RetrogeneDB ID:

retro_hsap_1560

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:15:43432350..43433007(-)
Located in intron of:ENSG00000137842
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:FDPS
Ensembl ID:ENSG00000160752
Aliases:FDPS, FPPS, FPS
Description:farnesyl diphosphate synthase [Source:HGNC Symbol;Acc:3631]


Retrocopy-Parental alignment summary:






>retro_hsap_1560
GAAGCATGTATGTACCGCCTGCTGAAGCTCTATTGCCATGAGCAGCCCTATTACCTGAACCTGATCCAGCTCTTCCGGCA
GAGTTTCTATCAGACTGAGATTGGGCAGACCCTGGATCTCATCATAGCCCCCCAGGGCAATGTGGATCTTGGCAGATTCA
CTGAAAAGAGGTACAAATCTAGTGTCACGTACAAGGCAGTTTCTACTCCTTCTACCTTCCTGTAGCTGCAGCCATGTATA
TGCAGGTATTGATAGAGAGAAGGAGAATACCAATGCCAAGAAGATCCTGCTGGAGATGGGAGAGGGAGAGTTCTTTCAGA
TCAGGATGATTACCCTCACCTCTTTGGGGACCCCAATGTGACCGCCAAAGTTGGCACTGACATCCAGGACAACAAATGCA
GCTGGCTGGTGGTTCAGTGTCTGCAACGGGCCACTCCAGAACAGTACCAGATTCTGAAGGAGAATTTTGGGCAGAAGGAG
GCCGAGAAGGTGGCCCCGGTGAAGGCAGTATATGAGGAGCTGGATCTGCCGGCCATGTTCTTGCAATAATAGGAAGACAG
TTACAGCCACGTTATGGGTCTCATTGAACAGTACGCAGCTCCCCTGCCCCCAGTCATCTTTCTGGGGTTGGCGCGCAAAA
TCTACAAGCGGAAAAAG

ORF - retro_hsap_1560 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 83.41 %
Parental protein coverage: 52.03 %
Number of stop codons detected: 2
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalEACIYRLLKLYCREQPYYLNLIELFLQSSYQTEIGQTLDLLTAPQGNVDLVRFTEKRYKSIVKYKT-AFY
EAC.YRLLKLYC.EQPYYLNLI.LF.QS.YQTEIGQTLDL..APQGNVDL.RFTEKRYKS.V.YK...FY
RetrocopyEACMYRLLKLYCHEQPYYLNLIQLFRQSFYQTEIGQTLDLIIAPQGNVDLGRFTEKRYKSSVTYKA<SFY
ParentalSFYLPIAAAMYM-AGIDGEKEHANAKKILLEMGE--FFQI-QDDYLDLFGDPSVTGKIGTDIQDNKCSWL
SFYLP.AAAMYM.AGID.EKE..NAKKILLEMGE..FFQI.QDDY..LFGDP.VT.K.GTDIQDNKCSWL
RetrocopySFYLPVAAAMYM<AGIDREKENTNAKKILLEMGEGEFFQI<QDDYPHLFGDPNVTAKVGTDIQDNKCSWL
ParentalVVQCLQRATPEQYQILKENYGQKEAEKVARVKALYEELDLPAVFLQYEEDSYSHIMALIEQYAAPLPPAV
VVQCLQRATPEQYQILKEN.GQKEAEKVA.VKA.YEELDLPA.FLQ..EDSYSH.M.LIEQYAAPLPP..
RetrocopyVVQCLQRATPEQYQILKENFGQKEAEKVAPVKAVYEELDLPAMFLQ**EDSYSHVMGLIEQYAAPLPPVI
ParentalFLGLARKIYKRRK
FLGLARKIYKR.K
RetrocopyFLGLARKIYKRKK

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 36 .87 RPM
bodymap2_adrenal 0 .18 RPM 72 .97 RPM
bodymap2_brain 0 .09 RPM 44 .33 RPM
bodymap2_breast 0 .14 RPM 36 .40 RPM
bodymap2_colon 0 .00 RPM 29 .89 RPM
bodymap2_heart 0 .06 RPM 13 .88 RPM
bodymap2_kidney 0 .00 RPM 46 .26 RPM
bodymap2_liver 0 .00 RPM 40 .22 RPM
bodymap2_lung 0 .00 RPM 35 .23 RPM
bodymap2_lymph_node 0 .00 RPM 35 .56 RPM
bodymap2_ovary 0 .00 RPM 40 .19 RPM
bodymap2_prostate 0 .00 RPM 23 .66 RPM
bodymap2_skeletal_muscle 0 .09 RPM 9 .69 RPM
bodymap2_testis 0 .00 RPM 35 .37 RPM
bodymap2_thyroid 0 .06 RPM 32 .62 RPM
bodymap2_white_blood_cells 0 .00 RPM 22 .92 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_1560 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_1560 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_1560 retrocopy 5' end.

Lab - click to see more details

retro_hsap_1560 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1560 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_1049
Gorilla gorilla retro_ggor_1185
Parental genes homology:
Parental genes homology involve 10 parental genes, and 49 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG0000000836411 retrocopies
retro_cjac_1066, retro_cjac_1217, retro_cjac_1395, retro_cjac_157, retro_cjac_2011, retro_cjac_2081, retro_cjac_2161, retro_cjac_299, retro_cjac_4154, retro_cjac_44, retro_cjac_70,
Echinops telfairi ENSETEG000000011546 retrocopies
retro_etel_1770, retro_etel_1818, retro_etel_2179, retro_etel_730, retro_etel_743, retro_etel_990,
Homo sapiens ENSG00000160752 6 retrocopies
retro_hsap_1519, retro_hsap_1558, retro_hsap_1560 , retro_hsap_3871, retro_hsap_3872, retro_hsap_502,
Microcebus murinus ENSMICG000000074681 retrocopy
retro_mmur_1148,
Macaca mulatta ENSMMUG000000231443 retrocopies
retro_mmul_1190, retro_mmul_2152, retro_mmul_565,
Nomascus leucogenys ENSNLEG000000120996 retrocopies
retro_nleu_1486, retro_nleu_1727, retro_nleu_2301, retro_nleu_2405, retro_nleu_2595, retro_nleu_2692,
Pongo abelii ENSPPYG000000007473 retrocopies
retro_pabe_1290, retro_pabe_1329, retro_pabe_235,
Pan troglodytes ENSPTRG000000014229 retrocopies
retro_ptro_1028, retro_ptro_1048, retro_ptro_1049, retro_ptro_2637, retro_ptro_2638, retro_ptro_2639, retro_ptro_2940, retro_ptro_2995, retro_ptro_377,
Rattus norvegicus ENSRNOG000000433773 retrocopies
retro_rnor_1175, retro_rnor_153, retro_rnor_2897,
Ictidomys tridecemlineatus ENSSTOG000000044751 retrocopy
retro_itri_488,

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 = 0.23 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .04 RPM
CEU_NA11843 0 .06 RPM
CEU_NA11930 0 .23 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .05 RPM
CEU_NA12760 0 .13 RPM
CEU_NA12827 0 .09 RPM
CEU_NA12872 0 .00 RPM
CEU_NA12873 0 .10 RPM
FIN_HG00183 0 .08 RPM
FIN_HG00277 0 .04 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .00 RPM
FIN_HG00328 0 .05 RPM
FIN_HG00338 0 .02 RPM
FIN_HG00349 0 .03 RPM
FIN_HG00375 0 .00 RPM
FIN_HG00377 0 .03 RPM
FIN_HG00378 0 .04 RPM
GBR_HG00099 0 .03 RPM
GBR_HG00111 0 .02 RPM
GBR_HG00114 0 .08 RPM
GBR_HG00119 0 .10 RPM
GBR_HG00131 0 .06 RPM
GBR_HG00133 0 .07 RPM
GBR_HG00134 0 .11 RPM
GBR_HG00137 0 .08 RPM
GBR_HG00142 0 .06 RPM
GBR_HG00143 0 .10 RPM
TSI_NA20512 0 .03 RPM
TSI_NA20513 0 .12 RPM
TSI_NA20518 0 .00 RPM
TSI_NA20532 0 .10 RPM
TSI_NA20538 0 .09 RPM
TSI_NA20756 0 .06 RPM
TSI_NA20765 0 .12 RPM
TSI_NA20771 0 .00 RPM
TSI_NA20786 0 .08 RPM
TSI_NA20798 0 .03 RPM
YRI_NA18870 0 .03 RPM
YRI_NA18907 0 .17 RPM
YRI_NA18916 0 .04 RPM
YRI_NA19093 0 .00 RPM
YRI_NA19099 0 .03 RPM
YRI_NA19114 0 .03 RPM
YRI_NA19118 0 .00 RPM
YRI_NA19213 0 .07 RPM
YRI_NA19214 0 .15 RPM
YRI_NA19223 0 .18 RPM

Indel association:

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





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