Gene loci information

Transcript annotation

  • This transcript has been annotated as Signal transducer and transcription activator.

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_2 g8992 g8992.t14 isoform g8992.t14 34414010 34418852
chr_2 g8992 g8992.t14 exon g8992.t14.exon1 34414010 34414656
chr_2 g8992 g8992.t14 cds g8992.t14.CDS1 34414047 34414656
chr_2 g8992 g8992.t14 exon g8992.t14.exon2 34414728 34415067
chr_2 g8992 g8992.t14 cds g8992.t14.CDS2 34414728 34415067
chr_2 g8992 g8992.t14 exon g8992.t14.exon3 34418266 34418852
chr_2 g8992 g8992.t14 cds g8992.t14.CDS3 34418266 34418374
chr_2 g8992 g8992.t14 TTS g8992.t14 34418829 34418829
chr_2 g8992 g8992.t14 TSS g8992.t14 NA NA

Sequences

>g8992.t14 Gene=g8992 Length=1574
TGAAACAACAAAGCAACTGTCAGTCAGTTTTCGTAACATGCAATTGAAGAAAATTAAGAG
AGCTGAAAAGAAAGGTACAGAGAGTGTGATGGATGAGAAGTTTGCATTGCTCTTCCAGTC
AAGCTTTGCCATTGGCCATGGTGATTTGGTATTTAGTGTTTGGGCACTTTCATTGCCTGT
TGTTGTTATTGTGCATGGCAATCAGGAACCACAGTCATGGGCCACAATCACATGGGATAA
TGCATTTGCCGAAATCAATCGTCAGCCATTCGCAGTGCCCGAAAAAGTGCCATGGAATCG
TTTAGCTGAGGCACTTAATATGAAATTCCGCGCATCAACTGGTCGCACACTAACACCAGA
AAATTTGCATTTTTTGGCTGAGAAAGCTTTTAAATTACAAGTTCCAATGCCGCCCACAGA
CGATTATCAAATCACTTGGTCACAATTCTGTAAAGAACCTTTGCCAGATCGCACATTCAC
TTTCTGGGAATGGTTTTATGCTGCAATGAAATTGACACGTGAACATTTGCGTGGACCTTG
GAATGATGGCTCAATTGTTGGTTTTATTCACAAACGCACAGCTGAAGATCAATTATTCAA
GTGTCAACGCGGAACTTTCTTGCTGCGATTCTCTGACAGCGAGTTAGGAGGCATAACAAT
TGCTTGGGTAAATGAAGGCAATGATGGAAATCCATGTGTGCTTCATATTCAGCCCTTCAC
AGCCAAGGACTTTGCAACACGCTCGTTATCAGATCGTATTCGTGATTTTGATGATCTAAC
AATTTTATATCCGAACAAGGCGAAGAATGAAGCTTTCGATAAATATACGACACCATCTGG
TCAACCTAAGAATAAGGATTACATCCCATCTGAAATTCGCGCCATTCTTTCGACATCAAA
TTCGAGCAATCTGTCATACGCCAACACACCGGCATCATTTATGCAGTCACCGGATCCATC
ACGTGACACGCCTTCTGTTCAGAGCGGTTATGGAATGGACGACGGTCAAATGAATCACAT
GAATCAGATACCAGGAATGGAGAACTTTGATCTTTCACTCGAGAACATTGACATGTACAC
TAGTTCATTTAATTAAATTAAAAGAGTTTATAATTGTGCATGTTTTTGTATGTGATTCGA
CAGCTAAAAACGGGATTCTTCCAACAAAATAATGAAAACCAAAATAACTTTCGACAAATG
ATTACAAAATTTTTATTTTTTTTATATGTTAATTTTTTTATTAAGTATATATAAATGAAA
AAGAGATGAAATCAAAAAAACAATTGAAAATTATAACGCCATGAATGTGTTTTGCATTGA
AAAAAAAATTAATTCTTCATTTTTGCAATATTAATAGATTTTTTTTTATTTGAGAGAAAA
ATTTTATTAGAGATTAGTTTTTACTCCTTCTTCCCTACTTAATTAAATTCCTTTGATGTA
ATCAATAATAAATATGTATGAATATTAATTGTAGTTCAGTGTCTTATCTATTTTTAGGCT
TTTAATTCTTTTTCTACTTCTTCTTCTACGCACACAATAAATAGCAAGATTAAAAAATTT
GTTTTTTGCATTTT

>g8992.t14 Gene=g8992 Length=352
MQLKKIKRAEKKGTESVMDEKFALLFQSSFAIGHGDLVFSVWALSLPVVVIVHGNQEPQS
WATITWDNAFAEINRQPFAVPEKVPWNRLAEALNMKFRASTGRTLTPENLHFLAEKAFKL
QVPMPPTDDYQITWSQFCKEPLPDRTFTFWEWFYAAMKLTREHLRGPWNDGSIVGFIHKR
TAEDQLFKCQRGTFLLRFSDSELGGITIAWVNEGNDGNPCVLHIQPFTAKDFATRSLSDR
IRDFDDLTILYPNKAKNEAFDKYTTPSGQPKNKDYIPSEIRAILSTSNSSNLSYANTPAS
FMQSPDPSRDTPSVQSGYGMDDGQMNHMNQIPGMENFDLSLENIDMYTSSFN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
16 g8992.t14 CDD cd09919 SH2_STAT_family 152 266 1.2284E-59
7 g8992.t14 Gene3D G3DSA:2.60.40.630 - 1 53 8.3E-22
8 g8992.t14 Gene3D G3DSA:1.10.238.10 - 54 172 6.6E-48
9 g8992.t14 Gene3D G3DSA:3.30.505.10 SHC Adaptor Protein 177 283 7.2E-34
3 g8992.t14 PANTHER PTHR11801 SIGNAL TRANSDUCER AND ACTIVATOR OF TRANSCRIPTION 1 306 2.2E-98
4 g8992.t14 PANTHER PTHR11801:SF48 SIGNAL TRANSDUCER AND ACTIVATOR OF TRANSCRIPTION 6 1 306 2.2E-98
2 g8992.t14 Pfam PF02864 STAT protein, DNA binding domain 1 51 1.0E-15
1 g8992.t14 Pfam PF00017 SH2 domain 174 247 2.1E-9
12 g8992.t14 Phobius SIGNAL_PEPTIDE Signal peptide region 1 43 -
13 g8992.t14 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 21 -
14 g8992.t14 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 22 32 -
15 g8992.t14 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 33 43 -
11 g8992.t14 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 44 352 -
10 g8992.t14 ProSiteProfiles PS50001 Src homology 2 (SH2) domain profile. 168 267 11.161
6 g8992.t14 SUPERFAMILY SSF49417 p53-like transcription factors 1 163 4.8E-63
5 g8992.t14 SUPERFAMILY SSF55550 SH2 domain 164 272 6.73E-35

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.

Raw TPM values