General information for g8992.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Signal transducer and activator of transcription 5A.
Parent gene
- The parent gene g8992 is located on chr_2: 34418374..34420073 (+ 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_2 | g8992 | g8992.t1 | TSS | g8992.t1 | 34411271 | 34411271 |
| chr_2 | g8992 | g8992.t1 | isoform | g8992.t1 | 34412312 | 34418374 |
| chr_2 | g8992 | g8992.t1 | exon | g8992.t1.exon1 | 34412312 | 34412439 |
| chr_2 | g8992 | g8992.t1 | cds | g8992.t1.CDS1 | 34412312 | 34412439 |
| chr_2 | g8992 | g8992.t1 | exon | g8992.t1.exon2 | 34412556 | 34413196 |
| chr_2 | g8992 | g8992.t1 | cds | g8992.t1.CDS2 | 34412556 | 34413196 |
| chr_2 | g8992 | g8992.t1 | exon | g8992.t1.exon3 | 34413276 | 34413528 |
| chr_2 | g8992 | g8992.t1 | cds | g8992.t1.CDS3 | 34413276 | 34413528 |
| chr_2 | g8992 | g8992.t1 | exon | g8992.t1.exon4 | 34413833 | 34414656 |
| chr_2 | g8992 | g8992.t1 | cds | g8992.t1.CDS4 | 34413833 | 34414656 |
| chr_2 | g8992 | g8992.t1 | exon | g8992.t1.exon5 | 34414728 | 34415067 |
| chr_2 | g8992 | g8992.t1 | cds | g8992.t1.CDS5 | 34414728 | 34415067 |
| chr_2 | g8992 | g8992.t1 | exon | g8992.t1.exon6 | 34418266 | 34418374 |
| chr_2 | g8992 | g8992.t1 | cds | g8992.t1.CDS6 | 34418266 | 34418374 |
| chr_2 | g8992 | g8992.t1 | TTS | g8992.t1 | 34418829 | 34418829 |
Sequences
>g8992.t1 Gene=g8992 Length=2295
ATGGCTTTGTGGAACAAGTTGCTGCAATCGCGGCCTGAAGTGATGGAGCAAATTCGTGTA
TCCTATGGAAACCATTTCCCCATGGAAGTTCGTCATTACCTATGCGATTGGCTTGAATCG
AGACTACTTTCCGGTCCAATGGTTTTAGATCATGATCCACAGTTGGAAATTGAATCTGCA
CGCTTTCTTAATGAACTACTTATTGAACTTGAAAGAAAAGCTAACGAAATGAGTTCAGAT
GAGCTAATTACCGCGAAATTACGTTTATTAGAATCAGCGAAAAATTTCCGTCAATTATTT
TCACACAATCCGAGTCAGCTGTATTCACATCTTCGTAATTGTCTGATGTTTGAAAAAAAT
ATGCTCTGTTATCCTGAGGAATGTGGTGTTACACAAAACAGTGAGTTTACGCAAATTTTT
CAAGCCCTTGAGGAACTTGTTTCACGTATTCGCGCCAATGAGAATGAAAATCGTAATTTG
AAGAAGCGTTATGAGATTTTCTGCTGTGAACTGCATGAAGTTACCAAAAACAATGCACAA
TATGATATACTTGATACTCAAAATCCTGAACATCGTGAAAGAATTGCACAATTGAGACGT
GAATCACAAGAGAAATTGCAATTGTCATTAAATCAACTGACTGGAATGCGATTGAATCTT
GTTGATAAATTTAAGGCAACAATCGAGCTTAGTGAGACTGTACAACAGAAAGTTATCGAC
AAGTACTTAAATCAATGGCGTATGAATCAAGGATTAGCTGGTAATGGAGCACCACCGTCA
AATGCCAATAATCTCGACATCATTCAAGGCTGGTGTGAACATCTTGCTGACATTTTATGG
AATACACGCGAGCAAATTAAAATGGTCTCTAAATATCGCAAACAAGTGAATGTTGATGAG
CAAAGTTTACCAGACTTTTTGCCCGAACTTTTTGCTAAAGTCACTGGTCTACTTGAACAT
TTGATTACACGTTCGTTTATCATTGAAAAACAACCACCGCAAGTTATGAAAACAAATACA
AGATTCGCATCAACAGTTCGTTTATTAATTGGAAATACTTTGAATATTAAAATGAATAGT
CCACTAGTAAAGGTAACAATCGTATCGGAACAACAGGCACAACAAACACAGCAGACAAAT
AAATGCTCAGAGCACACGTGTGGTGAAATCCTAAATAGCACTGGAAATATGGAATATAAT
GAAACAACAAAGCAACTGTCAGTCAGTTTTCGTAACATGCAATTGAAGAAAATTAAGAGA
GCTGAAAAGAAAGGTACAGAGAGTGTGATGGATGAGAAGTTTGCATTGCTCTTCCAGTCA
AGCTTTGCCATTGGCCATGGTGATTTGGTATTTAGTGTTTGGGCACTTTCATTGCCTGTT
GTTGTTATTGTGCATGGCAATCAGGAACCACAGTCATGGGCCACAATCACATGGGATAAT
GCATTTGCCGAAATCAATCGTCAGCCATTCGCAGTGCCCGAAAAAGTGCCATGGAATCGT
TTAGCTGAGGCACTTAATATGAAATTCCGCGCATCAACTGGTCGCACACTAACACCAGAA
AATTTGCATTTTTTGGCTGAGAAAGCTTTTAAATTACAAGTTCCAATGCCGCCCACAGAC
GATTATCAAATCACTTGGTCACAATTCTGTAAAGAACCTTTGCCAGATCGCACATTCACT
TTCTGGGAATGGTTTTATGCTGCAATGAAATTGACACGTGAACATTTGCGTGGACCTTGG
AATGATGGCTCAATTGTTGGTTTTATTCACAAACGCACAGCTGAAGATCAATTATTCAAG
TGTCAACGCGGAACTTTCTTGCTGCGATTCTCTGACAGCGAGTTAGGAGGCATAACAATT
GCTTGGGTAAATGAAGGCAATGATGGAAATCCATGTGTGCTTCATATTCAGCCCTTCACA
GCCAAGGACTTTGCAACACGCTCGTTATCAGATCGTATTCGTGATTTTGATGATCTAACA
ATTTTATATCCGAACAAGGCGAAGAATGAAGCTTTCGATAAATATACGACACCATCTGGT
CAACCTAAGAATAAGGATTACATCCCATCTGAAATTCGCGCCATTCTTTCGACATCAAAT
TCGAGCAATCTGTCATACGCCAACACACCGGCATCATTTATGCAGTCACCGGATCCATCA
CGTGACACGCCTTCTGTTCAGAGCGGTTATGGAATGGACGACGGTCAAATGAATCACATG
AATCAGATACCAGGAATGGAGAACTTTGATCTTTCACTCGAGAACATTGACATGTACACT
AGTTCATTTAATTAA
>g8992.t1 Gene=g8992 Length=764
MALWNKLLQSRPEVMEQIRVSYGNHFPMEVRHYLCDWLESRLLSGPMVLDHDPQLEIESA
RFLNELLIELERKANEMSSDELITAKLRLLESAKNFRQLFSHNPSQLYSHLRNCLMFEKN
MLCYPEECGVTQNSEFTQIFQALEELVSRIRANENENRNLKKRYEIFCCELHEVTKNNAQ
YDILDTQNPEHRERIAQLRRESQEKLQLSLNQLTGMRLNLVDKFKATIELSETVQQKVID
KYLNQWRMNQGLAGNGAPPSNANNLDIIQGWCEHLADILWNTREQIKMVSKYRKQVNVDE
QSLPDFLPELFAKVTGLLEHLITRSFIIEKQPPQVMKTNTRFASTVRLLIGNTLNIKMNS
PLVKVTIVSEQQAQQTQQTNKCSEHTCGEILNSTGNMEYNETTKQLSVSFRNMQLKKIKR
AEKKGTESVMDEKFALLFQSSFAIGHGDLVFSVWALSLPVVVIVHGNQEPQSWATITWDN
AFAEINRQPFAVPEKVPWNRLAEALNMKFRASTGRTLTPENLHFLAEKAFKLQVPMPPTD
DYQITWSQFCKEPLPDRTFTFWEWFYAAMKLTREHLRGPWNDGSIVGFIHKRTAEDQLFK
CQRGTFLLRFSDSELGGITIAWVNEGNDGNPCVLHIQPFTAKDFATRSLSDRIRDFDDLT
ILYPNKAKNEAFDKYTTPSGQPKNKDYIPSEIRAILSTSNSSNLSYANTPASFMQSPDPS
RDTPSVQSGYGMDDGQMNHMNQIPGMENFDLSLENIDMYTSSFN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 20 | g8992.t1 | CDD | cd16855 | STAT5_CCD | 134 | 323 | 1.24312E-49 |
| 19 | g8992.t1 | CDD | cd09919 | SH2_STAT_family | 564 | 678 | 5.30724E-57 |
| 17 | g8992.t1 | Coils | Coil | Coil | 60 | 80 | - |
| 18 | g8992.t1 | Coils | Coil | Coil | 143 | 163 | - |
| 16 | g8992.t1 | Coils | Coil | Coil | 181 | 201 | - |
| 12 | g8992.t1 | Gene3D | G3DSA:1.10.532.10 | Transcription Factor | 1 | 130 | 1.9E-32 |
| 13 | g8992.t1 | Gene3D | G3DSA:1.20.1050.20 | - | 131 | 326 | 4.3E-50 |
| 11 | g8992.t1 | Gene3D | G3DSA:2.60.40.630 | - | 327 | 465 | 1.8E-60 |
| 14 | g8992.t1 | Gene3D | G3DSA:1.10.238.10 | - | 466 | 584 | 2.6E-47 |
| 15 | g8992.t1 | Gene3D | G3DSA:3.30.505.10 | SHC Adaptor Protein | 589 | 695 | 2.6E-33 |
| 5 | g8992.t1 | PANTHER | PTHR11801 | SIGNAL TRANSDUCER AND ACTIVATOR OF TRANSCRIPTION | 1 | 720 | 1.5E-176 |
| 6 | g8992.t1 | PANTHER | PTHR11801:SF39 | SIGNAL TRANSDUCER AND ACTIVATOR OF TRANSCRIPTION 5B | 1 | 720 | 1.5E-176 |
| 1 | g8992.t1 | Pfam | PF02865 | STAT protein, protein interaction domain | 2 | 123 | 1.1E-27 |
| 3 | g8992.t1 | Pfam | PF01017 | STAT protein, all-alpha domain | 138 | 318 | 6.5E-38 |
| 4 | g8992.t1 | Pfam | PF02864 | STAT protein, DNA binding domain | 330 | 463 | 6.7E-49 |
| 2 | g8992.t1 | Pfam | PF00017 | SH2 domain | 586 | 659 | 7.1E-9 |
| 22 | g8992.t1 | ProSiteProfiles | PS50001 | Src homology 2 (SH2) domain profile. | 580 | 679 | 11.161 |
| 21 | g8992.t1 | SMART | SM00964 | STAT_int_2 | 2 | 128 | 3.5E-28 |
| 9 | g8992.t1 | SUPERFAMILY | SSF48092 | Transcription factor STAT-4 N-domain | 1 | 125 | 8.5E-24 |
| 7 | g8992.t1 | SUPERFAMILY | SSF47655 | STAT | 134 | 326 | 7.06E-40 |
| 10 | g8992.t1 | SUPERFAMILY | SSF49417 | p53-like transcription factors | 321 | 575 | 7.7E-91 |
| 8 | g8992.t1 | SUPERFAMILY | SSF55550 | SH2 domain | 576 | 684 | 2.56E-34 |
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 transcript has been annotated with K11224 (signal transducer and activator of transcription 5B)
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.
