General information for g1345.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Paired box pox-meso protein.
Parent gene
- The parent gene g1345 is located on chr_3: 9946997..9956589 (- 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 | g1345 | g1345.t1 | TTS | g1345.t1 | 9946309 | 9946309 |
| chr_3 | g1345 | g1345.t1 | isoform | g1345.t1 | 9946997 | 9956589 |
| chr_3 | g1345 | g1345.t1 | exon | g1345.t1.exon1 | 9946997 | 9947520 |
| chr_3 | g1345 | g1345.t1 | cds | g1345.t1.CDS1 | 9946997 | 9947520 |
| chr_3 | g1345 | g1345.t1 | exon | g1345.t1.exon2 | 9947581 | 9947676 |
| chr_3 | g1345 | g1345.t1 | cds | g1345.t1.CDS2 | 9947581 | 9947676 |
| chr_3 | g1345 | g1345.t1 | exon | g1345.t1.exon3 | 9947754 | 9947892 |
| chr_3 | g1345 | g1345.t1 | cds | g1345.t1.CDS3 | 9947754 | 9947892 |
| chr_3 | g1345 | g1345.t1 | exon | g1345.t1.exon4 | 9947983 | 9948044 |
| chr_3 | g1345 | g1345.t1 | cds | g1345.t1.CDS4 | 9947983 | 9948044 |
| chr_3 | g1345 | g1345.t1 | exon | g1345.t1.exon5 | 9956577 | 9956589 |
| chr_3 | g1345 | g1345.t1 | cds | g1345.t1.CDS5 | 9956577 | 9956589 |
| chr_3 | g1345 | g1345.t1 | TSS | g1345.t1 | 9957227 | 9957227 |
Sequences
>g1345.t1 Gene=g1345 Length=834
ATGGACCCGTCAGTCACAGACAATCACGTTCAGCAATATGGCGAAGTCAATCAACTAGGA
GGAGTTTTTGTAAATGGCCGTCCATTACCAAATGGCACACGAATGAGAATTGTTGAATTA
GCAAGATTAGGCATTCGTCCATGTGATATTTCTAGACAATTGCGTGTCTCACATGGATGT
GTGTCAAAGATATTAGCGAGATATCATGAGACAGGATCGATTCTTCCTGGTGCTATTGGT
GGATCAAAACCACGTGTAACTACACCGAAGGTTGTCAATTATATAAGAGAATTAAAAATG
AAAGATCCAGGCATTTTTGCATGGGAAATTCGCGATAGATTGCTAGCGGATGGTGTTTGT
GATAAAAATAATGTTCCTAGCGTCAGTTCAATATCTAGAATTTTAAGAAATAAAGTGACC
AATCATCATCATCACAATACAGCAATTTCGCACGCGCATACACATCCGCACTTGTATAAT
TCAATTTATCCAACTTATCCGTACGCAACGCCGCCATCAATTAAAAGTGAAAATTCACCA
AACACATCTTCATCTTGCGGTAGTCCATCACCGCCCAATAATATTATGCGAAATTGTCAT
CATTGGCCTCCACTGTCACACTCTGCCGCACATATCACACATTCAGTGAATGACATTTTA
AATTTTAATCAAAAATTCGTACAACCTCAAACGTCACCACAATTAGCAGCATCATCGCCC
ATGATGAATACACATGACACACAAAATTCGCATTCACAAAATTACAACTACTACATGTAC
TTTCAAAACACAGCAATGCATAGCAATGGAATCTCAACTGGAGCCAATTTATAA
>g1345.t1 Gene=g1345 Length=277
MDPSVTDNHVQQYGEVNQLGGVFVNGRPLPNGTRMRIVELARLGIRPCDISRQLRVSHGC
VSKILARYHETGSILPGAIGGSKPRVTTPKVVNYIRELKMKDPGIFAWEIRDRLLADGVC
DKNNVPSVSSISRILRNKVTNHHHHNTAISHAHTHPHLYNSIYPTYPYATPPSIKSENSP
NTSSSCGSPSPPNNIMRNCHHWPPLSHSAAHITHSVNDILNFNQKFVQPQTSPQLAASSP
MMNTHDTQNSHSQNYNYYMYFQNTAMHSNGISTGANL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g1345.t1 | CDD | cd00131 | PAX | 13 | 138 | 3.21257E-83 |
| 9 | g1345.t1 | Gene3D | G3DSA:1.10.10.10 | winged helix repressor DNA binding domain | 5 | 80 | 1.5E-37 |
| 10 | g1345.t1 | Gene3D | G3DSA:1.10.10.10 | winged helix repressor DNA binding domain | 81 | 160 | 7.3E-35 |
| 2 | g1345.t1 | PANTHER | PTHR45636 | PAIRED BOX PROTEIN PAX-6-RELATED-RELATED | 7 | 258 | 4.4E-113 |
| 3 | g1345.t1 | PANTHER | PTHR45636:SF16 | PAIRED BOX POX-MESO PROTEIN | 7 | 258 | 4.4E-113 |
| 6 | g1345.t1 | PRINTS | PR00027 | Paired box signature | 16 | 31 | 1.4E-40 |
| 5 | g1345.t1 | PRINTS | PR00027 | Paired box signature | 34 | 52 | 1.4E-40 |
| 7 | g1345.t1 | PRINTS | PR00027 | Paired box signature | 54 | 71 | 1.4E-40 |
| 4 | g1345.t1 | PRINTS | PR00027 | Paired box signature | 72 | 89 | 1.4E-40 |
| 1 | g1345.t1 | Pfam | PF00292 | ‘Paired box’ domain | 14 | 136 | 7.8E-66 |
| 12 | g1345.t1 | ProSitePatterns | PS00034 | Paired DNA-binding domain signature. | 46 | 62 | - |
| 14 | g1345.t1 | ProSiteProfiles | PS51057 | Paired DNA-binding domain profile. | 12 | 138 | 62.015 |
| 13 | g1345.t1 | SMART | SM00351 | pax3 | 12 | 136 | 3.0E-87 |
| 8 | g1345.t1 | SUPERFAMILY | SSF46689 | Homeodomain-like | 15 | 137 | 3.58E-38 |
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:0003677 | DNA binding | MF |
| GO:0006355 | regulation of transcription, DNA-templated | BP |
KEGG
Orthology
- This transcript has been annotated with K09382 (paired box protein 1/9)
Pathway
This gene does not belong to any 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.
