General information for g11122.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Protein ultraspiracle.
Parent gene
- The parent gene g11122 is located on chr_1: 14253699..14270414 (- 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 | g11122 | g11122.t1 | TTS | g11122.t1 | 14253663 | 14253663 |
| chr_1 | g11122 | g11122.t1 | isoform | g11122.t1 | 14253699 | 14270414 |
| chr_1 | g11122 | g11122.t1 | exon | g11122.t1.exon1 | 14253699 | 14253943 |
| chr_1 | g11122 | g11122.t1 | cds | g11122.t1.CDS1 | 14253699 | 14253943 |
| chr_1 | g11122 | g11122.t1 | exon | g11122.t1.exon2 | 14254000 | 14254228 |
| chr_1 | g11122 | g11122.t1 | cds | g11122.t1.CDS2 | 14254000 | 14254228 |
| chr_1 | g11122 | g11122.t1 | exon | g11122.t1.exon3 | 14254296 | 14254466 |
| chr_1 | g11122 | g11122.t1 | cds | g11122.t1.CDS3 | 14254296 | 14254466 |
| chr_1 | g11122 | g11122.t1 | exon | g11122.t1.exon4 | 14254551 | 14254730 |
| chr_1 | g11122 | g11122.t1 | cds | g11122.t1.CDS4 | 14254551 | 14254730 |
| chr_1 | g11122 | g11122.t1 | exon | g11122.t1.exon5 | 14254807 | 14255005 |
| chr_1 | g11122 | g11122.t1 | cds | g11122.t1.CDS5 | 14254807 | 14255005 |
| chr_1 | g11122 | g11122.t1 | exon | g11122.t1.exon6 | 14258034 | 14258565 |
| chr_1 | g11122 | g11122.t1 | cds | g11122.t1.CDS6 | 14258034 | 14258565 |
| chr_1 | g11122 | g11122.t1 | exon | g11122.t1.exon7 | 14270297 | 14270414 |
| chr_1 | g11122 | g11122.t1 | cds | g11122.t1.CDS7 | 14270297 | 14270414 |
| chr_1 | g11122 | g11122.t1 | TSS | g11122.t1 | 14271315 | 14271315 |
Sequences
>g11122.t1 Gene=g11122 Length=1674
ATGTTGAAGAAAGAGAAGCCTATGATGACAGTAGCCGCTATAATTGAGCAGGCACAAAAT
CGTTGGATGGAGCATCCGCTTGTCTATAATCGAAGTCTACAATTCCAAGGATCTTACTGC
ATCGATTCATCATTGATTGGACATATGGGTCCATTATCACCGCCAGATCTAAAGCCAGAT
ATTTCACTATTAAATTGCAATAATAATAATAATAACAATACAAATAATAATAACAGTAGT
AATAGCATTAATCATATTATTTTAAATAATCACAACACATCACCAATACCGACAACGACG
GGTATGAACACATTTTCGCCGATTCAGTCGATGAATAATAATGGTCCGAGTAGTCCTATC
AGTTCACTCGGCAGTGGGAGTGGAACGATTGTCACATTTAATCAGATCAAACTGCAATCA
CCATCGCCCTCAAATGCATCATCGTCATCAACTCTAAGCGGTCCATTGACAACGACACCG
CCTGCAACGAATGTCAACAATATTCTTGTAATGAATAATAATGGCAGTGGAAATGCTACG
AATGGGAAAAATCAACAGCAATATCCGCCCAATCATCCTCTCTCGGGATCGAAACATCTA
TGCTCAATTTGTGGTGATCGTGCAAGTGGAAAGCATTATGGTGTATATAGTTGTGAAGGC
TGTAAAGGCTTTTTCAAAAGAACAGTAAGAAAGGACTTGTCATATGCATGTCGAGAGGAT
CGAAATTGTGTGATTGATAAAAAACAAAGGAATCGTTGTCAATATTGTCGTTACCAGAAA
TGCTTAAATTGTGGTATGAAACGAGAAGCCGTTCAAGAAGAACGACAGCGAGGTGGAAAG
TCACAAAAGAGTGGCGACGATATGAATATTTCATCAACGCCGCCTTTCGTGAATAATGGA
CCTGCTCGAGAATTTACATTGGAGCGTCTAATGGAAGCAGAACAAATGAGCGAATCAAAA
TGCGGGGATAAATCTATACAATATTTACGTATAGCCAGCTCTAATGCAATGATTCCAAAT
GAATACAGGGCGCCTGTTTCATCAATTTGTGCAATGGTAAATAGACTGTCCTTTCAACTA
ATGGACTTTTGTCGACGACTGCCTCACTTCACAAAATTACCTCATGACGATCAGATAGAA
CTACTAAAACATAGTTTTAATGAATTGCTGATAATTTCCGTTGCATACATGAGCATTCCG
TATATTGAACCTGATCGACGGAATGCCGATGGAACGCTGGAAAGACGAACAATATCGCAA
CAGATGTGTCTTGGACGTAATTACACATTAGGCAGAAACATGGCAGTGCAAGCGGGTGTT
GTGCAAATATTTGATAGAATTTTATCGGAATTAAGTGTCAAAGTTAAAAGAATGGAAATT
GATCTTACTGAACTGTGCTTACTTAAGGCAATTATTGTCTTTAATCCAGATGTAAGAAAA
CTTACAGAACGCACAGATATCGATTTAGTGCGTGCAAAAATTTACGCCTGTCTCGACGAG
TACTGTCGACAGAAACATCCAACAGAAGACGGTCGTTTTGCTCAACTTCTACTTCGACTG
CCAGCTCTCCGATCCATAAGTCTCAAGTGTGTAGATCATTTGTTCTATTTTCAACTTATT
GATGACAAACATGTTGAAGAAATTCTTGAAGAGGAATTAGGAAGGTGCACCTAA
>g11122.t1 Gene=g11122 Length=557
MLKKEKPMMTVAAIIEQAQNRWMEHPLVYNRSLQFQGSYCIDSSLIGHMGPLSPPDLKPD
ISLLNCNNNNNNNTNNNNSSNSINHIILNNHNTSPIPTTTGMNTFSPIQSMNNNGPSSPI
SSLGSGSGTIVTFNQIKLQSPSPSNASSSSTLSGPLTTTPPATNVNNILVMNNNGSGNAT
NGKNQQQYPPNHPLSGSKHLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACRED
RNCVIDKKQRNRCQYCRYQKCLNCGMKREAVQEERQRGGKSQKSGDDMNISSTPPFVNNG
PAREFTLERLMEAEQMSESKCGDKSIQYLRIASSNAMIPNEYRAPVSSICAMVNRLSFQL
MDFCRRLPHFTKLPHDDQIELLKHSFNELLIISVAYMSIPYIEPDRRNADGTLERRTISQ
QMCLGRNYTLGRNMAVQAGVVQIFDRILSELSVKVKRMEIDLTELCLLKAIIVFNPDVRK
LTERTDIDLVRAKIYACLDEYCRQKHPTEDGRFAQLLLRLPALRSISLKCVDHLFYFQLI
DDKHVEEILEEELGRCT
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 23 | g11122.t1 | CDD | cd06956 | NR_DBD_RXR | 199 | 275 | 1.01418E-50 |
| 22 | g11122.t1 | CDD | cd06943 | NR_LBD_RXR_like | 304 | 538 | 9.65384E-107 |
| 21 | g11122.t1 | Gene3D | G3DSA:3.30.50.10 | - | 194 | 293 | 8.7E-36 |
| 20 | g11122.t1 | Gene3D | G3DSA:1.10.565.10 | Retinoid X Receptor | 298 | 555 | 9.4E-75 |
| 27 | g11122.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 138 | 162 | - |
| 3 | g11122.t1 | PANTHER | PTHR24083:SF103 | PROTEIN ULTRASPIRACLE | 133 | 553 | 4.5E-141 |
| 4 | g11122.t1 | PANTHER | PTHR24083 | NUCLEAR HORMONE RECEPTOR | 133 | 553 | 4.5E-141 |
| 9 | g11122.t1 | PRINTS | PR00047 | C4-type steroid receptor zinc finger signature | 201 | 217 | 2.2E-18 |
| 12 | g11122.t1 | PRINTS | PR00047 | C4-type steroid receptor zinc finger signature | 217 | 232 | 2.2E-18 |
| 10 | g11122.t1 | PRINTS | PR00047 | C4-type steroid receptor zinc finger signature | 250 | 258 | 2.2E-18 |
| 11 | g11122.t1 | PRINTS | PR00047 | C4-type steroid receptor zinc finger signature | 258 | 266 | 2.2E-18 |
| 15 | g11122.t1 | PRINTS | PR00398 | Steroid hormone receptor signature | 262 | 272 | 7.7E-24 |
| 8 | g11122.t1 | PRINTS | PR00545 | Retinoid X receptor signature | 269 | 282 | 2.7E-22 |
| 17 | g11122.t1 | PRINTS | PR00398 | Steroid hormone receptor signature | 352 | 373 | 7.7E-24 |
| 14 | g11122.t1 | PRINTS | PR00398 | Steroid hormone receptor signature | 373 | 389 | 7.7E-24 |
| 5 | g11122.t1 | PRINTS | PR00545 | Retinoid X receptor signature | 420 | 445 | 2.7E-22 |
| 6 | g11122.t1 | PRINTS | PR00545 | Retinoid X receptor signature | 446 | 464 | 2.7E-22 |
| 13 | g11122.t1 | PRINTS | PR00398 | Steroid hormone receptor signature | 458 | 473 | 7.7E-24 |
| 7 | g11122.t1 | PRINTS | PR00545 | Retinoid X receptor signature | 487 | 506 | 2.7E-22 |
| 16 | g11122.t1 | PRINTS | PR00398 | Steroid hormone receptor signature | 515 | 532 | 7.7E-24 |
| 2 | g11122.t1 | Pfam | PF00105 | Zinc finger, C4 type (two domains) | 200 | 268 | 1.1E-30 |
| 1 | g11122.t1 | Pfam | PF00104 | Ligand-binding domain of nuclear hormone receptor | 341 | 540 | 1.4E-32 |
| 26 | g11122.t1 | ProSitePatterns | PS00031 | Nuclear hormones receptors DNA-binding region signature. | 201 | 227 | - |
| 29 | g11122.t1 | ProSiteProfiles | PS51030 | Nuclear hormone receptors DNA-binding domain profile. | 198 | 273 | 21.275 |
| 28 | g11122.t1 | ProSiteProfiles | PS51843 | Nuclear receptor (NR) ligand-binding (LBD) domain profile. | 306 | 556 | 47.156 |
| 25 | g11122.t1 | SMART | SM00399 | c4gold | 198 | 269 | 6.2E-38 |
| 24 | g11122.t1 | SMART | SM00430 | holi | 351 | 527 | 1.9E-41 |
| 19 | g11122.t1 | SUPERFAMILY | SSF57716 | Glucocorticoid receptor-like (DNA-binding domain) | 199 | 280 | 1.73E-29 |
| 18 | g11122.t1 | SUPERFAMILY | SSF48508 | Nuclear receptor ligand-binding domain | 307 | 551 | 1.7E-56 |
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:0003707 | steroid hormone receptor activity | MF |
| GO:0005634 | nucleus | CC |
| GO:0003677 | DNA binding | MF |
| 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
- This transcript has been annotated with K14030 (nuclear receptor subfamily 2 group B member 4)
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.
