Gene loci information

Transcript annotation

  • This transcript has been annotated as Nuclear receptor subfamily 2 group E member 1.

Parent gene

Gene structure

  • The exon-intron structure of all isoforms are indicated below. CDS regions are colored in green. TSS and TTs that were predicted with CTR-Seq data are indicated in solid circle and squares, respectively. More specific data are shown in the table below.

Chromosome Gene Transcript Category ID Start End
chr_3 g247 g247.t1 isoform g247.t1 2003037 2006558
chr_3 g247 g247.t1 exon g247.t1.exon1 2003037 2003118
chr_3 g247 g247.t1 cds g247.t1.CDS1 2003037 2003118
chr_3 g247 g247.t1 exon g247.t1.exon2 2005228 2006558
chr_3 g247 g247.t1 cds g247.t1.CDS2 2005228 2006558
chr_3 g247 g247.t1 TSS g247.t1 NA NA
chr_3 g247 g247.t1 TTS g247.t1 NA NA

Sequences

>g247.t1 Gene=g247 Length=1413
ATGATGCAATCACCAATAAGTTCGTCTCCTGAATTAATGGATCCGAGATTTAGTCAATTA
AGATTACCAGCATCTTCATCAAGTCGAATTCTTTATGATGTACCATGTAAAGTTTGTCGT
GATCATAGTTCTGGTAAACATTATGGCATTTATGCATGTGATGGATGTGCAGGATTTTTT
AAACGATCAATTCGTCGTAATCGTCAATATGTTTGTAAATCAAAATCTGATGGACTTTGT
CAAGTTGATAAAACACATCGAAATCAATGCAGAGCATGCAGACTTAAGAAATGTTTTGAA
GTTGGAATGAATCGTGATGCAGTGCAACATGAACGTGGACCAAGAAATTCAACATTAAGA
AAACAAATGGCAATGTTTATAAATAAAGATGCAGCAATAAGACATCATGAAGCTTACATT
ATGGCCAGCATTCCAGGACCAGCACCTTTGCCATTACCAATTGGTCTTGATTTAACTGTG
CCACGACTTACAACAAATCCATTCATCACACCAACTTCTTATATTTCAAATTTCTCAACT
GGCAGCACTTCACCGCCATCAACAATTTCATCAACACCACCACCATCAGTTCCACCACTT
CTTCATATTCCATCATCACCACAACATCATCATCTTAATAATGTTGAACCAATTCGTGAA
GCAGCAGCTCAATTATTATTTTTAAATGTGAATTTTCTTAAAAATCTTACACCATTCACT
CAACTTCCACTTGGTGATCAATTGTTGCTATTTGAAGAATCATGGCGTGAATTTTTCATT
ATGGGTATTGCTGAGCACTTACTGCCTATCAATTTCACACAGCTTCTTTTCGCCTACGAA
ATTCTCAATAGTACATGCCATGAGCCAAAGTCAAAAAGCGCAACTGAGTCGATGATAAGA
GAAATTCAAGCATTTCAGCAGGTGCTGAATAAATTCATACAGATGAGGGTTGACAGCAAT
GAATATGTTTATTTGCGAGCAATTGTTTTATATAAGAGTGAATTAAGCAATAATAATAAT
AACAATAATAACAATAATGTTATCAAGACAGAAAGAGATAAGGACAGCAGTCAAGATGTC
ATTACAAGCACTAGCGATGATTCTTCTTCTGATGTGTCACATAATAATTCATCAAATACA
ATCAAAACAACATCAACTAATAATGGAAAAGTTTTAGAAGAACCAATGAAAGTTAGAGCA
CTTGAAACTAATGCAAAAGATGCACTGGCTGCATATGAACAAAATTATTATGGTGTTTCA
CATCAATTGAGGTATAAAAATTTACTCTCACTTTTACCAACATTGAAATCTGTCTCACCA
TATACAATAGAAGAATTATTCTTTAGACGCAATATTGGACATGTTTCATTAATGAAATTA
CTCGTTGACATGTATCTACAGAAGAAGCCATAA

>g247.t1 Gene=g247 Length=470
MMQSPISSSPELMDPRFSQLRLPASSSSRILYDVPCKVCRDHSSGKHYGIYACDGCAGFF
KRSIRRNRQYVCKSKSDGLCQVDKTHRNQCRACRLKKCFEVGMNRDAVQHERGPRNSTLR
KQMAMFINKDAAIRHHEAYIMASIPGPAPLPLPIGLDLTVPRLTTNPFITPTSYISNFST
GSTSPPSTISSTPPPSVPPLLHIPSSPQHHHLNNVEPIREAAAQLLFLNVNFLKNLTPFT
QLPLGDQLLLFEESWREFFIMGIAEHLLPINFTQLLFAYEILNSTCHEPKSKSATESMIR
EIQAFQQVLNKFIQMRVDSNEYVYLRAIVLYKSELSNNNNNNNNNNVIKTERDKDSSQDV
ITSTSDDSSSDVSHNNSSNTIKTTSTNNGKVLEEPMKVRALETNAKDALAAYEQNYYGVS
HQLRYKNLLSLLPTLKSVSPYTIEELFFRRNIGHVSLMKLLVDMYLQKKP

Protein features from InterProScan

Transcript Database ID Name Start End E.value
18 g247.t1 CDD cd07163 NR_DBD_TLX 27 119 9.35158E-69
17 g247.t1 Gene3D G3DSA:3.30.50.10 - 27 140 9.9E-35
15 g247.t1 Gene3D G3DSA:1.10.565.10 Retinoid X Receptor 199 367 2.2E-35
16 g247.t1 Gene3D G3DSA:1.10.565.10 Retinoid X Receptor 381 470 4.1E-15
23 g247.t1 MobiDBLite mobidb-lite consensus disorder prediction 341 389 -
22 g247.t1 MobiDBLite mobidb-lite consensus disorder prediction 361 389 -
3 g247.t1 PANTHER PTHR24083 NUCLEAR HORMONE RECEPTOR 32 467 1.7E-113
4 g247.t1 PANTHER PTHR24083:SF98 NUCLEAR RECEPTOR SUBFAMILY 2 GROUP E MEMBER 1 32 467 1.7E-113
8 g247.t1 PRINTS PR00047 C4-type steroid receptor zinc finger signature 36 52 3.2E-16
6 g247.t1 PRINTS PR00047 C4-type steroid receptor zinc finger signature 52 67 3.2E-16
7 g247.t1 PRINTS PR00047 C4-type steroid receptor zinc finger signature 87 95 3.2E-16
5 g247.t1 PRINTS PR00047 C4-type steroid receptor zinc finger signature 95 103 3.2E-16
12 g247.t1 PRINTS PR00398 Steroid hormone receptor signature 99 109 5.3E-14
11 g247.t1 PRINTS PR00398 Steroid hormone receptor signature 221 242 5.3E-14
10 g247.t1 PRINTS PR00398 Steroid hormone receptor signature 242 258 5.3E-14
9 g247.t1 PRINTS PR00398 Steroid hormone receptor signature 315 330 5.3E-14
2 g247.t1 Pfam PF00105 Zinc finger, C4 type (two domains) 35 105 8.0E-29
1 g247.t1 Pfam PF00104 Ligand-binding domain of nuclear hormone receptor 207 448 3.8E-15
21 g247.t1 ProSitePatterns PS00031 Nuclear hormones receptors DNA-binding region signature. 36 62 -
25 g247.t1 ProSiteProfiles PS51030 Nuclear hormone receptors DNA-binding domain profile. 33 110 20.156
24 g247.t1 ProSiteProfiles PS51843 Nuclear receptor (NR) ligand-binding (LBD) domain profile. 173 468 31.582
20 g247.t1 SMART SM00399 c4gold 33 106 1.6E-36
19 g247.t1 SMART SM00430 holi 220 439 6.9E-18
14 g247.t1 SUPERFAMILY SSF57716 Glucocorticoid receptor-like (DNA-binding domain) 32 120 2.75E-28
13 g247.t1 SUPERFAMILY SSF48508 Nuclear receptor ligand-binding domain 104 465 1.3E-40

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0006355 regulation of transcription, DNA-templated BP
GO:0043565 sequence-specific DNA binding MF
GO:0008270 zinc ion binding MF
GO:0003700 DNA-binding transcription factor activity MF

KEGG

Orthology

Pathway

  • This transcript belongs to the following pathways

Expression

Transcript expression in Pv11 cells

TPM values are indicated as average +/- STDEV.

Differential expression

Differentially expressed genes were identified with DESeq2 using the ‘run_DE_analysis.pl’ script from Trinity. Transcripts were determined as differentially expressed when (1) FDR < 0.05 (2) fold change > 2 (TPM calculated by RSEM). DE information and fold change between conditions are indicated in the plot below. There were no conditions that were differentially expressed