General information for g3109.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Catenin alpha.
Parent gene
- The parent gene g3109 is located on chr_3: 22859128..22860043 (+ 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 | g3109 | g3109.t2 | isoform | g3109.t2 | 22858202 | 22860043 |
| chr_3 | g3109 | g3109.t2 | exon | g3109.t2.exon1 | 22858202 | 22858274 |
| chr_3 | g3109 | g3109.t2 | cds | g3109.t2.CDS1 | 22858250 | 22858274 |
| chr_3 | g3109 | g3109.t2 | exon | g3109.t2.exon2 | 22858383 | 22858450 |
| chr_3 | g3109 | g3109.t2 | cds | g3109.t2.CDS2 | 22858383 | 22858450 |
| chr_3 | g3109 | g3109.t2 | exon | g3109.t2.exon3 | 22858646 | 22859068 |
| chr_3 | g3109 | g3109.t2 | cds | g3109.t2.CDS3 | 22858646 | 22859068 |
| chr_3 | g3109 | g3109.t2 | exon | g3109.t2.exon4 | 22859132 | 22859248 |
| chr_3 | g3109 | g3109.t2 | cds | g3109.t2.CDS4 | 22859132 | 22859248 |
| chr_3 | g3109 | g3109.t2 | exon | g3109.t2.exon5 | 22859326 | 22860043 |
| chr_3 | g3109 | g3109.t2 | cds | g3109.t2.CDS5 | 22859326 | 22859490 |
| chr_3 | g3109 | g3109.t2 | TTS | g3109.t2 | 22860146 | 22860146 |
| chr_3 | g3109 | g3109.t2 | TSS | g3109.t2 | NA | NA |
Sequences
>g3109.t2 Gene=g3109 Length=1399
AGCTCAGAAGAATTGGATACAGACACAGAGTTTGAGCCAGTAGAAGATATGACAATTGAA
ACACGTAGTCGTTCAAGCGCTCATACAGGCGATCAAACAATTGATGAATATCCTGATATT
AGTGGAATTACAACAGCAAGAGAAGCGATGCGCAAGATGAATGAGGAAGACAAGCAAAAG
ATTATGCAACAAGTCGAGTTATTCCGTAGAGAAAAACTCACATTCGATTCAGAAGTTGCT
AAATGGGACGACACTGGCAATGATATCATCTATCTTGCTAAACATATGTGTATGATTATG
ATGGAAATGACTGATTTCACACGTGGTCGTGGTCCATTAAAGACAACTATGGATGTCATC
AATGCAGCTAAGAAAATTTCAGAAGCTGGAACAAAACTTGATAAATTAACTCGCGAAATT
GCTGATCAATGTCCTGAAAGTTCTACAAAGAAAGATCTTTTGGCCTACATTCAACGAATC
GTTCTCTATTGTCATCAAATTCAAATTACGTCGAAGGTCAAAGCTGATGTGCAAAATATT
TCTGGTGAATTGATTGTTTCTGGGCTCGACAGTGCAACATCCTTGATTCAAGCTGCCAAA
AATTTAATGAATGCTGTCGTTTATACGGTAAAATATTCCTATGTAGCATCAACTAAATAC
ACCAGACAAGGAACAGTTTCGTCACCAATAGTTGTATGGAAGATGAAAGCACCAGAAAAG
AAACCACTTGTAAGGCCTGAAAAACCTGAAGAAGTTCGTGCAAAAGTCAGACGAGCATCA
CAGAAAAAGACACAAAATCCAGTGCACGCCCTTTCGGAATTTCAGAGCCCTGCCGACAAC
ATTTAAAACAATTAATTTAAAGCTACTTTTTCTTAATGAATGAAAAATCTCTCATATAAA
AAAATGTTTTCTAGATCATTCTCAAGGAGCCTAAAATAACTTAAGTAAATAATTGAACTA
CATTAAAAGATTTGATCAATGATAATCATAAATTGAGGATGACAAAATCATAAATTAAAC
GAAGAATTTCTATAAAATTTTATTAATATTTAAGTATGCATTTTCAAAGCTATCAAATAA
ATTTTTTACATTTTTCAATTATAGAAACACACAAACAAAAATATTTTAGTTTTAAATGAA
CTTTGCAATCATTTTATATATACACATTTGATTTTATACCATTTTAAGTATTATTTTTTG
GATGTCTGGTGATCATAAAAGTAAATTCCAGACTCATTGCTTCCGTTTTGTTCATTAATA
ATCAAAAAAGAGGAAGAAAAATTTATTTTTAATGTACTAATAAATTATTTTATTTTTATT
TAGTCATAATTGACATCAAAACATTGAGACAATTTTCCATTTTTAAAAAATAAATATAAT
TGTAGGAAAAAAATGAAAA
>g3109.t2 Gene=g3109 Length=265
MTIETRSRSSAHTGDQTIDEYPDISGITTAREAMRKMNEEDKQKIMQQVELFRREKLTFD
SEVAKWDDTGNDIIYLAKHMCMIMMEMTDFTRGRGPLKTTMDVINAAKKISEAGTKLDKL
TREIADQCPESSTKKDLLAYIQRIVLYCHQIQITSKVKADVQNISGELIVSGLDSATSLI
QAAKNLMNAVVYTVKYSYVASTKYTRQGTVSSPIVVWKMKAPEKKPLVRPEKPEEVRAKV
RRASQKKTQNPVHALSEFQSPADNI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 13 | g3109.t2 | Gene3D | G3DSA:1.20.120.230 | - | 25 | 220 | 5.5E-80 |
| 9 | g3109.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 16 | - |
| 12 | g3109.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 25 | - |
| 10 | g3109.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 225 | 242 | - |
| 11 | g3109.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 225 | 265 | - |
| 8 | g3109.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 245 | 265 | - |
| 2 | g3109.t2 | PANTHER | PTHR18914:SF9 | CATENIN ALPHA | 3 | 262 | 1.1E-140 |
| 3 | g3109.t2 | PANTHER | PTHR18914 | ALPHA CATENIN | 3 | 262 | 1.1E-140 |
| 4 | g3109.t2 | PRINTS | PR00805 | Alpha-catenin signature | 72 | 94 | 2.4E-34 |
| 6 | g3109.t2 | PRINTS | PR00805 | Alpha-catenin signature | 136 | 160 | 2.4E-34 |
| 5 | g3109.t2 | PRINTS | PR00805 | Alpha-catenin signature | 213 | 231 | 2.4E-34 |
| 1 | g3109.t2 | Pfam | PF01044 | Vinculin family | 11 | 225 | 1.1E-90 |
| 7 | g3109.t2 | SUPERFAMILY | SSF47220 | alpha-catenin/vinculin-like | 39 | 220 | 1.57E-53 |
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:0051015 | actin filament binding | MF |
| GO:0007155 | cell adhesion | BP |
| GO:0045296 | cadherin 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.
