RetrogeneDB ID:

retro_hsap_4724

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:X:85736517..85736817(+)
Located in intron of:ENSG00000126733
Retrocopy
information
Ensembl ID:ENSG00000231478
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:FCF1
Ensembl ID:ENSG00000119616
Aliases:FCF1, Bka, C14orf111, UTP24
Description:FCF1 rRNA-processing protein [Source:HGNC Symbol;Acc:20220]


Retrocopy-Parental alignment summary:






>retro_hsap_4724
CTGTATACCAAGTATATCCCTATATAAATGACTTCATAATGGCTGAAATTGAAAAATTTAGGCAGAAATAGCTAGTTTCT
CTAAGGATCACCAAGTATAGAAGATTTGAATAATTAGCATGCACACATTAAATCACTTATGCAGATGACTGCTTCATACG
AGAGTAATTCAGCACAAGTTTACATTGTGCTCACAGTTGATCAGGACCTGAAATGAATCTGGAAGATCCCTGGAGCTCAT
ATCATGTACATTCCTAACTATAGATACAACGTTGAATGGATGACAGATAATTATGGAGCC

ORF - retro_hsap_4724 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 62.86 %
Parental protein coverage: 55.74 %
Number of stop codons detected: 4
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalLYAKCIPC-ITDCVMAEIEKLGQKYRVALRIAKDPRFERLPCTHKGTYADDCLVQ-RVTQHK-CYIVATV
LY.K.IP..I.D..MAEIEK..QK..V.LRI.K..RFE.L.CTH..TYADDC....RV.QHK..YIV.TV
RetrocopyLYTKYIPI<INDFIMAEIEKFRQK*LVSLRITKYRRFE*LACTH*ITYADDCFIR<RVIQHK<VYIVLTV
ParentalDRDLKRRIRKIPGVPIMYISNHRYNIERMPDDYGA
D.DLK..I.KIPG..IMYI.N.RYN.E.M.D.YGA
RetrocopyDQDLK-*IWKIPGAHIMYIPNYRYNVEWMTDNYGA

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 30 .15 RPM
bodymap2_adrenal 0 .00 RPM 30 .25 RPM
bodymap2_brain 0 .00 RPM 22 .03 RPM
bodymap2_breast 0 .00 RPM 40 .53 RPM
bodymap2_colon 0 .00 RPM 40 .24 RPM
bodymap2_heart 0 .00 RPM 21 .80 RPM
bodymap2_kidney 0 .00 RPM 29 .99 RPM
bodymap2_liver 0 .00 RPM 16 .56 RPM
bodymap2_lung 0 .00 RPM 19 .23 RPM
bodymap2_lymph_node 0 .00 RPM 23 .79 RPM
bodymap2_ovary 0 .00 RPM 55 .13 RPM
bodymap2_prostate 0 .00 RPM 44 .01 RPM
bodymap2_skeletal_muscle 0 .00 RPM 16 .73 RPM
bodymap2_testis 0 .00 RPM 37 .16 RPM
bodymap2_thyroid 0 .00 RPM 71 .30 RPM
bodymap2_white_blood_cells 0 .00 RPM 53 .98 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_4724 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_4724 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_4724 retrocopy 5' end.

Lab - click to see more details

retro_hsap_4724 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_4724 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_3142
Parental genes homology:
Parental genes homology involve 29 parental genes, and 164 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000182967 retrocopies
retro_amel_1447, retro_amel_1574, retro_amel_435, retro_amel_458, retro_amel_481, retro_amel_526, retro_amel_932,
Bos taurus ENSBTAG000000203811 retrocopy
retro_btau_446,
Canis familiaris ENSCAFG000000169713 retrocopies
retro_cfam_142, retro_cfam_205, retro_cfam_95,
Callithrix jacchus ENSCJAG000000205189 retrocopies
retro_cjac_1432, retro_cjac_1615, retro_cjac_1711, retro_cjac_1926, retro_cjac_2158, retro_cjac_3094, retro_cjac_3125, retro_cjac_4092, retro_cjac_4148,
Cavia porcellus ENSCPOG000000011496 retrocopies
retro_cpor_1205, retro_cpor_212, retro_cpor_336, retro_cpor_351, retro_cpor_51, retro_cpor_634,
Equus caballus ENSECAG000000082611 retrocopy
retro_ecab_423,
Erinaceus europaeus ENSEEUG000000071731 retrocopy
retro_eeur_491,
Felis catus ENSFCAG000000227533 retrocopies
retro_fcat_1461, retro_fcat_523, retro_fcat_685,
Homo sapiens ENSG00000119616 6 retrocopies
retro_hsap_2686, retro_hsap_3040, retro_hsap_383, retro_hsap_3912, retro_hsap_4724 , retro_hsap_535,
Gorilla gorilla ENSGGOG000000163183 retrocopies
retro_ggor_1872, retro_ggor_2507, retro_ggor_3080,
Latimeria chalumnae ENSLACG000000188791 retrocopy
retro_lcha_9,
Loxodonta africana ENSLAFG000000007241 retrocopy
retro_lafr_81,
Microcebus murinus ENSMICG000000060615 retrocopies
retro_mmur_1175, retro_mmur_832, retro_mmur_86, retro_mmur_906, retro_mmur_968,
Macaca mulatta ENSMMUG000000088878 retrocopies
retro_mmul_1306, retro_mmul_1422, retro_mmul_1704, retro_mmul_1737, retro_mmul_1891, retro_mmul_459, retro_mmul_492, retro_mmul_685,
Monodelphis domestica ENSMODG000000061795 retrocopies
retro_mdom_1729, retro_mdom_622, retro_mdom_635, retro_mdom_820, retro_mdom_846,
Mustela putorius furoENSMPUG000000093217 retrocopies
retro_mputfur_1002, retro_mputfur_1131, retro_mputfur_1306, retro_mputfur_1315, retro_mputfur_1621, retro_mputfur_532, retro_mputfur_891,
Mus musculus ENSMUSG000000212433 retrocopies
retro_mmus_1575, retro_mmus_2358, retro_mmus_3268,
Nomascus leucogenys ENSNLEG000000163117 retrocopies
retro_nleu_1145, retro_nleu_1185, retro_nleu_1789, retro_nleu_1927, retro_nleu_1994, retro_nleu_686, retro_nleu_874,
Oryctolagus cuniculus ENSOCUG000000141201 retrocopy
retro_ocun_96,
Otolemur garnettii ENSOGAG0000000271119 retrocopies
retro_ogar_1007, retro_ogar_1114, retro_ogar_1666, retro_ogar_1955, retro_ogar_2035, retro_ogar_2167, retro_ogar_2240, retro_ogar_2336, retro_ogar_2482, retro_ogar_2939, retro_ogar_3232, retro_ogar_3432, retro_ogar_3486, retro_ogar_3488, retro_ogar_503, retro_ogar_651, retro_ogar_739, retro_ogar_79, retro_ogar_972,
Pongo abelii ENSPPYG0000000599110 retrocopies
retro_pabe_1758, retro_pabe_214, retro_pabe_2295, retro_pabe_2437, retro_pabe_2613, retro_pabe_2685, retro_pabe_3188, retro_pabe_326, retro_pabe_3668, retro_pabe_3830,
Pan troglodytes ENSPTRG000000065406 retrocopies
retro_ptro_1813, retro_ptro_1998, retro_ptro_2660, retro_ptro_297, retro_ptro_3142, retro_ptro_401,
Pteropus vampyrus ENSPVAG000000006573 retrocopies
retro_pvam_1169, retro_pvam_1272, retro_pvam_454,
Rattus norvegicus ENSRNOG000000047235 retrocopies
retro_rnor_2539, retro_rnor_2591, retro_rnor_2658, retro_rnor_771, retro_rnor_818,
Sorex araneus ENSSARG000000032703 retrocopies
retro_sara_126, retro_sara_177, retro_sara_375,
Ictidomys tridecemlineatus ENSSTOG000000080834 retrocopies
retro_itri_1149, retro_itri_297, retro_itri_599, retro_itri_850,
Tupaia belangeri ENSTBEG0000001355730 retrocopies
retro_tbel_1190, retro_tbel_1261, retro_tbel_135, retro_tbel_1397, retro_tbel_1457, retro_tbel_1576, retro_tbel_182, retro_tbel_222, retro_tbel_2578, retro_tbel_2996, retro_tbel_3037, retro_tbel_3060, retro_tbel_3075, retro_tbel_3105, retro_tbel_3152, retro_tbel_3360, retro_tbel_342, retro_tbel_3564, retro_tbel_3568, retro_tbel_3661, retro_tbel_3694, retro_tbel_3797, retro_tbel_3923, retro_tbel_4463, retro_tbel_4506, retro_tbel_4571, retro_tbel_4645, retro_tbel_580, retro_tbel_776, retro_tbel_966,
Tarsius syrichta ENSTSYG000000063273 retrocopies
retro_tsyr_1016, retro_tsyr_1418, retro_tsyr_621,
Tursiops truncatus ENSTTRG000000024403 retrocopies
retro_ttru_1447, retro_ttru_1691, retro_ttru_584,

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 ) 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 .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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