General information for g2402.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative 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.t2 | isoform | g2402.t2 | 17656848 | 17657993 |
| chr_3 | g2402 | g2402.t2 | exon | g2402.t2.exon1 | 17656848 | 17657993 |
| chr_3 | g2402 | g2402.t2 | cds | g2402.t2.CDS1 | 17656888 | 17657328 |
| chr_3 | g2402 | g2402.t2 | TSS | g2402.t2 | NA | NA |
| chr_3 | g2402 | g2402.t2 | TTS | g2402.t2 | NA | NA |
Sequences
>g2402.t2 Gene=g2402 Length=1146
TTATTGCAGATTAGATTAATCATATTTTTTATAAATGACAATGTCATTGAACGAAAAACG
AATGCTGGATCGCGAAGCATTGCGTTCAGTAATTCAGCAATGGAATGCAAATCGACTAGA
TTTATTTGAATTGTCAGAGCCAAGTGAAAATCTTGAATTCCATGGCGTAATGCGTTTCTA
TTTTCAAGATGTTGGTCAGAAAGTCGCTACCAAATGTATACGCGTGCAATCTGATGCAAC
AGTTGCCGATGTGATCGAGACATTAATCGAAAAATTCCGTCCTGATATGCGCATGTTATC
CGTCCCAAATTATGCACTTTATGAAGTGCATGCAAATGGTGAGGAAAGAAAATTAAATCC
AGATGAAAAGCCATTGCTTGTGCAGCTCAATTGGCACGTCGATGACCGCGAAGGAAGGTT
TTTATTGAAAGATCTCGATCAAAAACCAACTGTAAGTTTTAATCTTTTATTAATGACATA
GAATTTAACTCAATTTCTGTCGTCACAGACATTAGACAACACAGACACAAACTTTAAACG
AAAATTATCGAAACGTGAAAAGAAGGAGCAAAAGAAGAAGGAAAAATTGCAAAAACTCAA
CTCAAATGCTGACGAGTCAGAAAACCATGTTGCTGAAAAATTGTATACCGGTAAGTAGCA
TGCAATTTGTCAAATGAGACAGTTTGTTTTTAAATCTACTGTGCGTCATTGTAGAGCTTC
CAGAAACATCGTTTACGCGCTCAATATCAAATCCAGAAGCAGTCATGCGACGAAGAAGAC
AGCAAAAACTTGAGAAGAAATTGCAACAATTTAGATCAAGAGATGGAGGGCCTGATACGG
GTGGAACGTTAAAAATTTATGGTGAAAGTCTCTGCCGCGATGTGCCTTATAAAACACTAC
TGCTGTCAATACGTGATTGCGCACAAGCAGTTGTTAGAGAAATGTTGGCAAAATATGGTA
TGGACAAAGCTGATCCACTACATTATTGTCTTGTGCAGGTAAAAAAATTTGAATAATTGC
TCTTCCACCATAAACTAATGTGTCTCTCGTTTAAACTATTTTAGGTTAATAGTGATGGCT
CCGAATATATTCTTGATGATGATGAATGTCCATTATCAATACTAATGAATCATCCGACGT
CTAGAG
>g2402.t2 Gene=g2402 Length=146
MSLNEKRMLDREALRSVIQQWNANRLDLFELSEPSENLEFHGVMRFYFQDVGQKVATKCI
RVQSDATVADVIETLIEKFRPDMRMLSVPNYALYEVHANGEERKLNPDEKPLLVQLNWHV
DDREGRFLLKDLDQKPTVSFNLLLMT
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g2402.t2 | CDD | cd01782 | RA1_Afadin | 21 | 130 | 0.000 |
| 6 | g2402.t2 | Gene3D | G3DSA:3.10.20.90 | - | 7 | 139 | 0.000 |
| 2 | g2402.t2 | PANTHER | PTHR10398 | AFADIN | 7 | 137 | 0.000 |
| 3 | g2402.t2 | PANTHER | PTHR10398:SF1 | CANOE, ISOFORM E | 7 | 137 | 0.000 |
| 1 | g2402.t2 | Pfam | PF00788 | Ras association (RalGDS/AF-6) domain | 41 | 130 | 0.000 |
| 7 | g2402.t2 | ProSiteProfiles | PS50200 | Ras-associating (RA) domain profile. | 40 | 134 | 30.884 |
| 5 | g2402.t2 | SMART | SM00314 | RA_5 | 40 | 134 | 0.000 |
| 4 | g2402.t2 | SUPERFAMILY | SSF54236 | Ubiquitin-like | 41 | 131 | 0.000 |
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:0007165 | signal transduction | BP |
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.
