RetrogeneDB ID:

retro_hsap_1225

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:13:90823333..90824161(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000235879
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:FAR1
Ensembl ID:ENSG00000197601
Aliases:FAR1, MLSTD2, SDR10E1
Description:fatty acyl CoA reductase 1 [Source:HGNC Symbol;Acc:26222]


Retrocopy-Parental alignment summary:






>retro_hsap_1225
TTTCCAGGATGGATTGATAACTTTAATGGACCAAGTGGTCTCTTTATTGTGGCAGGGAAAGGAATTCTTTGAACAATGCG
CGTCTCCAATAATGCCCTTGAAGATCTTGTTCCTGTAGATGTAGTTGTCAACAACAGTCTTGTGGCAGCCTGGTATTCCG
GAGTTAATAGAACAAGAAACCTCATGTCATATAATTGTACAACAGATAGCACTAATCATTTCCACTGGGGTGAAGTTTAA
TACCATGTAATTTCTACTTTCAAGAGGAATCCTCTCGAACAGGCCTTCAGATGGCCCAATGTAAATCTAACCTCCAATCA
CCTTTTATATCATTACTGGATTGCTGTAAGCCATAAGGCCTCAGCATTCCTGGATGATATCTACCTCAGGATGACTGGAA
GAAGCCCAAGGATGATGAAAACAATAATTCATCTTCACAAAGCTGTGATGTTACTTGAGTATTTCACAAGTAATTCTTGG
GTTTGGAATACGGACAATGTCAATATGTTAATGAATCAACTAAACCTTGAAGATAAAAAGACTTTCAATATTGATGTACG
GCAGTTACATTAGGCAGAATATATAGAGAACTACTGCATGGGAACTGAGAAGTACATATTGAATAAAGAAACGTCTGGCC
TCCCTGCAGTCAGAAAACATCTGAACAAGTTGCATAATATATCTTATGATTTTAATACTATCCTTGTGATCCTCATCTGA
CACATTTTTATTGCAAGACCACAAATGGCAAGAAACATCTGATACTTTGTGGTTAGTCTGTGTTACAAGTTTCTGTCATA
GTTTCAAGCATCCAGCACTATGAGATAC

ORF - retro_hsap_1225 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 85.87 %
Parental protein coverage: 53.59 %
Number of stop codons detected: 6
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalFPGWIDNFNGPSGLFIAAGKGILRTIRASNNALADLVPVDVVVNMSLAAAWYSGVNRPRNIMVYNCTTGS
FPGWIDNFNGPSGLFI.AGKGIL.T.R.SNNAL.DLVPVDVVVN.SL.AAWYSGVNR.RN.M.YNCTT.S
RetrocopyFPGWIDNFNGPSGLFIVAGKGIL*TMRVSNNALEDLVPVDVVVNNSLVAAWYSGVNRTRNLMSYNCTTDS
ParentalTNPFHWGEVEYHVISTFKRNPLEQAFRRPNVNLTSNHLLYHYWIAVSHKAPAFLYDIYLRMTGRSPRMMK
TN.FHWGEV.YHVISTFKRNPLEQAFR.PNVNLTSNHLLYHYWIAVSHKA.AFL.DIYLRMTGRSPRMMK
RetrocopyTNHFHWGEV*YHVISTFKRNPLEQAFRWPNVNLTSNHLLYHYWIAVSHKASAFLDDIYLRMTGRSPRMMK
ParentalTITRLHKAMVFLEYFTSNSWVWNTENVNMLMNQLNPEDKKTFNIDVRQLHWAEYIENYCLGTKKYVLNEE
TI..LHKA...LEYFTSNSWVWNT.NVNMLMNQLN.EDKKTFNIDVRQLH.AEYIENYC.GT.KY.LN.E
RetrocopyTIIHLHKAVMLLEYFTSNSWVWNTDNVNMLMNQLNLEDKKTFNIDVRQLH*AEYIENYCMGTEKYILNKE
ParentalMSGLPAARKHLNKLRNIRYGFNTILVILIWRIFIARSQMARNIWYFVVSLCYKFLSYFRASSTMRY
.SGLPA.RKHLNKL.NI.Y.FNTILVILI..IFIAR.QMARNI.YFVVSLCYKFLS.F.ASSTMRY
RetrocopyTSGLPAVRKHLNKLHNISYDFNTILVILI*HIFIARPQMARNI*YFVVSLCYKFLS*FQASSTMRY

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 51 .68 RPM
bodymap2_adrenal 0 .00 RPM 63 .89 RPM
bodymap2_brain 0 .02 RPM 141 .48 RPM
bodymap2_breast 0 .00 RPM 74 .13 RPM
bodymap2_colon 0 .00 RPM 61 .57 RPM
bodymap2_heart 0 .00 RPM 48 .37 RPM
bodymap2_kidney 0 .00 RPM 77 .10 RPM
bodymap2_liver 0 .00 RPM 5 .17 RPM
bodymap2_lung 0 .00 RPM 53 .69 RPM
bodymap2_lymph_node 0 .00 RPM 58 .00 RPM
bodymap2_ovary 0 .00 RPM 97 .91 RPM
bodymap2_prostate 0 .00 RPM 78 .29 RPM
bodymap2_skeletal_muscle 0 .00 RPM 31 .17 RPM
bodymap2_testis 0 .08 RPM 70 .49 RPM
bodymap2_thyroid 0 .00 RPM 71 .24 RPM
bodymap2_white_blood_cells 0 .00 RPM 166 .05 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_1225 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_1225 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_1225 retrocopy 5' end.

Lab - click to see more details

retro_hsap_1225 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1225 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_840
Gorilla gorilla retro_ggor_958
Pongo abelii retro_pabe_1019
Macaca mulatta retro_mmul_1301
Parental genes homology:
Parental genes homology involve 12 parental genes, and 15 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG000000034902 retrocopies
retro_chof_1358, retro_chof_1733,
Callithrix jacchus ENSCJAG000000100771 retrocopy
retro_cjac_545,
Cavia porcellus ENSCPOG000000026541 retrocopy
retro_cpor_267,
Homo sapiens ENSG00000197601 1 retrocopy
retro_hsap_1225 ,
Gorilla gorilla ENSGGOG000000011801 retrocopy
retro_ggor_958,
Macaca mulatta ENSMMUG000000119901 retrocopy
retro_mmul_1301,
Nomascus leucogenys ENSNLEG000000176951 retrocopy
retro_nleu_698,
Oryctolagus cuniculus ENSOCUG000000043362 retrocopies
retro_ocun_1056, retro_ocun_790,
Otolemur garnettii ENSOGAG000000050642 retrocopies
retro_ogar_1353, retro_ogar_341,
Pongo abelii ENSPPYG000000034701 retrocopy
retro_pabe_1019,
Pan troglodytes ENSPTRG000000241901 retrocopy
retro_ptro_840,
Rattus norvegicus ENSRNOG000000131761 retrocopy
retro_rnor_467,

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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