RetrogeneDB ID:

retro_hsap_3001

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:4:161739590..161739999(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000242635
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RPS14
Ensembl ID:ENSG00000164587
Aliases:RPS14, EMTB, S14
Description:ribosomal protein S14 [Source:HGNC Symbol;Acc:10387]


Retrocopy-Parental alignment summary:






>retro_hsap_3001
GAAGGAAATGAAGAACAAGTCATCGGCTTTGAATTTCAGGGGCTGAAGTAGAGAATATATTTGATGTCTGCCACATTTTT
TTACCCTTCAGTGACACTTCTGTCCATGTTATTGATATCACTGACAAATAAACTATCTGCTGCATGACTGGGGGATGAAG
AATAAGGGTGATCGAAATGAATTCTCACCTTAAACTACCATGTTGGCCATCCACAATGTGGCCCAGAAGTGCAAGGGTCT
GGACATTGTTGCAATACATATCATATTACAGACCACAGGAGGAAATACAGCCAAGATCCCTGGGCCTGGGGCTCAGTCAG
TTCTCAGTGCCTTTGCTCATTAAGGAAAGGAGACTGGACAGATTAAAGATGTCATTGACATCTTATGACAGCACTCACAG
GAAGAAGGG

ORF - retro_hsap_3001 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 53.96 %
Parental protein coverage: 90.73 %
Number of stop codons detected: 4
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalEKKEEQVISLGPQV-AEGENVFGVCHIFASFNDTFVHVTDLSGKETICRVTGG-MKVKADRDESSPYAAM
E..EEQVI....Q..AE.EN.F.VCHIF..F.DT.VHV.D...K.TIC..TGG.MK.K.DR.E.SP...M
RetrocopyEGNEEQVIGFEFQG<AEVENIFDVCHIFLPFSDTSVHVIDITDK*TICCMTGG<MKNKGDRNEFSP*TTM
ParentalLAAQDVAQRCKELGITALHIKLRATGGNRTKTPGPGAQSALRALARSGMKIGRIEDVTPIPSDSTRRKG
LA...VAQ.CK.L.I.A.HI.L..TGGN..K.PGPGAQS.L.A.A..G...G.I.DV..I........G
RetrocopyLAIHNVAQKCKGLDIVAIHIILQTTGGNTAKIPGPGAQSVLSAFAH*GKETGQIKDVIDIL*QHSQEEG

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 639 .89 RPM
bodymap2_adrenal 0 .00 RPM 859 .94 RPM
bodymap2_brain 0 .00 RPM 215 .93 RPM
bodymap2_breast 0 .00 RPM 544 .48 RPM
bodymap2_colon 0 .00 RPM 825 .31 RPM
bodymap2_heart 0 .00 RPM 153 .10 RPM
bodymap2_kidney 0 .00 RPM 313 .72 RPM
bodymap2_liver 0 .00 RPM 140 .62 RPM
bodymap2_lung 0 .00 RPM 540 .54 RPM
bodymap2_lymph_node 0 .00 RPM 522 .77 RPM
bodymap2_ovary 0 .00 RPM 754 .52 RPM
bodymap2_prostate 0 .00 RPM 706 .05 RPM
bodymap2_skeletal_muscle 0 .00 RPM 380 .07 RPM
bodymap2_testis 0 .41 RPM 469 .12 RPM
bodymap2_thyroid 0 .00 RPM 478 .14 RPM
bodymap2_white_blood_cells 0 .00 RPM 888 .14 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3001 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3001 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_3001 retrocopy 5' end.

Lab - click to see more details

retro_hsap_3001 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3001 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2030
Gorilla gorilla retro_ggor_2080
Pongo abelii retro_pabe_2487
Parental genes homology:
Parental genes homology involve 19 parental genes, and 72 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000150041 retrocopy
retro_acar_201,
Ailuropoda melanoleuca ENSAMEG000000046442 retrocopies
retro_amel_1390, retro_amel_524,
Bos taurus ENSBTAG000000085702 retrocopies
retro_btau_1109, retro_btau_213,
Canis familiaris ENSCAFG000000180942 retrocopies
retro_cfam_1589, retro_cfam_301,
Callithrix jacchus ENSCJAG000000209811 retrocopy
retro_cjac_89,
Cavia porcellus ENSCPOG000000244082 retrocopies
retro_cpor_253, retro_cpor_284,
Echinops telfairi ENSETEG000000028996 retrocopies
retro_etel_1270, retro_etel_1358, retro_etel_1851, retro_etel_1995, retro_etel_293, retro_etel_967,
Homo sapiens ENSG00000164587 8 retrocopies
retro_hsap_119, retro_hsap_1622, retro_hsap_268, retro_hsap_3001 , retro_hsap_3113, retro_hsap_3232, retro_hsap_3495, retro_hsap_3789,
Gorilla gorilla ENSGGOG000000245938 retrocopies
retro_ggor_1225, retro_ggor_2080, retro_ggor_2135, retro_ggor_2199, retro_ggor_222, retro_ggor_2362, retro_ggor_2548, retro_ggor_316,
Latimeria chalumnae ENSLACG000000161641 retrocopy
retro_lcha_12,
Macaca mulatta ENSMMUG000000028485 retrocopies
retro_mmul_1921, retro_mmul_1983, retro_mmul_358, retro_mmul_570, retro_mmul_90,
Mustela putorius furoENSMPUG000000137761 retrocopy
retro_mputfur_127,
Nomascus leucogenys ENSNLEG000000103661 retrocopy
retro_nleu_101,
Oryctolagus cuniculus ENSOCUG000000115091 retrocopy
retro_ocun_128,
Otolemur garnettii ENSOGAG000000007211 retrocopy
retro_ogar_286,
Pongo abelii ENSPPYG000000159507 retrocopies
retro_pabe_1340, retro_pabe_2487, retro_pabe_2571, retro_pabe_2888, retro_pabe_3204, retro_pabe_401, retro_pabe_494,
Rattus norvegicus ENSRNOG0000001877410 retrocopies
retro_rnor_1313, retro_rnor_1467, retro_rnor_1532, retro_rnor_1759, retro_rnor_1875, retro_rnor_1918, retro_rnor_2181, retro_rnor_228, retro_rnor_2728, retro_rnor_873,
Sarcophilus harrisii ENSSHAG000000180523 retrocopies
retro_shar_380, retro_shar_381, retro_shar_503,
Tupaia belangeri ENSTBEG0000000636810 retrocopies
retro_tbel_1147, retro_tbel_1332, retro_tbel_1603, retro_tbel_1868, retro_tbel_202, retro_tbel_3517, retro_tbel_3619, retro_tbel_416, retro_tbel_519, retro_tbel_740,

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 = 0.05 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .00 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .00 RPM
CEU_NA12760 0 .00 RPM
CEU_NA12827 0 .05 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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