General information for g10390.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as GATA-binding factor A.
Parent gene
- The parent gene g10390 is located on chr_1: 9486973..9488522 (- 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 | g10390 | g10390.t1 | TTS | g10390.t1 | 9486353 | 9486353 |
| chr_1 | g10390 | g10390.t1 | isoform | g10390.t1 | 9486973 | 9488522 |
| chr_1 | g10390 | g10390.t1 | exon | g10390.t1.exon1 | 9486973 | 9487833 |
| chr_1 | g10390 | g10390.t1 | cds | g10390.t1.CDS1 | 9486973 | 9487833 |
| chr_1 | g10390 | g10390.t1 | exon | g10390.t1.exon2 | 9487899 | 9488071 |
| chr_1 | g10390 | g10390.t1 | cds | g10390.t1.CDS2 | 9487899 | 9488071 |
| chr_1 | g10390 | g10390.t1 | exon | g10390.t1.exon3 | 9488163 | 9488255 |
| chr_1 | g10390 | g10390.t1 | cds | g10390.t1.CDS3 | 9488163 | 9488255 |
| chr_1 | g10390 | g10390.t1 | exon | g10390.t1.exon4 | 9488324 | 9488522 |
| chr_1 | g10390 | g10390.t1 | cds | g10390.t1.CDS4 | 9488324 | 9488522 |
| chr_1 | g10390 | g10390.t1 | TSS | g10390.t1 | NA | NA |
Sequences
>g10390.t1 Gene=g10390 Length=1326
ATGTTTCATTCCACACCATCATCGTACTCTGAAATGACCTCAGTAGCTAGCAATACTGCA
TCATTTCATCAAACAACAAACACGACGGCAAACACACCTGTCTACGTGCCATCAAATCGT
GCTATACATTCACAGTATGCCGGACATGCTGGTAATTACACAAATGCACAGAATGCGTGG
CCCACTGAAAGTGCCTTTGGTTCAACACATTCCCCATTTTACGCACAAAACATGATGTAC
ATGCGAGCCTACGATCCATCCGGATTTCAACGAACTTCACCATATGGAATGGAAAGTGCA
ATGGACTTTCAATTTGGCGAAGGTCGTGAATGTGTCAACTGCGGTGCAATAAGTACACCA
TTATGGCGTCGTGATGGAACTGGACACTATTTATGTAATGCTTGTGGACTTTATCATAAA
ATGAATGGCATGAATCGACCACTGATTAAACCCAGTAAAAGACTGCAAACAGCAACAAGA
CGATTGGGATTGTGTTGTACAAATTGTGGTACAAGAACAACAACATTATGGCGTAGAAAT
AATGAGGGTGAACCAGTATGTAATGCATGCGGTCTCTATTTTAAGTTGCATGGAATTAAT
CGACCACTTGCTATGCGAAAAGATGGAATTCAAACACGAAAAAGAAAGCCGAAGAAGGCT
GGAACAAGTGGACCAGAATTATTGGGACTTGTTAAGAAGGAAGACTTCCATCATCATCAT
GATGACTTGAAATCAACAAGTTTAACTGATCGTAATGGAAATGCAAAGTTATTATTGCCT
GGCAGTCCAAAATTACTTCAAAAAAGTCACATTTCACCAATTCACACGCACCATCATCAT
CCGCATCATCATCAATCATCTTATTCATTGACATCGCCAATGCAAAATGTAAACACACCA
TCTAAATTCGATTTACAGCCATCATCAAATACTGTGGCTGCTTCATCTACTGCTACTGCC
ATTTCATCAAGTGCATCATCACACAATAACACAAATAATAATCATTCATCAACAGTCTCA
TCGCATCTTTATACTTCACCGTTGATATCGTCAACACAGAGCAATTTGCATAGCTCGTAT
TTGCATAATAACAGCTTAACGAGTTCGTCATATGGCGCAATCAAGTCTGAATCCAACATT
CCCGGCATCACGAATCCAGCAAGCATGATAAGTGGAAATTATGACTATATGAGTAATTGC
ATACAGAATGGATATTTTGGAGGCACATTTGGTTTGCCCAATGGTACTGCACATCATACA
GATTTGAGTGGATATCATCATCAGCATAATGTTATACAAGCTGCAAAATTGATGGCAACA
TCTTAG
>g10390.t1 Gene=g10390 Length=441
MFHSTPSSYSEMTSVASNTASFHQTTNTTANTPVYVPSNRAIHSQYAGHAGNYTNAQNAW
PTESAFGSTHSPFYAQNMMYMRAYDPSGFQRTSPYGMESAMDFQFGEGRECVNCGAISTP
LWRRDGTGHYLCNACGLYHKMNGMNRPLIKPSKRLQTATRRLGLCCTNCGTRTTTLWRRN
NEGEPVCNACGLYFKLHGINRPLAMRKDGIQTRKRKPKKAGTSGPELLGLVKKEDFHHHH
DDLKSTSLTDRNGNAKLLLPGSPKLLQKSHISPIHTHHHHPHHHQSSYSLTSPMQNVNTP
SKFDLQPSSNTVAASSTATAISSSASSHNNTNNNHSSTVSSHLYTSPLISSTQSNLHSSY
LHNNSLTSSSYGAIKSESNIPGITNPASMISGNYDYMSNCIQNGYFGGTFGLPNGTAHHT
DLSGYHHQHNVIQAAKLMATS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 12 | g10390.t1 | CDD | cd00202 | ZnF_GATA | 110 | 154 | 5.18324E-18 |
| 11 | g10390.t1 | CDD | cd00202 | ZnF_GATA | 166 | 216 | 1.49527E-22 |
| 9 | g10390.t1 | Gene3D | G3DSA:3.30.50.10 | - | 101 | 159 | 2.2E-27 |
| 10 | g10390.t1 | Gene3D | G3DSA:3.30.50.10 | - | 160 | 216 | 4.8E-29 |
| 3 | g10390.t1 | PANTHER | PTHR10071:SF320 | PANNIER | 1 | 357 | 3.3E-133 |
| 4 | g10390.t1 | PANTHER | PTHR10071 | TRANSCRIPTION FACTOR GATA FAMILY MEMBER | 1 | 357 | 3.3E-133 |
| 6 | g10390.t1 | PRINTS | PR00619 | Transcription factor GATA zinc finger signature | 107 | 124 | 2.1E-15 |
| 5 | g10390.t1 | PRINTS | PR00619 | Transcription factor GATA zinc finger signature | 125 | 142 | 2.1E-15 |
| 2 | g10390.t1 | Pfam | PF00320 | GATA zinc finger | 111 | 143 | 3.3E-14 |
| 1 | g10390.t1 | Pfam | PF00320 | GATA zinc finger | 166 | 198 | 1.7E-14 |
| 13 | g10390.t1 | ProSitePatterns | PS00344 | GATA-type zinc finger domain. | 111 | 135 | - |
| 14 | g10390.t1 | ProSitePatterns | PS00344 | GATA-type zinc finger domain. | 166 | 190 | - |
| 18 | g10390.t1 | ProSiteProfiles | PS50114 | GATA-type zinc finger domain profile. | 105 | 160 | 27.853 |
| 17 | g10390.t1 | ProSiteProfiles | PS50114 | GATA-type zinc finger domain profile. | 160 | 213 | 28.209 |
| 15 | g10390.t1 | SMART | SM00401 | GATA_3 | 105 | 155 | 8.0E-19 |
| 16 | g10390.t1 | SMART | SM00401 | GATA_3 | 160 | 210 | 1.1E-22 |
| 7 | g10390.t1 | SUPERFAMILY | SSF57716 | Glucocorticoid receptor-like (DNA-binding domain) | 104 | 159 | 1.9E-16 |
| 8 | g10390.t1 | SUPERFAMILY | SSF57716 | Glucocorticoid receptor-like (DNA-binding domain) | 159 | 219 | 1.38E-17 |
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:0006357 | regulation of transcription by RNA polymerase II | BP |
| 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 K09183 (GATA-binding protein 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.
