Gene loci information

Transcript annotation

  • This transcript has been annotated as Ecdysone receptor.

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_1 g10955 g10955.t1 isoform g10955.t1 12999107 13001000
chr_1 g10955 g10955.t1 exon g10955.t1.exon1 12999107 12999661
chr_1 g10955 g10955.t1 cds g10955.t1.CDS1 12999107 12999661
chr_1 g10955 g10955.t1 exon g10955.t1.exon2 12999746 12999895
chr_1 g10955 g10955.t1 cds g10955.t1.CDS2 12999746 12999895
chr_1 g10955 g10955.t1 exon g10955.t1.exon3 12999958 13000478
chr_1 g10955 g10955.t1 cds g10955.t1.CDS3 12999958 13000478
chr_1 g10955 g10955.t1 exon g10955.t1.exon4 13000537 13000820
chr_1 g10955 g10955.t1 cds g10955.t1.CDS4 13000537 13000820
chr_1 g10955 g10955.t1 exon g10955.t1.exon5 13000879 13001000
chr_1 g10955 g10955.t1 cds g10955.t1.CDS5 13000879 13001000
chr_1 g10955 g10955.t1 TSS g10955.t1 13001290 13001290
chr_1 g10955 g10955.t1 TTS g10955.t1 NA NA

Sequences

>g10955.t1 Gene=g10955 Length=1632
ATGAAGACAGAAAATCTAATTGTAACAACAGTAAAAGTTGAACCATTGAATTATGCTGCT
ACACAATCTTATGGTGAAAATAACATTTATGGCGGTGCAGCTAAGAAACAACGATTAGAA
AGTGATGAATGGATGAATCAATCAAATATGAATCTCGAATCTTCCAATATGAATCATAAC
ACAATTAGTGGCTTTTCATCGTCACCAGATAACTACGAGGCATATAGCCCAAATGGTAAA
ATGGGAATGGATGATAACAACATGAGCTCACATTTGAGTGATTGCCTCGACTCAAAAAAG
TCCAAAAAAGGACCCGTTCCAAGACAACAGGAAGAGTTGTGCCTCGTTTGTGGAGATCGT
GCCTCGGGATATCATTATAACGCGTTGACGTGTGAAGGGTGCAAAGGATTTTTCCGACGT
AGTGTAACTAAAAATGCTGTTTATTGTTGTAAATTTGGTCATGAATGTGAAATGGATATG
TATATGAGACGAAAGTGCCAGGAGTGTCGATTAAAAAAATGTTTGGCTGTGGGTATGCGA
CCAGAATGCGTTGTACCAGAGAATCAATGTGCTATTAAGCGAAAAGAGAAAAAAGCACAG
AAAGAAAAGGACAAGGACAAAGGAGTTGGAGGCGGTGGTGGTGGTGCAAGTTTAAGCAAC
AGCAGCGCCTCGTTAACAAATCAAAATAACAATATAATGAAAACGACAGAGGTCTTATAT
AAGGAAGAAATTCTACCGCAGCTTATGAAGTGCGAATCACCACCACACACAATGCACCAG
TTACTACCCGAGAAATTGCTGATTGAAAATCGCAGTAAGGGACTGCCTCAATTAACATCA
AATCAATTGGCTGTTATTTACAAACTCATATGGTATCAAGATGGTTATGAACAACCATCT
GAAGAAGACTTGAAACGAATTAGCAATGACCTCGCTGATGAAGAAGATAACAATGATGCA
CACTTTAGATACATAACTGAGATCACAATATTGACAGTACAACTGATCGTTGAATTTGCT
AAAGGGCTTCCAGCATTTACGAAAATTCCACAAGAAGATCAAATTACATTATTAAAGGCT
TGCTCCAGTGAAGTTATGATGTTGCGCATGGCTCGACGTTACGATTCGCATAGCGATTCC
ATTTTGTTTGCGAATAATACCACATATACGAAACAAACGTATCAGTTGGCTGGCATGGAA
GACACCATTGATGACTTGTTACACTTTTGTCGACAAATGTACGCTTTATCGATCGATAAT
GTGGAATATGCACTTCTCACTGCAATCGTCATATTCTCTGATCGACCTGGTCTTGAAAAA
GCAGAAATGGTTGAATTCATTCAATCCTATTATATTGAAACACTCAAAGTTTACATCATC
AATCGGCACGGTGGCGAGCAAAAATGTAGCATTCAATTTGCAAAGCTACTAGGCATCCTC
ACTGAGCTGAGAACAATGGGCAATAAGAACTCTGAAATGTGCTTTTCATTAAAATTAAAG
AACCGAAAACTGCCAAAATTTTTAGAAGAGGTTTGGGACGTTGGCGACAGTAGTATTGGC
CATCATTCAGGCTCTGTCACAACCAATATAACAACTGAGAATATAGTTCGTGACCGAATC
AATCGAAATTAA

>g10955.t1 Gene=g10955 Length=543
MKTENLIVTTVKVEPLNYAATQSYGENNIYGGAAKKQRLESDEWMNQSNMNLESSNMNHN
TISGFSSSPDNYEAYSPNGKMGMDDNNMSSHLSDCLDSKKSKKGPVPRQQEELCLVCGDR
ASGYHYNALTCEGCKGFFRRSVTKNAVYCCKFGHECEMDMYMRRKCQECRLKKCLAVGMR
PECVVPENQCAIKRKEKKAQKEKDKDKGVGGGGGGASLSNSSASLTNQNNNIMKTTEVLY
KEEILPQLMKCESPPHTMHQLLPEKLLIENRSKGLPQLTSNQLAVIYKLIWYQDGYEQPS
EEDLKRISNDLADEEDNNDAHFRYITEITILTVQLIVEFAKGLPAFTKIPQEDQITLLKA
CSSEVMMLRMARRYDSHSDSILFANNTTYTKQTYQLAGMEDTIDDLLHFCRQMYALSIDN
VEYALLTAIVIFSDRPGLEKAEMVEFIQSYYIETLKVYIINRHGGEQKCSIQFAKLLGIL
TELRTMGNKNSEMCFSLKLKNRKLPKFLEEVWDVGDSSIGHHSGSVTTNITTENIVRDRI
NRN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
26 g10955.t1 CDD cd07161 NR_DBD_EcR 111 201 3.36676E-60
27 g10955.t1 CDD cd06938 NR_LBD_EcR 282 514 1.72763E-136
25 g10955.t1 Gene3D G3DSA:3.30.50.10 - 106 188 1.8E-32
24 g10955.t1 Gene3D G3DSA:1.10.565.10 Retinoid X Receptor 270 515 1.7E-89
31 g10955.t1 MobiDBLite mobidb-lite consensus disorder prediction 195 227 -
32 g10955.t1 MobiDBLite mobidb-lite consensus disorder prediction 195 209 -
3 g10955.t1 PANTHER PTHR48092:SF9 ECDYSONE RECEPTOR-LIKE PROTEIN 27 514 3.3E-157
4 g10955.t1 PANTHER PTHR48092 KNIRPS-RELATED PROTEIN-RELATED 27 514 3.3E-157
12 g10955.t1 PRINTS PR01283 Ecdysteroid receptor (1H nuclear receptor) signature 102 113 1.9E-69
5 g10955.t1 PRINTS PR00047 C4-type steroid receptor zinc finger signature 114 130 1.4E-18
8 g10955.t1 PRINTS PR00047 C4-type steroid receptor zinc finger signature 130 145 1.4E-18
6 g10955.t1 PRINTS PR00047 C4-type steroid receptor zinc finger signature 163 171 1.4E-18
7 g10955.t1 PRINTS PR00047 C4-type steroid receptor zinc finger signature 171 179 1.4E-18
20 g10955.t1 PRINTS PR00398 Steroid hormone receptor signature 175 185 3.5E-25
16 g10955.t1 PRINTS PR01283 Ecdysteroid receptor (1H nuclear receptor) signature 180 189 1.9E-69
15 g10955.t1 PRINTS PR01283 Ecdysteroid receptor (1H nuclear receptor) signature 281 306 1.9E-69
13 g10955.t1 PRINTS PR01283 Ecdysteroid receptor (1H nuclear receptor) signature 313 332 1.9E-69
17 g10955.t1 PRINTS PR00398 Steroid hormone receptor signature 328 349 3.5E-25
19 g10955.t1 PRINTS PR00398 Steroid hormone receptor signature 349 365 3.5E-25
11 g10955.t1 PRINTS PR01283 Ecdysteroid receptor (1H nuclear receptor) signature 375 388 1.9E-69
14 g10955.t1 PRINTS PR01283 Ecdysteroid receptor (1H nuclear receptor) signature 403 421 1.9E-69
18 g10955.t1 PRINTS PR00398 Steroid hormone receptor signature 416 431 3.5E-25
21 g10955.t1 PRINTS PR00398 Steroid hormone receptor signature 475 492 3.5E-25
10 g10955.t1 PRINTS PR01283 Ecdysteroid receptor (1H nuclear receptor) signature 477 494 1.9E-69
9 g10955.t1 PRINTS PR01283 Ecdysteroid receptor (1H nuclear receptor) signature 496 514 1.9E-69
2 g10955.t1 Pfam PF00105 Zinc finger, C4 type (two domains) 113 180 2.9E-29
1 g10955.t1 Pfam PF00104 Ligand-binding domain of nuclear hormone receptor 318 499 2.7E-28
30 g10955.t1 ProSitePatterns PS00031 Nuclear hormones receptors DNA-binding region signature. 114 140 -
34 g10955.t1 ProSiteProfiles PS51030 Nuclear hormone receptors DNA-binding domain profile. 111 186 19.432
33 g10955.t1 ProSiteProfiles PS51843 Nuclear receptor (NR) ligand-binding (LBD) domain profile. 281 516 56.526
29 g10955.t1 SMART SM00399 c4gold 111 182 2.8E-37
28 g10955.t1 SMART SM00430 holi 327 487 3.1E-41
23 g10955.t1 SUPERFAMILY SSF57716 Glucocorticoid receptor-like (DNA-binding domain) 112 194 8.97E-28
22 g10955.t1 SUPERFAMILY SSF48508 Nuclear receptor ligand-binding domain 296 514 1.15E-68

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:0005634 nucleus CC
GO:0003677 DNA binding MF
GO:0035100 ecdysone binding MF
GO:0006355 regulation of transcription, DNA-templated BP
GO:0004879 nuclear receptor activity MF
GO:0035076 ecdysone receptor-mediated signaling pathway 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.

Raw TPM values