General information for g14920.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Protein pangolin, isoform J.
Parent gene
- The parent gene g14920 is located on chr_4: 3055407..3066712 (+ 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_4 | g14920 | g14920.t2 | isoform | g14920.t2 | 3055407 | 3066712 |
| chr_4 | g14920 | g14920.t2 | exon | g14920.t2.exon1 | 3055407 | 3056308 |
| chr_4 | g14920 | g14920.t2 | cds | g14920.t2.CDS1 | 3055407 | 3056308 |
| chr_4 | g14920 | g14920.t2 | exon | g14920.t2.exon2 | 3056633 | 3056774 |
| chr_4 | g14920 | g14920.t2 | cds | g14920.t2.CDS2 | 3056633 | 3056774 |
| chr_4 | g14920 | g14920.t2 | exon | g14920.t2.exon3 | 3057205 | 3057264 |
| chr_4 | g14920 | g14920.t2 | cds | g14920.t2.CDS3 | 3057205 | 3057264 |
| chr_4 | g14920 | g14920.t2 | exon | g14920.t2.exon4 | 3057833 | 3057998 |
| chr_4 | g14920 | g14920.t2 | cds | g14920.t2.CDS4 | 3057833 | 3057998 |
| chr_4 | g14920 | g14920.t2 | exon | g14920.t2.exon5 | 3066549 | 3066712 |
| chr_4 | g14920 | g14920.t2 | cds | g14920.t2.CDS5 | 3066549 | 3066712 |
| chr_4 | g14920 | g14920.t2 | TSS | g14920.t2 | NA | NA |
| chr_4 | g14920 | g14920.t2 | TTS | g14920.t2 | NA | NA |
Sequences
>g14920.t2 Gene=g14920 Length=1434
ATGGACATCAGTAATGAGCCATTAAATCTTTGTACTAAAAACTCTTCTGATGAGCAGCAA
GAAGTTCATAGAGAGCACATAATTGACTATGATGATGCGTGTCTGCCAAAAAACTGTGAT
AAGAAATTAAACGGCGGCACATCACCAACGCCGGATGAGTCAGAATTGGATACAGAAAGC
AGCGCGCCATTTAATCCGAATTTATTATTACAACAGCATCAACTTGAGCAGTATTTACTG
CTACAACAACAACAGCAAGTGCAACAACATATGATAGATGGAACACAAGCAAAAATGCAT
TTAGACAAATATTTAAAATTGACAAATCGTTATCTCAATACAATGTCACCATTTTTACAG
CATTTTCAGCAAGGACCAGTTGTTAATGCACAAGCAGCAGCTAATGCAGCAGCAACATTA
TTATTGGCAAATCATCAGTCAACAAGTGGTGATCGTGTTGATGATGGTGATGATTCATGT
GATGGCTCAATGACATCATCATCAACACAACAACAACAAGATGGTGTTAGACTTTTTCTC
CATAAATTGATTGAATATAATTTCTTACAACAATTGCAACAACAACAGCAAATCAATGAC
CTGATAAATAATAATAATAATAATAATAACAATCAAAGTAATAACAAAAATGGTAGTCAT
AGTAATCATAATAATAATACAAATGGGCACAATCATAGCAAGGCAAACAAAAGTCCGACC
AATAGTAATGATGGTGATAGTGACTACTACAATCATCATAATATAATGCCAACGCCAACT
AGTGCAACAAAAACTTTCTTTGATTTTCTTAAAAATGCTAGTGCTGCAAATAGTGGCACT
ACTAGTGGGCAACAGAGTGGAAGTAGTAATGGTCATAATAGTCGCATTCAAGCTTTTAAG
AGATCGTCATCAGAGAACAGTAAAAACACATCTAGTTCAATATCATCAGAAAATATGAAA
ACTTCGGAAGCAGACAAGAAAAAACCACATATCAAGAAGCCGCTAAATGCATTTATGCTT
TACATGAAAGAAATGAGAGCGCAGGTGGTGGCAGAATGTACGCTTAAAGAATCAGCAGCC
ATAAATCAGATACTAGGGAGAAAGTGGCACTCGCTGAGCCGTGAAGAACAGAGTGTCTAT
TATGAAAAGGCACGACAAGAACGACAGCTACATATGGAACTTTATCCGGGGTGGAGTGCA
CGCGACAACTATGGTTATGGTAGCAAGAAAAAGAAACGAAAAAAAGATCGATCACCCGCG
GATTCGGGAGGTGAAACAATTGCTGAAATAGAGTTGCAAAAGAGCTTTGTCATTTCGGAT
TATTTGTTTTCCTCAGGTTACGAAAAACATCCACAAACAGTACTTAAAAAGTCATTTGTA
ACAACTCTGGTGATGATAAATTTAAACACTCTTTCAAAATGGATTAACAATTAA
>g14920.t2 Gene=g14920 Length=477
MDISNEPLNLCTKNSSDEQQEVHREHIIDYDDACLPKNCDKKLNGGTSPTPDESELDTES
SAPFNPNLLLQQHQLEQYLLLQQQQQVQQHMIDGTQAKMHLDKYLKLTNRYLNTMSPFLQ
HFQQGPVVNAQAAANAAATLLLANHQSTSGDRVDDGDDSCDGSMTSSSTQQQQDGVRLFL
HKLIEYNFLQQLQQQQQINDLINNNNNNNNNQSNNKNGSHSNHNNNTNGHNHSKANKSPT
NSNDGDSDYYNHHNIMPTPTSATKTFFDFLKNASAANSGTTSGQQSGSSNGHNSRIQAFK
RSSSENSKNTSSSISSENMKTSEADKKKPHIKKPLNAFMLYMKEMRAQVVAECTLKESAA
INQILGRKWHSLSREEQSVYYEKARQERQLHMELYPGWSARDNYGYGSKKKKRKKDRSPA
DSGGETIAEIELQKSFVISDYLFSSGYEKHPQTVLKKSFVTTLVMINLNTLSKWINN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g14920.t2 | CDD | cd01388 | SOX-TCF_HMG-box | 330 | 401 | 1.39547E-36 |
| 5 | g14920.t2 | Gene3D | G3DSA:1.10.30.10 | DNA Binding (I) | 329 | 417 | 2.3E-24 |
| 8 | g14920.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 147 | 173 | - |
| 9 | g14920.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 299 | 330 | - |
| 10 | g14920.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 299 | 319 | - |
| 2 | g14920.t2 | PANTHER | PTHR10373 | TRANSCRIPTION FACTOR 7 FAMILY MEMBER | 96 | 426 | 7.7E-72 |
| 3 | g14920.t2 | PANTHER | PTHR10373:SF38 | PROTEIN PANGOLIN, ISOFORM J | 96 | 426 | 7.7E-72 |
| 1 | g14920.t2 | Pfam | PF00505 | HMG (high mobility group) box | 331 | 398 | 9.8E-21 |
| 11 | g14920.t2 | ProSiteProfiles | PS50118 | HMG boxes A and B DNA-binding domains profile. | 331 | 399 | 15.28 |
| 7 | g14920.t2 | SMART | SM00398 | hmgende2 | 330 | 400 | 1.5E-21 |
| 4 | g14920.t2 | SUPERFAMILY | SSF47095 | HMG-box | 319 | 399 | 8.25E-21 |
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:0016055 | Wnt signaling pathway | BP |
KEGG
Orthology
- This transcript has been annotated with K04491 (transcription factor 7-like 2)
Pathway
- This transcript belongs to the following 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.
