RetrogeneDB ID:

retro_hsap_3242

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:5:133603130..133603528(+)
Located in intron of:ENSG00000006837
Retrocopy
information
Ensembl ID:ENSG00000239615
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RPS13
Ensembl ID:ENSG00000110700
Aliases:RPS13, S13
Description:ribosomal protein S13 [Source:HGNC Symbol;Acc:10386]


Retrocopy-Parental alignment summary:






>retro_hsap_3242
GCTCTGCCCTATCGCTGCAGGATCCCCACTCAGCTGAAGTTGATACCTGATGACATGAAGGAGCAGATTTACAAACTGGC
CAAAAAGGGCCTGACTCCCTCACAAGTCAGTGTGATCCTGAGAGATGCACATGTGTTGCACAAGTACGCTTTGTGACAGG
CAATGAAATCTTAAGAATTCTTAAGTCCAAGGGACTTGCTCTTGATCTCCCTGATGATCTGTACCATTCAATCAAGAAAG
CAGTTGCTATTTGAAAGCATCTCAAACAAAACAGAAAGGATAAGGATGCTAAACTATGCCTGATTCTGACAGAGAGCCGG
ATTCACCATTTGGCTAGATATTATAAGACCAAGTGAATCCTCCCTCCCAGTTGGAAATATGAGTCATCAACAAACAGC

ORF - retro_hsap_3242 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 79.1 %
Parental protein coverage: 88.08 %
Number of stop codons detected: 2
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalALPYRRSVPTWLKLTSDDVKEQIYKLAKKGLTPSQIGVILRDSHG-VAQVRFVTGNKILRILKSKGLAPD
ALPYR...PT.LKL..DD.KEQIYKLAKKGLTPSQ..VILRD.H..VAQVRFVTGN.ILRILKSKGLA.D
RetrocopyALPYRCRIPTQLKLIPDDMKEQIYKLAKKGLTPSQVSVILRDAHV<VAQVRFVTGNEILRILKSKGLALD
ParentalLPEDLYHLIKKAVAVRKHLERNRKDKDAKFRLILIESRIHRLARYYKTKRVLPPNWKYESSTAS
LP.DLYH.IKKAVA..KHL..NRKDKDAK..LIL.ESRIH.LARYYKTK..LPP.WKYESST.S
RetrocopyLPDDLYHSIKKAVAI*KHLKQNRKDKDAKLCLILTESRIHHLARYYKTK*ILPPSWKYESSTNS

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 .00 RPM 277 .42 RPM
bodymap2_adrenal 0 .00 RPM 358 .44 RPM
bodymap2_brain 0 .02 RPM 139 .02 RPM
bodymap2_breast 0 .00 RPM 257 .34 RPM
bodymap2_colon 0 .00 RPM 443 .26 RPM
bodymap2_heart 0 .00 RPM 160 .81 RPM
bodymap2_kidney 0 .00 RPM 247 .11 RPM
bodymap2_liver 0 .00 RPM 202 .26 RPM
bodymap2_lung 0 .00 RPM 467 .39 RPM
bodymap2_lymph_node 0 .00 RPM 596 .29 RPM
bodymap2_ovary 0 .00 RPM 457 .52 RPM
bodymap2_prostate 0 .00 RPM 694 .12 RPM
bodymap2_skeletal_muscle 0 .00 RPM 407 .68 RPM
bodymap2_testis 0 .15 RPM 254 .63 RPM
bodymap2_thyroid 0 .00 RPM 191 .66 RPM
bodymap2_white_blood_cells 0 .00 RPM 679 .39 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3242 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3242 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_3242 retrocopy 5' end.

Lab - click to see more details

retro_hsap_3242 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3242 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pongo abelii retro_pabe_2689
Parental genes homology:
Parental genes homology involve 34 parental genes, and 157 retrocopies.

Species Parental gene accession Retrocopies number
Caenorhabditis elegans C16A3.91 retrocopy
retro_cele_6,
Ailuropoda melanoleuca ENSAMEG000000028953 retrocopies
retro_amel_1451, retro_amel_1788, retro_amel_694,
Bos taurus ENSBTAG000000403085 retrocopies
retro_btau_1286, retro_btau_266, retro_btau_284, retro_btau_46, retro_btau_784,
Choloepus hoffmanni ENSCHOG000000087214 retrocopies
retro_chof_1484, retro_chof_1497, retro_chof_1644, retro_chof_2359,
Callithrix jacchus ENSCJAG000000095641 retrocopy
retro_cjac_356,
Cavia porcellus ENSCPOG000000000233 retrocopies
retro_cpor_1535, retro_cpor_400, retro_cpor_526,
Dipodomys ordii ENSDORG000000025073 retrocopies
retro_dord_397, retro_dord_57, retro_dord_759,
Equus caballus ENSECAG0000001492812 retrocopies
retro_ecab_1037, retro_ecab_1047, retro_ecab_1065, retro_ecab_1066, retro_ecab_170, retro_ecab_304, retro_ecab_696, retro_ecab_777, retro_ecab_804, retro_ecab_822, retro_ecab_891, retro_ecab_954,
Felis catus ENSFCAG000000053702 retrocopies
retro_fcat_407, retro_fcat_598,
Homo sapiens ENSG00000110700 6 retrocopies
retro_hsap_1499, retro_hsap_1574, retro_hsap_2098, retro_hsap_251, retro_hsap_3242 , retro_hsap_388,
Gorilla gorilla ENSGGOG000000074503 retrocopies
retro_ggor_127, retro_ggor_2207, retro_ggor_303,
Latimeria chalumnae ENSLACG000000171741 retrocopy
retro_lcha_2,
Loxodonta africana ENSLAFG000000268813 retrocopies
retro_lafr_1179, retro_lafr_382, retro_lafr_511,
Macropus eugenii ENSMEUG000000149862 retrocopies
retro_meug_635, retro_meug_797,
Microcebus murinus ENSMICG000000037168 retrocopies
retro_mmur_1109, retro_mmur_1620, retro_mmur_172, retro_mmur_460, retro_mmur_588, retro_mmur_85, retro_mmur_880, retro_mmur_904,
Myotis lucifugus ENSMLUG000000097513 retrocopies
retro_mluc_174, retro_mluc_2470, retro_mluc_899,
Macaca mulatta ENSMMUG000000225472 retrocopies
retro_mmul_330, retro_mmul_40,
Monodelphis domestica ENSMODG000000070786 retrocopies
retro_mdom_1108, retro_mdom_1150, retro_mdom_1895, retro_mdom_1965, retro_mdom_566, retro_mdom_599,
Mustela putorius furoENSMPUG000000133161 retrocopy
retro_mputfur_181,
Mus musculus ENSMUSG0000009086219 retrocopies
retro_mmus_1062, retro_mmus_1124, retro_mmus_1526, retro_mmus_1563, retro_mmus_1980, retro_mmus_2210, retro_mmus_2642, retro_mmus_2830, retro_mmus_2831, retro_mmus_2832, retro_mmus_2906, retro_mmus_3050, retro_mmus_3092, retro_mmus_3153, retro_mmus_3236, retro_mmus_328, retro_mmus_3423, retro_mmus_775, retro_mmus_807,
Ornithorhynchus anatinus ENSOANG000000076871 retrocopy
retro_oana_98,
Oryctolagus cuniculus ENSOCUG000000055366 retrocopies
retro_ocun_1337, retro_ocun_1523, retro_ocun_1929, retro_ocun_673, retro_ocun_740, retro_ocun_909,
Otolemur garnettii ENSOGAG000000021287 retrocopies
retro_ogar_1567, retro_ogar_1595, retro_ogar_1818, retro_ogar_2751, retro_ogar_3441, retro_ogar_502, retro_ogar_844,
Ochotona princeps ENSOPRG000000001625 retrocopies
retro_opri_1107, retro_opri_239, retro_opri_390, retro_opri_487, retro_opri_57,
Pongo abelii ENSPPYG000000034566 retrocopies
retro_pabe_1250, retro_pabe_1298, retro_pabe_2001, retro_pabe_2012, retro_pabe_2689, retro_pabe_408,
Pteropus vampyrus ENSPVAG000000128063 retrocopies
retro_pvam_1143, retro_pvam_698, retro_pvam_880,
Rattus norvegicus ENSRNOG000000205022 retrocopies
retro_rnor_190, retro_rnor_377,
Sarcophilus harrisii ENSSHAG000000040523 retrocopies
retro_shar_183, retro_shar_298, retro_shar_589,
Sus scrofa ENSSSCG000000133815 retrocopies
retro_sscr_1209, retro_sscr_264, retro_sscr_333, retro_sscr_711, retro_sscr_738,
Ictidomys tridecemlineatus ENSSTOG000000089965 retrocopies
retro_itri_1011, retro_itri_1905, retro_itri_329, retro_itri_493, retro_itri_881,
Tupaia belangeri ENSTBEG000000077177 retrocopies
retro_tbel_1777, retro_tbel_2022, retro_tbel_3850, retro_tbel_3913, retro_tbel_4204, retro_tbel_661, retro_tbel_902,
Tarsius syrichta ENSTSYG0000001311411 retrocopies
retro_tsyr_133, retro_tsyr_1352, retro_tsyr_1447, retro_tsyr_1460, retro_tsyr_1712, retro_tsyr_1900, retro_tsyr_1967, retro_tsyr_247, retro_tsyr_51, retro_tsyr_887, retro_tsyr_904,
Tursiops truncatus ENSTTRG000000163213 retrocopies
retro_ttru_1168, retro_ttru_1435, retro_ttru_737,
Vicugna pacos ENSVPAG000000014635 retrocopies
retro_vpac_117, retro_vpac_247, retro_vpac_415, retro_vpac_473, retro_vpac_525,

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 = 0.03 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .03 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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