RetrogeneDB ID:

retro_hsap_3508

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:6:113902702..113903166(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000218208
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RPS27A
Ensembl ID:ENSG00000143947
Aliases:RPS27A, CEP80, HEL112, S27A, UBA80, UBC, UBCEP1, UBCEP80
Description:ribosomal protein S27a [Source:HGNC Symbol;Acc:10417]


Retrocopy-Parental alignment summary:






>retro_hsap_3508
ATGCAGATTTTCTTGAAAACCCTTACGGAGAAGACCATCACCCTCGAGGCTGAACCCTTGGATACGATAGAAAATGTAAA
GGCCAAGATCCAGGATAAGGAAGGAATTCCTCCTGATCAGCAAAGACTGATCTTTGCTGGAAAGCAACTGGAAGATGGAT
GTACTTTGTCTGACTACAGTATTCAAAAGGAGTCTACTCTTCATCTTGTGTTGAGACTTCGTGGTGGTGATAAGAAAAGG
AAGAAGTCTTACACCACTCCCAAGAAGAATAAGCACAAGAGAAAGAAGGTTAAGCTGGCTGTCCTGAAATATTATAAGGT
GGATGAGAATGGCAAAATTAGTTGCCTTCGTCGAGAGTGACCTTCTGATGAATGTGGTGCTGAGGTGTTTATGGCAAGCC
ACTTTGACAGACATTATTGTGGCAAATGTTGTCTGACTTACTGCTTAACAAACCAGAAGACAAG

ORF - retro_hsap_3508 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 91.72 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLV
MQIF.KTLT.KTITLE.EP.DTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDG.TLSDY.IQKESTLHLV
RetrocopyMQIFLKTLTEKTITLEAEPLDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGCTLSDYSIQKESTLHLV
ParentalLRLRGGAKKRKKKSYTTPKKNKHKRKKVKLAVLKYYKVDENGKISRLRRECPSDECGAGVFMASHFDRHY
LRLRGG.KKR.KKSYTTPKKNKHKRKKVKLAVLKYYKVDENGKIS.LRRE.PSDECGA.VFMASHFDRHY
RetrocopyLRLRGGDKKR-KKSYTTPKKNKHKRKKVKLAVLKYYKVDENGKISCLRRE*PSDECGAEVFMASHFDRHY
ParentalCGKCCLTYC-FNKPEDK
CGKCCLTYC..NKPEDK
RetrocopyCGKCCLTYC<LNKPEDK

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 .74 RPM 241 .34 RPM
bodymap2_adrenal 0 .92 RPM 445 .31 RPM
bodymap2_brain 0 .00 RPM 168 .49 RPM
bodymap2_breast 0 .84 RPM 255 .72 RPM
bodymap2_colon 0 .37 RPM 539 .62 RPM
bodymap2_heart 0 .00 RPM 135 .97 RPM
bodymap2_kidney 0 .00 RPM 283 .70 RPM
bodymap2_liver 0 .00 RPM 197 .57 RPM
bodymap2_lung 0 .12 RPM 575 .35 RPM
bodymap2_lymph_node 0 .04 RPM 651 .95 RPM
bodymap2_ovary 0 .85 RPM 554 .21 RPM
bodymap2_prostate 0 .02 RPM 709 .26 RPM
bodymap2_skeletal_muscle 0 .02 RPM 147 .09 RPM
bodymap2_testis 0 .43 RPM 329 .65 RPM
bodymap2_thyroid 0 .51 RPM 244 .64 RPM
bodymap2_white_blood_cells 0 .06 RPM 847 .09 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3508 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3508 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_3508 retrocopy 5' end.

Lab - click to see more details

retro_hsap_3508 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3508 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Gorilla gorilla retro_ggor_2373
Parental genes homology:
Parental genes homology involve 19 parental genes, and 92 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000040175 retrocopies
retro_amel_1565, retro_amel_175, retro_amel_598, retro_amel_661, retro_amel_844,
Canis familiaris ENSCAFG000000234713 retrocopies
retro_cfam_1048, retro_cfam_640, retro_cfam_81,
Callithrix jacchus ENSCJAG000000100525 retrocopies
retro_cjac_200, retro_cjac_229, retro_cjac_344, retro_cjac_74, retro_cjac_88,
Felis catus ENSFCAG000000239391 retrocopy
retro_fcat_1542,
Homo sapiens ENSG00000143947 10 retrocopies
retro_hsap_1694, retro_hsap_1715, retro_hsap_2217, retro_hsap_2416, retro_hsap_276, retro_hsap_3344, retro_hsap_3508 , retro_hsap_4272, retro_hsap_4649, retro_hsap_4650,
Loxodonta africana ENSLAFG000000231332 retrocopies
retro_lafr_1122, retro_lafr_185,
Macropus eugenii ENSMEUG0000000891713 retrocopies
retro_meug_107, retro_meug_1184, retro_meug_1460, retro_meug_1514, retro_meug_1544, retro_meug_1657, retro_meug_183, retro_meug_1866, retro_meug_209, retro_meug_521, retro_meug_594, retro_meug_937, retro_meug_94,
Myotis lucifugus ENSMLUG0000001706410 retrocopies
retro_mluc_1201, retro_mluc_1255, retro_mluc_1298, retro_mluc_1646, retro_mluc_1730, retro_mluc_1865, retro_mluc_1867, retro_mluc_2264, retro_mluc_37, retro_mluc_380,
Myotis lucifugus ENSMLUG000000294491 retrocopy
retro_mluc_1585,
Macaca mulatta ENSMMUG000000155638 retrocopies
retro_mmul_1198, retro_mmul_193, retro_mmul_2189, retro_mmul_222, retro_mmul_2470, retro_mmul_282, retro_mmul_606, retro_mmul_73,
Monodelphis domestica ENSMODG000000018193 retrocopies
retro_mdom_1367, retro_mdom_1751, retro_mdom_205,
Mustela putorius furoENSMPUG000000104686 retrocopies
retro_mputfur_1512, retro_mputfur_242, retro_mputfur_319, retro_mputfur_332, retro_mputfur_499, retro_mputfur_777,
Oryctolagus cuniculus ENSOCUG0000000361310 retrocopies
retro_ocun_1087, retro_ocun_1163, retro_ocun_1209, retro_ocun_1259, retro_ocun_1268, retro_ocun_1339, retro_ocun_164, retro_ocun_288, retro_ocun_381, retro_ocun_851,
Pongo abelii ENSPPYG000000258711 retrocopy
retro_pabe_117,
Pan troglodytes ENSPTRG000000119281 retrocopy
retro_ptro_32,
Rattus norvegicus ENSRNOG000000044262 retrocopies
retro_rnor_117, retro_rnor_161,
Sus scrofa ENSSSCG000000223571 retrocopy
retro_sscr_145,
Ictidomys tridecemlineatus ENSSTOG000000095665 retrocopies
retro_itri_1583, retro_itri_1765, retro_itri_26, retro_itri_635, retro_itri_962,
Tursiops truncatus ENSTTRG000000139475 retrocopies
retro_ttru_1199, retro_ttru_1279, retro_ttru_533, retro_ttru_705, retro_ttru_838,

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 = 0.28 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .09 RPM
CEU_NA11843 0 .17 RPM
CEU_NA11930 0 .16 RPM
CEU_NA12004 0 .04 RPM
CEU_NA12400 0 .25 RPM
CEU_NA12751 0 .10 RPM
CEU_NA12760 0 .13 RPM
CEU_NA12827 0 .05 RPM
CEU_NA12872 0 .05 RPM
CEU_NA12873 0 .06 RPM
FIN_HG00183 0 .05 RPM
FIN_HG00277 0 .18 RPM
FIN_HG00315 0 .03 RPM
FIN_HG00321 0 .09 RPM
FIN_HG00328 0 .07 RPM
FIN_HG00338 0 .13 RPM
FIN_HG00349 0 .28 RPM
FIN_HG00375 0 .12 RPM
FIN_HG00377 0 .15 RPM
FIN_HG00378 0 .19 RPM
GBR_HG00099 0 .12 RPM
GBR_HG00111 0 .13 RPM
GBR_HG00114 0 .13 RPM
GBR_HG00119 0 .02 RPM
GBR_HG00131 0 .14 RPM
GBR_HG00133 0 .14 RPM
GBR_HG00134 0 .07 RPM
GBR_HG00137 0 .03 RPM
GBR_HG00142 0 .17 RPM
GBR_HG00143 0 .13 RPM
TSI_NA20512 0 .11 RPM
TSI_NA20513 0 .05 RPM
TSI_NA20518 0 .11 RPM
TSI_NA20532 0 .14 RPM
TSI_NA20538 0 .05 RPM
TSI_NA20756 0 .17 RPM
TSI_NA20765 0 .12 RPM
TSI_NA20771 0 .06 RPM
TSI_NA20786 0 .08 RPM
TSI_NA20798 0 .03 RPM
YRI_NA18870 0 .17 RPM
YRI_NA18907 0 .07 RPM
YRI_NA18916 0 .19 RPM
YRI_NA19093 0 .00 RPM
YRI_NA19099 0 .08 RPM
YRI_NA19114 0 .05 RPM
YRI_NA19118 0 .06 RPM
YRI_NA19213 0 .17 RPM
YRI_NA19214 0 .05 RPM
YRI_NA19223 0 .04 RPM

Indel association:

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



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