General information for g2402.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Afadin.
Parent gene
- The parent gene g2402 is located on chr_3: 17670253..17674280 (+ 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 | g2402 | g2402.t3 | isoform | g2402.t3 | 17670253 | 17671193 |
| chr_3 | g2402 | g2402.t3 | exon | g2402.t3.exon1 | 17670253 | 17670928 |
| chr_3 | g2402 | g2402.t3 | cds | g2402.t3.CDS1 | 17670287 | 17670928 |
| chr_3 | g2402 | g2402.t3 | exon | g2402.t3.exon2 | 17671030 | 17671193 |
| chr_3 | g2402 | g2402.t3 | cds | g2402.t3.CDS2 | 17671030 | 17671191 |
| chr_3 | g2402 | g2402.t3 | TSS | g2402.t3 | NA | NA |
| chr_3 | g2402 | g2402.t3 | TTS | g2402.t3 | NA | NA |
Sequences
>g2402.t3 Gene=g2402 Length=840
TCGTTCACAATCATTTGCAAAGCAGCCAGCAGGAATGTCTGCTGCAACACCAACAATGGA
ACCACAAGGACAGGAGGCGATTTTACCGGCAGTTCTTGAGTTTCCCGAGCATAGCCAGGA
ACAATTTTTAAAAGCTGTCATTACTGATCTCGATGTGAATGCTCCAAATTTTAAACTCGC
GCCCGTTTATACACTTTATTTGTGTGCGCGATATCGTGCCTCAACACATTACCGTCCCGA
CCTGCAGCCAACTGAACGTGCTCACAAATTGACTGTTTTTCTTCACCATGTGGCAAATCT
TATTCATAACATCATTCAAGAGAAATATAACGATCCAAAAATTCTCTCATTTTGGATGGC
CAACAGCAGCGAATTTTTGCATTTCCTAAAATCTGACCGACATATTTCGGCTTTCAGTGT
GCAAGCACAGGAAGTATTAGCCGAATGTGTACAAGCAGCTTTTCAAAATCTCGTATCGAT
TTTCCATTCAGAATTATCACAAACACTCAATCAATTTCTGTCGGAAAATATTGACCATGA
TTCGGCCGCTGGACTTGTGCTTTCAGTTCTTGGATCTGCGATGGCATTGCTGAGGAGATG
CCGTGTAAATGCAGCACTCACTATTCAGCTATTTTCGCAATTGTTCCATTATATAAATGT
TGTTTGTTTCAATAAGTTTGTCACAACATCACATTTATGTACGAATGTATGGGGAAAAGC
ATTAAGTGATAGACTAGCATTGCTAGAATTGTGGGCAGAAAAACAAGGACTTGAGCTTGC
AGCTGATTGTCATCTAGCCAAAATCAACCAGTGTGCCGAGTTTTTACAAGCACCAAAAAC
>g2402.t3 Gene=g2402 Length=268
MSAATPTMEPQGQEAILPAVLEFPEHSQEQFLKAVITDLDVNAPNFKLAPVYTLYLCARY
RASTHYRPDLQPTERAHKLTVFLHHVANLIHNIIQEKYNDPKILSFWMANSSEFLHFLKS
DRHISAFSVQAQEVLAECVQAAFQNLVSIFHSELSQTLNQFLSENIDHDSAAGLVLSVLG
SAMALLRRCRVNAALTIQLFSQLFHYINVVCFNKFVTTSHLCTNVWGKALSDRLALLELW
AEKQGLELAADCHLAKINQCAEFLQAPK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g2402.t3 | CDD | cd15471 | Myo5p-like_CBD_afadin | 27 | 268 | 0.00000 |
| 2 | g2402.t3 | PANTHER | PTHR10398 | AFADIN | 8 | 268 | 0.00000 |
| 3 | g2402.t3 | PANTHER | PTHR10398:SF1 | CANOE, ISOFORM E | 8 | 268 | 0.00000 |
| 1 | g2402.t3 | Pfam | PF01843 | DIL domain | 198 | 268 | 0.00000 |
| 5 | g2402.t3 | ProSiteProfiles | PS51126 | Dilute domain profile. | 84 | 268 | 28.39500 |
| 4 | g2402.t3 | SMART | SM01132 | DIL_2 | 198 | 268 | 0.00014 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
There are no GO annotations for this transcript.
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.
