RetrogeneDB ID:

retro_hsap_6

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:3:93779791..93780355(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000178700
Aliases:DHFRL1, DHFRP4
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:DHFR
Ensembl ID:ENSG00000228716
Aliases:DHFR, DHFRP1, DYR
Description:dihydrofolate reductase [Source:HGNC Symbol;Acc:2861]


Retrocopy-Parental alignment summary:






>retro_hsap_6
ATGTTTCTTTTGCTAAACTGCATCGTCGCTGTGTCCCAAAACATGGGCATCGGCAAGAACGGGGACCTGCCCAGGCCGCC
GCTCAGGAATGAATTCAGGTATTTCCAGAGAATGACCACAACTTCTTCAGTAGAGGGTAAACAGAATCTGGTGATTATGG
GTAGGAAGACCTGGTTCTCCATTCCTGAGAAGAATCGACCTTTAAAGGATAGAATTAATTTAGTTCTCAGCAGAGAACTC
AAGGAACCTCCACAAGGAGCTCATTTTCTTGCCAGAAGTTTGGATGATGCCTTAAAACTTACTGAACGACCAGAATTAGC
AAATAAAGTAGACATGATTTGGATAGTTGGTGGCAGTTCTGTTTATAAGGAAGCCATGAATCACCTAGGCCATCTTAAAC
TATTTGTGACAAGGATCATGCAGGACTTTGAAAGTGACACGTTTTTTTCAGAAATTGACTTGGAGAAATATAAACTTCTG
CCTGAATACCCAGGTGTTCTCTCTGATGTCCAGGAGGGGAAACACATCAAGTACAAATTTGAAGTATGTGAGAAGGATGA
TTAA

ORF - retro_hsap_6 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 93.44 %
Parental protein coverage: 97.86 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalLNCIVAVSQNMGIGKNGDLPWPPLRNEFRYFQRMTTTSSVEGKQNLVIMGKKTWFSIPEKNRPLKGRINL
LNCIVAVSQNMGIGKNGDLP.PPLRNEFRYFQRMTTTSSVEGKQNLVIMG.KTWFSIPEKNRPLK.RINL
RetrocopyLNCIVAVSQNMGIGKNGDLPRPPLRNEFRYFQRMTTTSSVEGKQNLVIMGRKTWFSIPEKNRPLKDRINL
ParentalVLSRELKEPPQGAHFLSRSLDDALKLTEQPELANKVDMVWIVGGSSVYKEAMNHPGHLKLFVTRIMQDFE
VLSRELKEPPQGAHFL.RSLDDALKLTE.PELANKVDM.WIVGGSSVYKEAMNH.GHLKLFVTRIMQDFE
RetrocopyVLSRELKEPPQGAHFLARSLDDALKLTERPELANKVDMIWIVGGSSVYKEAMNHLGHLKLFVTRIMQDFE
ParentalSDTFFPEIDLEKYKLLPEYPGVLSDVQEEKGIKYKFEVYEKND
SDTFF.EIDLEKYKLLPEYPGVLSDVQE.K.IKYKFEV.EK.D
RetrocopySDTFFSEIDLEKYKLLPEYPGVLSDVQEGKHIKYKFEVCEKDD

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 .99 RPM 5 .11 RPM
bodymap2_adrenal 1 .74 RPM 11 .85 RPM
bodymap2_brain 3 .00 RPM 6 .75 RPM
bodymap2_breast 1 .17 RPM 25 .29 RPM
bodymap2_colon 1 .24 RPM 6 .90 RPM
bodymap2_heart 0 .66 RPM 1 .51 RPM
bodymap2_kidney 2 .32 RPM 4 .55 RPM
bodymap2_liver 0 .76 RPM 6 .25 RPM
bodymap2_lung 0 .26 RPM 1 .99 RPM
bodymap2_lymph_node 1 .01 RPM 7 .80 RPM
bodymap2_ovary 3 .49 RPM 7 .96 RPM
bodymap2_prostate 3 .01 RPM 4 .57 RPM
bodymap2_skeletal_muscle 0 .16 RPM 3 .07 RPM
bodymap2_testis 2 .38 RPM 12 .14 RPM
bodymap2_thyroid 2 .75 RPM 13 .69 RPM
bodymap2_white_blood_cells 2 .68 RPM 7 .58 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity may be related with retro_hsap_6 in 7 libraries
ENCODE library ID Target ChIP-Seq Peak coordinates
ENCFF002CXN POLR2A 3:93781296..93781792
ENCFF002CZY POLR2A 3:93781351..93781852
ENCFF002DAK POLR2A 3:93781342..93781842
ENCFF002DAV POLR2A 3:93781322..93781866
ENCFF002DAY POLR2A 3:93781293..93781929
ENCFF002CSY POLR2A 3:93781327..93782327
ENCFF002CZW POLR2A 3:93781341..93782168

EST - click to see more details

No EST(s) were mapped for retro_hsap_6 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_6 retrocopy 5' end.

Lab - click to see more details

retro_hsap_6 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_6 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_109
Gorilla gorilla retro_ggor_1959
Macaca mulatta retro_mmul_1496
Callithrix jacchus retro_cjac_2017
Parental genes homology:
Parental genes homology involve 19 parental genes, and 52 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000157502 retrocopies
retro_amel_218, retro_amel_842,
Bos taurus ENSBTAG000000076811 retrocopy
retro_btau_351,
Callithrix jacchus ENSCJAG000000195564 retrocopies
retro_cjac_2017, retro_cjac_2298, retro_cjac_2446, retro_cjac_531,
Equus caballus ENSECAG000000268271 retrocopy
retro_ecab_513,
Felis catus ENSFCAG000000267453 retrocopies
retro_fcat_579, retro_fcat_705, retro_fcat_841,
Homo sapiens ENSG00000228716 4 retrocopies
retro_hsap_1927, retro_hsap_2119, retro_hsap_3602, retro_hsap_6 ,
Gorilla gorilla ENSGGOG000000223662 retrocopies
retro_ggor_1959, retro_ggor_2429,
Myotis lucifugus ENSMLUG000000122002 retrocopies
retro_mluc_1109, retro_mluc_2577,
Macaca mulatta ENSMMUG0000001828313 retrocopies
retro_mmul_1496, retro_mmul_425, retro_mmul_692, retro_mmul_693, retro_mmul_695, retro_mmul_700, retro_mmul_701, retro_mmul_704, retro_mmul_738, retro_mmul_760, retro_mmul_768, retro_mmul_82, retro_mmul_994,
Monodelphis domestica ENSMODG000000248603 retrocopies
retro_mdom_1685, retro_mdom_604, retro_mdom_703,
Mustela putorius furoENSMPUG000000087041 retrocopy
retro_mputfur_1107,
Mus musculus ENSMUSG000000217071 retrocopy
retro_mmus_3326,
Nomascus leucogenys ENSNLEG000000129893 retrocopies
retro_nleu_1193, retro_nleu_2314, retro_nleu_2631,
Oryctolagus cuniculus ENSOCUG000000051273 retrocopies
retro_ocun_1351, retro_ocun_1640, retro_ocun_650,
Otolemur garnettii ENSOGAG000000253201 retrocopy
retro_ogar_222,
Pongo abelii ENSPPYG000000156002 retrocopies
retro_pabe_2959, retro_pabe_41,
Pan troglodytes ENSPTRG000000170423 retrocopies
retro_ptro_109, retro_ptro_1551, retro_ptro_2988,
Rattus norvegicus ENSRNOG000000135211 retrocopy
retro_rnor_2030,
Sus scrofa ENSSSCG000000141252 retrocopies
retro_sscr_104, retro_sscr_1131,

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 = 2.3 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .88 RPM
CEU_NA11843 0 .82 RPM
CEU_NA11930 1 .79 RPM
CEU_NA12004 1 .18 RPM
CEU_NA12400 0 .81 RPM
CEU_NA12751 1 .87 RPM
CEU_NA12760 1 .44 RPM
CEU_NA12827 0 .94 RPM
CEU_NA12872 1 .42 RPM
CEU_NA12873 1 .21 RPM
FIN_HG00183 1 .24 RPM
FIN_HG00277 1 .22 RPM
FIN_HG00315 1 .71 RPM
FIN_HG00321 1 .60 RPM
FIN_HG00328 1 .23 RPM
FIN_HG00338 1 .11 RPM
FIN_HG00349 0 .77 RPM
FIN_HG00375 1 .39 RPM
FIN_HG00377 0 .66 RPM
FIN_HG00378 1 .72 RPM
GBR_HG00099 1 .25 RPM
GBR_HG00111 0 .77 RPM
GBR_HG00114 0 .97 RPM
GBR_HG00119 1 .41 RPM
GBR_HG00131 2 .13 RPM
GBR_HG00133 1 .30 RPM
GBR_HG00134 1 .40 RPM
GBR_HG00137 1 .13 RPM
GBR_HG00142 1 .50 RPM
GBR_HG00143 1 .56 RPM
TSI_NA20512 0 .40 RPM
TSI_NA20513 1 .43 RPM
TSI_NA20518 1 .17 RPM
TSI_NA20532 1 .12 RPM
TSI_NA20538 1 .29 RPM
TSI_NA20756 1 .11 RPM
TSI_NA20765 1 .82 RPM
TSI_NA20771 1 .33 RPM
TSI_NA20786 1 .26 RPM
TSI_NA20798 1 .15 RPM
YRI_NA18870 1 .29 RPM
YRI_NA18907 1 .21 RPM
YRI_NA18916 1 .60 RPM
YRI_NA19093 0 .75 RPM
YRI_NA19099 1 .25 RPM
YRI_NA19114 1 .68 RPM
YRI_NA19118 2 .30 RPM
YRI_NA19213 1 .96 RPM
YRI_NA19214 1 .52 RPM
YRI_NA19223 1 .87 RPM

Indel association:

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



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