General information for g1348.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Signal transducer and activator of transcription 5B.
Parent gene
- The parent gene g1348 is located on chr_3: 9967579..9970724 (+ 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_3 | g1348 | g1348.t1 | TSS | g1348.t1 | 9967510 | 9967510 |
| chr_3 | g1348 | g1348.t1 | isoform | g1348.t1 | 9967579 | 9970724 |
| chr_3 | g1348 | g1348.t1 | exon | g1348.t1.exon1 | 9967579 | 9967706 |
| chr_3 | g1348 | g1348.t1 | cds | g1348.t1.CDS1 | 9967579 | 9967706 |
| chr_3 | g1348 | g1348.t1 | exon | g1348.t1.exon2 | 9967797 | 9968422 |
| chr_3 | g1348 | g1348.t1 | cds | g1348.t1.CDS2 | 9967797 | 9968422 |
| chr_3 | g1348 | g1348.t1 | exon | g1348.t1.exon3 | 9968489 | 9968747 |
| chr_3 | g1348 | g1348.t1 | cds | g1348.t1.CDS3 | 9968489 | 9968747 |
| chr_3 | g1348 | g1348.t1 | exon | g1348.t1.exon4 | 9968961 | 9969024 |
| chr_3 | g1348 | g1348.t1 | cds | g1348.t1.CDS4 | 9968961 | 9969024 |
| chr_3 | g1348 | g1348.t1 | exon | g1348.t1.exon5 | 9969196 | 9969964 |
| chr_3 | g1348 | g1348.t1 | cds | g1348.t1.CDS5 | 9969196 | 9969964 |
| chr_3 | g1348 | g1348.t1 | exon | g1348.t1.exon6 | 9970278 | 9970575 |
| chr_3 | g1348 | g1348.t1 | cds | g1348.t1.CDS6 | 9970278 | 9970575 |
| chr_3 | g1348 | g1348.t1 | exon | g1348.t1.exon7 | 9970637 | 9970724 |
| chr_3 | g1348 | g1348.t1 | cds | g1348.t1.CDS7 | 9970637 | 9970724 |
| chr_3 | g1348 | g1348.t1 | TTS | g1348.t1 | 9970987 | 9970987 |
Sequences
>g1348.t1 Gene=g1348 Length=2232
ATGTCTCTGTGGAATCAACTTGTGCAGTTGCAGCCATCAGTGATTAATCATTTAACCGCA
AATTATGGTGATCATTTTCCGATAGAAATTCGCCAATATTTAGCTGAATGGCTTGAAAAT
CGATTAATAAAAACTGTGCCTGAAAATGAACAATCAGTCGAGTGTTTGATATTTTTTGAG
GAGTTTCTTCAACAATTGCAAAAAAAGGCTTCAGAAATGGACAATATTGCTATCAGTTTT
CGTTTATCTGAAGCAGCTCGAAATATTGGTCAAACTTACGCATCTGATAAACTTCAATTG
TATAAACGTCTTCGTCAAAATCTTCAATATGAGGAAAATTTATTACGAAATCCACGAGTA
TATTTGAGAAGAGATATTAATAGGGAAGAATATAATGAACTTTCACAAGTACTCGAAACA
TTGATATTAAAAACTCGCGAAATTGAAAATGAAAATCGTGCATTGAAAAATGGTTATGAG
AGATTCTACCTTCAGTATTATAAAGTTGCAAAGAAGAACAGGCAATATGAAATTTGGATT
TCTCAACAACCTGAAAATAGAACTGAAATTGAAGCACGAAGAAATGAACATAATGAAAGT
GTGCAGCAATTATTAAATTTTTTGAAGCATAAGAAGTTGAGTTTAATTGATAAATTAAAA
ATTGTGATTGCGGAAACTGATGGTGTCCAAAATACAGTTTTAGAAAAATATTTACATGAG
TGGTTATTGAGTCAAAGGTCAATTGCTATGGGAGGTTTTATAAAAACATCAATCAGACTT
GAAACTATTCAAAAATGGTGTGAATACTTAGCAGAAATTCTTTGGACCGTTCGCGAACAA
GTTAAAATTTTGCGAAATTCAAGTCAACAGATGTTTCAAGTTTATAACGATCAAATTTTA
TGTGATACTTTGCATGAAATTTTTGAAACTGTTACAAAGTTAGTGGAGAAACTGATAATA
CGATCTTTTATAATTGAAAAGCAACCACCACAAGTAATTGGAACAAGGAAAAAGTTTGAA
TCAACTGTTCGTCTTTTAATTGGCAATAAATTAAACATTAACATGTTTAATCCACAGGTT
ACAGCAAAAATTATATCTGAGAAGCAAGCAAGAGAAATTCGTATAACAAATCAATGTTAT
GAAGGTTGTGAAACAATTATCAACAATACCGGCTACATGGAATATTCTGAAACATTAAAA
CAAATGTCTTTAAGCTTTAATAACATGATACTTCCTATTATGAAAAAAGAAATGTGTAAA
ATAAGGAAAGAAAGAACTGGAATGGAAAGTGTTTCTGATAAGAAGTTTGCATTGTTATTT
CAATCAACATTTTCAACTGGTGATATGAGTTTTAATGTCTGGGCTATTTCCTTACCAATC
GTGGTTACTTCACATACAAATCAAAAACCAGAAGCTTTGGCAACGATTACATGGGATAAT
GCTTTCTCAGAAATCAATCGTGAACCATTTGTTGTACCTGAAAAAGTACCAGTTACTCGT
TTTGCAGAAGCTTTGAATGTCATATTTCGCTCAAAAACTGATCGCAACTTGACTGATGAA
AATTTGCACTTTTTGTGTGAAAAAGTAACAAGAATGAAATTACCAATGCCACTTCCTGAC
GATGTTGAAGTTTCTTGGCAGATGTTTTGTAAAGATCCTCTACCAAATCGGGCTTTTAAT
TTTTGGACATGGTTTTACGAAACAATGGAATTGACAAAAAGTTTCCTTTCTGGTCCTTGG
AAAGATGGATTAATTATGGGTTTTGTCGAAAGAGAATCAGTTGAAAGGAAGCTTCTTCAT
TGTCAGAATGGCACGTTTCTACTTAGATTCGCAGAAAGTGAATTAGGTGGTGTAACAATT
GCTGTTGTTCAAAATAATTTTGTTACACACATTGAGCCGTTCACAGAGACTGTGTTGAAA
ATTCGCAGTTTGGCTGATGCAGTGCGTGATATTGAAGGCTTGACTTATCTTTATCCATGT
AAACCGATTAATGAAGCATTTAAAAGTCATATCACACCCAAATCATCAGCTATAAAAGGG
CCATATGTAAAAAGTGAATTACGAATGTCAGTTCCTGCAACATCGACGGCTGCTAACAAT
CAAATTACAGATGATACTTTTACAATTTATGATGATCAACAATTTTATTCAAATTGTTCT
AATTTTTTGCCAAACTTTACCTCATCATTTTCGCCTACCTCAAGTTACCAAGTTTTTACT
TCAAGTTGTTGA
>g1348.t1 Gene=g1348 Length=743
MSLWNQLVQLQPSVINHLTANYGDHFPIEIRQYLAEWLENRLIKTVPENEQSVECLIFFE
EFLQQLQKKASEMDNIAISFRLSEAARNIGQTYASDKLQLYKRLRQNLQYEENLLRNPRV
YLRRDINREEYNELSQVLETLILKTREIENENRALKNGYERFYLQYYKVAKKNRQYEIWI
SQQPENRTEIEARRNEHNESVQQLLNFLKHKKLSLIDKLKIVIAETDGVQNTVLEKYLHE
WLLSQRSIAMGGFIKTSIRLETIQKWCEYLAEILWTVREQVKILRNSSQQMFQVYNDQIL
CDTLHEIFETVTKLVEKLIIRSFIIEKQPPQVIGTRKKFESTVRLLIGNKLNINMFNPQV
TAKIISEKQAREIRITNQCYEGCETIINNTGYMEYSETLKQMSLSFNNMILPIMKKEMCK
IRKERTGMESVSDKKFALLFQSTFSTGDMSFNVWAISLPIVVTSHTNQKPEALATITWDN
AFSEINREPFVVPEKVPVTRFAEALNVIFRSKTDRNLTDENLHFLCEKVTRMKLPMPLPD
DVEVSWQMFCKDPLPNRAFNFWTWFYETMELTKSFLSGPWKDGLIMGFVERESVERKLLH
CQNGTFLLRFAESELGGVTIAVVQNNFVTHIEPFTETVLKIRSLADAVRDIEGLTYLYPC
KPINEAFKSHITPKSSAIKGPYVKSELRMSVPATSTAANNQITDDTFTIYDDQQFYSNCS
NFLPNFTSSFSPTSSYQVFTSSC
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 17 | g1348.t1 | CDD | cd09919 | SH2_STAT_family | 564 | 673 | 2.35626E-38 |
| 16 | g1348.t1 | Coils | Coil | Coil | 131 | 151 | - |
| 12 | g1348.t1 | Gene3D | G3DSA:1.10.532.10 | Transcription Factor | 1 | 120 | 4.3E-25 |
| 13 | g1348.t1 | Gene3D | G3DSA:1.20.1050.20 | - | 121 | 323 | 4.4E-31 |
| 11 | g1348.t1 | Gene3D | G3DSA:2.60.40.630 | - | 324 | 465 | 1.0E-40 |
| 14 | g1348.t1 | Gene3D | G3DSA:1.10.238.10 | - | 466 | 586 | 2.0E-37 |
| 15 | g1348.t1 | Gene3D | G3DSA:3.30.505.10 | SHC Adaptor Protein | 587 | 668 | 4.4E-24 |
| 5 | g1348.t1 | PANTHER | PTHR11801 | SIGNAL TRANSDUCER AND ACTIVATOR OF TRANSCRIPTION | 1 | 713 | 4.4E-127 |
| 6 | g1348.t1 | PANTHER | PTHR11801:SF39 | SIGNAL TRANSDUCER AND ACTIVATOR OF TRANSCRIPTION 5B | 1 | 713 | 4.4E-127 |
| 1 | g1348.t1 | Pfam | PF02865 | STAT protein, protein interaction domain | 2 | 117 | 1.8E-23 |
| 3 | g1348.t1 | Pfam | PF01017 | STAT protein, all-alpha domain | 132 | 314 | 1.2E-26 |
| 4 | g1348.t1 | Pfam | PF02864 | STAT protein, DNA binding domain | 327 | 463 | 1.8E-35 |
| 2 | g1348.t1 | Pfam | PF00017 | SH2 domain | 585 | 638 | 8.7E-9 |
| 19 | g1348.t1 | ProSiteProfiles | PS50001 | Src homology 2 (SH2) domain profile. | 580 | 631 | 9.989 |
| 18 | g1348.t1 | SMART | SM00964 | STAT_int_2 | 2 | 121 | 2.3E-17 |
| 9 | g1348.t1 | SUPERFAMILY | SSF48092 | Transcription factor STAT-4 N-domain | 1 | 116 | 2.62E-21 |
| 7 | g1348.t1 | SUPERFAMILY | SSF47655 | STAT | 129 | 323 | 2.75E-26 |
| 10 | g1348.t1 | SUPERFAMILY | SSF49417 | p53-like transcription factors | 320 | 574 | 5.72E-69 |
| 8 | g1348.t1 | SUPERFAMILY | SSF55550 | SH2 domain | 577 | 685 | 3.37E-23 |
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:0042025 | host cell nucleus | CC |
| GO:0003677 | DNA binding | MF |
| GO:0007165 | signal transduction | BP |
| GO:0006355 | regulation of transcription, DNA-templated | BP |
| GO:0003700 | DNA-binding transcription factor 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. There were no conditions that were differentially expressed