology:
Parental genes homology involve 11 parental genes, and 122 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000176341 retrocopy
retro_acar_20,
Cavia porcellus ENSCPOG000000037504 retrocopies
retro_cpor_1244, retro_cpor_22, retro_cpor_317, retro_cpor_486,
Echinops telfairi ENSETEG0000000158418 retrocopies
retro_etel_1143, retro_etel_1281, retro_etel_1410, retro_etel_1430, retro_etel_1575, retro_etel_167, retro_etel_1822, retro_etel_188, retro_etel_1964, retro_etel_2004, retro_etel_2041, retro_etel_2194, retro_etel_263, retro_etel_337, retro_etel_378, retro_etel_541, retro_etel_809, retro_etel_825,
Homo sapiens ENSG00000137154 16 retrocopies
retro_hsap_1009, retro_hsap_1067, retro_hsap_1231, retro_hsap_1310, retro_hsap_1967, retro_hsap_2184, retro_hsap_2298, retro_hsap_3045, retro_hsap_3996, retro_hsap_4122, retro_hsap_4235 , retro_hsap_4279, retro_hsap_4860, retro_hsap_731, retro_hsap_818, retro_hsap_966,
Loxodonta africana ENSLAFG000000107664 retrocopies
retro_lafr_1021, retro_lafr_1239, retro_lafr_59, retro_lafr_667,
Myotis lucifugus ENSMLUG0000000758827 retrocopies
retro_mluc_1041, retro_mluc_1146, retro_mluc_1169, retro_mluc_1393, retro_mluc_1411, retro_mluc_1448, retro_mluc_1472, retro_mluc_1532, retro_mluc_1566, retro_mluc_1593, retro_mluc_1629, retro_mluc_1635, retro_mluc_1723, retro_mluc_1799, retro_mluc_1909, retro_mluc_1928, retro_mluc_1933, retro_mluc_2110, retro_mluc_2129, retro_mluc_490, retro_mluc_493, retro_mluc_514, retro_mluc_557, retro_mluc_652, retro_mluc_678, retro_mluc_722, retro_mluc_830,
Monodelphis domestica ENSMODG000000040951 retrocopy
retro_mdom_301,
Ochotona princeps ENSOPRG000000122905 retrocopies
retro_opri_123, retro_opri_642, retro_opri_78, retro_opri_862, retro_opri_895,
Pan troglodytes ENSPTRG0000003915319 retrocopies
retro_ptro_1313, retro_ptro_1442, retro_ptro_1627, retro_ptro_1662, retro_ptro_1994, retro_ptro_2442, retro_ptro_2713, retro_ptro_2799, retro_ptro_2878, retro_ptro_2902, retro_ptro_2938, retro_ptro_3235, retro_ptro_519, retro_ptro_569, retro_ptro_669, retro_ptro_749, retro_ptro_785, retro_ptro_799, retro_ptro_845,
Rattus norvegicus ENSRNOG0000000766321 retrocopies
retro_rnor_1092, retro_rnor_1093, retro_rnor_1269, retro_rnor_1484, retro_rnor_1556, retro_rnor_1564, retro_rnor_1845, retro_rnor_1901, retro_rnor_1991, retro_rnor_2071, retro_rnor_2073, retro_rnor_2187, retro_rnor_2332, retro_rnor_2447, retro_rnor_2781, retro_rnor_2790, retro_rnor_558, retro_rnor_756, retro_rnor_896, retro_rnor_942, retro_rnor_943,
Sorex araneus ENSSARG000000065496 retrocopies
retro_sara_284, retro_sara_369, retro_sara_392, retro_sara_436, retro_sara_512, retro_sara_710,

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 = 4.3 RPM Legend:


Library Retrogene expression
CEU_NA11831 2 .44 RPM
CEU_NA11843 2 .62 RPM
CEU_NA11930 2 .31 RPM
CEU_NA12004 1 .90 RPM
CEU_NA12400 3 .16 RPM
CEU_NA12751 1 .89 RPM
CEU_NA12760 2 .60 RPM
CEU_NA12827 2 .12 RPM
CEU_NA12872 2 .91 RPM
CEU_NA12873 2 .39 RPM
FIN_HG00183 2 .09 RPM
FIN_HG00277 3 .51 RPM
FIN_HG00315 2 .32 RPM
FIN_HG00321 2 .60 RPM
FIN_HG00328 2 .89 RPM
FIN_HG00338 2 .75 RPM
FIN_HG00349 3 .02 RPM
FIN_HG00375 2 .52 RPM
FIN_HG00377 2 .42 RPM
FIN_HG00378 1 .85 RPM
GBR_HG00099 2 .44 RPM
GBR_HG00111 2 .86 RPM
GBR_HG00114 1 .92 RPM
GBR_HG00119 2 .18 RPM
GBR_HG00131 1 .70 RPM
GBR_HG00133 2 .73 RPM
GBR_HG00134 1 .68 RPM
GBR_HG00137 2 .56 RPM
GBR_HG00142 2 .22 RPM
GBR_HG00143 1 .63 RPM
TSI_NA20512 2 .63 RPM
TSI_NA20513 1 .23 RPM
TSI_NA20518 4 .30 RPM
TSI_NA20532 1 .70 RPM
TSI_NA20538 3 .41 RPM
TSI_NA20756 2 .30 RPM
TSI_NA20765 1 .35 RPM
TSI_NA20771 3 .57 RPM
TSI_NA20786 2 .48 RPM
TSI_NA20798 1 .22 RPM
YRI_NA18870 2 .00 RPM
YRI_NA18907 1 .66 RPM
YRI_NA18916 1 .71 RPM
YRI_NA19093 1 .04 RPM
YRI_NA19099 1 .57 RPM
YRI_NA19114 1 .76 RPM
YRI_NA19118 1 .72 RPM
YRI_NA19213 1 .96 RPM
YRI_NA19214 1 .30 RPM
YRI_NA19223 1 .63 RPM

Indel association:

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



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