General information for g2780.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Cytospin-A.
Parent gene
- The parent gene g2780 is located on chr_3: 20226015..20226517 (+ 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 | g2780 | g2780.t4 | isoform | g2780.t4 | 20224261 | 20226015 |
| chr_3 | g2780 | g2780.t4 | exon | g2780.t4.exon1 | 20224261 | 20224678 |
| chr_3 | g2780 | g2780.t4 | exon | g2780.t4.exon2 | 20225224 | 20225349 |
| chr_3 | g2780 | g2780.t4 | exon | g2780.t4.exon3 | 20225414 | 20225543 |
| chr_3 | g2780 | g2780.t4 | exon | g2780.t4.exon4 | 20225716 | 20225860 |
| chr_3 | g2780 | g2780.t4 | cds | g2780.t4.CDS1 | 20225744 | 20225860 |
| chr_3 | g2780 | g2780.t4 | exon | g2780.t4.exon5 | 20225920 | 20226015 |
| chr_3 | g2780 | g2780.t4 | cds | g2780.t4.CDS2 | 20225920 | 20226015 |
| chr_3 | g2780 | g2780.t4 | TTS | g2780.t4 | 20226544 | 20226544 |
| chr_3 | g2780 | g2780.t4 | TSS | g2780.t4 | NA | NA |
Sequences
>g2780.t4 Gene=g2780 Length=915
AGAAAACAAAAAAGTAACGGAAGTACAGTAAAAAATGGAACTAGCAATTCTATTGGCAGC
AACAACAACAATATCAACAACACCACTATCACAAATAACAGTAATAATGGTATTGTGGCA
AATTCAGTTTCTTATATAACGCGACAAGATTCACGATTGTCTGTAAAAAGTTTGATTGAG
AGCATCGAGAATACTTCAAAGCAGACCAAAGTTTCGTCGTCTGGATCACAATCGGGATCG
CAAACGAGTCTAAACAACTTGTCCGTTATAGAGCAGCAGCAGTGTGAAAAGTTAACAACA
AACATTGATGAAGAGAAGCAACAAAAGAATTTGAATAATAATTCCATCACGAGTAATCAC
AGCAATATTCTTACTACGTCAAATAATGTTAATTTGAATGGAACGCAAAAGAGTGGAGTG
GCAATTCCACAAAAGACTGATGATCATGATCAATTCTATTCATCGATTTTAACATCACAC
AAGCACGATTACAATTTAAACCACAAACACGATTATGTGAGACGAAACAGCTACGGTGAT
ATAAGCGAACGAAAAGATCCATTAAATGCACTAGTGAAGAATGGCGGGTCGAAACGAAAT
GCTTTACTCAAATGGTGTCAAAATAAAGTTGTTGGGTATCGAAATATCGACATAACCAAC
TTCAGTTCATCATGGAATGATGGTTTGGCTTTATGTGCTCTAATGCATTCATATTTACCT
GAAAAAATTCCATATGACGAACTTACACCACTTGACAAGAAGAAAAATTTTAGTTTAGCC
TTCGATGCTGCAGAAACAGTTGGAATTAAGACAACTTTGAATATCAATGAAATGTGTCAA
CAGGAAAGACCAGATTGGCAATCAATAATGTCATATGTGACACAAATTTACAAGCATTTT
GAGTCGCAGCCCTAA
>g2780.t4 Gene=g2780 Length=70
MHSYLPEKIPYDELTPLDKKKNFSLAFDAAETVGIKTTLNINEMCQQERPDWQSIMSYVT
QIYKHFESQP
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g2780.t4 | Gene3D | G3DSA:1.10.418.10 | - | 1 | 70 | 0.0000000 |
| 2 | g2780.t4 | PANTHER | PTHR23167 | CALPONIN HOMOLOGY DOMAIN-CONTAINING PROTEIN DDB_G0272472-RELATED | 1 | 66 | 0.0000000 |
| 3 | g2780.t4 | PANTHER | PTHR23167:SF18 | CYTOSPIN-A | 1 | 66 | 0.0000000 |
| 1 | g2780.t4 | Pfam | PF00307 | Calponin homology (CH) domain | 2 | 67 | 0.0000009 |
| 6 | g2780.t4 | ProSiteProfiles | PS50021 | Calponin homology (CH) domain profile. | 1 | 67 | 13.2580000 |
| 4 | g2780.t4 | SUPERFAMILY | SSF47576 | Calponin-homology domain, CH-domain | 1 | 66 | 0.0000000 |
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:0005515 | protein binding | 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.
