General information for g10955.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Ecdysone receptor.
Parent gene
- The parent gene g10955 is located on chr_1: 13001000..13004105 (- strand)
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.t3 | isoform | g10955.t3 | 12999107 | 13000236 |
| chr_1 | g10955 | g10955.t3 | exon | g10955.t3.exon1 | 12999107 | 12999661 |
| chr_1 | g10955 | g10955.t3 | cds | g10955.t3.CDS1 | 12999107 | 12999661 |
| chr_1 | g10955 | g10955.t3 | exon | g10955.t3.exon2 | 12999746 | 12999895 |
| chr_1 | g10955 | g10955.t3 | cds | g10955.t3.CDS2 | 12999746 | 12999895 |
| chr_1 | g10955 | g10955.t3 | exon | g10955.t3.exon3 | 12999958 | 13000236 |
| chr_1 | g10955 | g10955.t3 | cds | g10955.t3.CDS3 | 12999958 | 13000188 |
| chr_1 | g10955 | g10955.t3 | TSS | g10955.t3 | NA | NA |
| chr_1 | g10955 | g10955.t3 | TTS | g10955.t3 | NA | NA |
Sequences
>g10955.t3 Gene=g10955 Length=984
AGTTTAAGCAACAGCAGCGCCTCGTTAACAAATCAAAATAACAATATAATGAAAACGACA
GAGGTCTTATATAAGGAAGAAATTCTACCGCAGCTTATGAAGTGCGAATCACCACCACAC
ACAATGCACCAGTTACTACCCGAGAAATTGCTGATTGAAAATCGCAGTAAGGGACTGCCT
CAATTAACATCAAATCAATTGGCTGTTATTTACAAACTCATATGGTATCAAGATGGTTAT
GAACAACCATCTGAAGAAGACTTGAAACGAATTAGCAATGACCTCGCTGATGAAGAAGAT
AACAATGATGCACACTTTAGATACATAACTGAGATCACAATATTGACAGTACAACTGATC
GTTGAATTTGCTAAAGGGCTTCCAGCATTTACGAAAATTCCACAAGAAGATCAAATTACA
TTATTAAAGGCTTGCTCCAGTGAAGTTATGATGTTGCGCATGGCTCGACGTTACGATTCG
CATAGCGATTCCATTTTGTTTGCGAATAATACCACATATACGAAACAAACGTATCAGTTG
GCTGGCATGGAAGACACCATTGATGACTTGTTACACTTTTGTCGACAAATGTACGCTTTA
TCGATCGATAATGTGGAATATGCACTTCTCACTGCAATCGTCATATTCTCTGATCGACCT
GGTCTTGAAAAAGCAGAAATGGTTGAATTCATTCAATCCTATTATATTGAAACACTCAAA
GTTTACATCATCAATCGGCACGGTGGCGAGCAAAAATGTAGCATTCAATTTGCAAAGCTA
CTAGGCATCCTCACTGAGCTGAGAACAATGGGCAATAAGAACTCTGAAATGTGCTTTTCA
TTAAAATTAAAGAACCGAAAACTGCCAAAATTTTTAGAAGAGGTTTGGGACGTTGGCGAC
AGTAGTATTGGCCATCATTCAGGCTCTGTCACAACCAATATAACAACTGAGAATATAGTT
CGTGACCGAATCAATCGAAATTAA
>g10955.t3 Gene=g10955 Length=311
MKTTEVLYKEEILPQLMKCESPPHTMHQLLPEKLLIENRSKGLPQLTSNQLAVIYKLIWY
QDGYEQPSEEDLKRISNDLADEEDNNDAHFRYITEITILTVQLIVEFAKGLPAFTKIPQE
DQITLLKACSSEVMMLRMARRYDSHSDSILFANNTTYTKQTYQLAGMEDTIDDLLHFCRQ
MYALSIDNVEYALLTAIVIFSDRPGLEKAEMVEFIQSYYIETLKVYIINRHGGEQKCSIQ
FAKLLGILTELRTMGNKNSEMCFSLKLKNRKLPKFLEEVWDVGDSSIGHHSGSVTTNITT
ENIVRDRINRN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 16 | g10955.t3 | CDD | cd06938 | NR_LBD_EcR | 50 | 282 | 0.000 |
| 15 | g10955.t3 | Gene3D | G3DSA:1.10.565.10 | Retinoid X Receptor | 38 | 283 | 0.000 |
| 2 | g10955.t3 | PANTHER | PTHR48092:SF9 | ECDYSONE RECEPTOR-LIKE PROTEIN | 38 | 282 | 0.000 |
| 3 | g10955.t3 | PANTHER | PTHR48092 | KNIRPS-RELATED PROTEIN-RELATED | 38 | 282 | 0.000 |
| 6 | g10955.t3 | PRINTS | PR01283 | Ecdysteroid receptor (1H nuclear receptor) signature | 49 | 74 | 0.000 |
| 5 | g10955.t3 | PRINTS | PR01283 | Ecdysteroid receptor (1H nuclear receptor) signature | 81 | 100 | 0.000 |
| 12 | g10955.t3 | PRINTS | PR00398 | Steroid hormone receptor signature | 96 | 117 | 0.000 |
| 13 | g10955.t3 | PRINTS | PR00398 | Steroid hormone receptor signature | 117 | 133 | 0.000 |
| 4 | g10955.t3 | PRINTS | PR01283 | Ecdysteroid receptor (1H nuclear receptor) signature | 143 | 156 | 0.000 |
| 8 | g10955.t3 | PRINTS | PR01283 | Ecdysteroid receptor (1H nuclear receptor) signature | 171 | 189 | 0.000 |
| 10 | g10955.t3 | PRINTS | PR00398 | Steroid hormone receptor signature | 184 | 199 | 0.000 |
| 11 | g10955.t3 | PRINTS | PR00398 | Steroid hormone receptor signature | 243 | 260 | 0.000 |
| 9 | g10955.t3 | PRINTS | PR01283 | Ecdysteroid receptor (1H nuclear receptor) signature | 245 | 262 | 0.000 |
| 7 | g10955.t3 | PRINTS | PR01283 | Ecdysteroid receptor (1H nuclear receptor) signature | 264 | 282 | 0.000 |
| 1 | g10955.t3 | Pfam | PF00104 | Ligand-binding domain of nuclear hormone receptor | 86 | 267 | 0.000 |
| 18 | g10955.t3 | ProSiteProfiles | PS51843 | Nuclear receptor (NR) ligand-binding (LBD) domain profile. | 49 | 284 | 56.526 |
| 17 | g10955.t3 | SMART | SM00430 | holi | 95 | 255 | 0.000 |
| 14 | g10955.t3 | SUPERFAMILY | SSF48508 | Nuclear receptor ligand-binding domain | 64 | 282 | 0.000 |
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:0035076 | ecdysone receptor-mediated signaling pathway | BP |
| GO:0006355 | regulation of transcription, DNA-templated | BP |
| GO:0004879 | nuclear receptor activity | MF |
KEGG
Orthology
This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).
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.
