General information for g6946.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Periodic tryptophan protein 2-like protein.
Parent gene
- The parent gene g6946 is located on chr_2: 20095348..20096229 (+ 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_2 | g6946 | g6946.t3 | TSS | g6946.t3 | 20093115 | 20093115 |
| chr_2 | g6946 | g6946.t3 | isoform | g6946.t3 | 20093200 | 20094259 |
| chr_2 | g6946 | g6946.t3 | exon | g6946.t3.exon1 | 20093200 | 20093217 |
| chr_2 | g6946 | g6946.t3 | cds | g6946.t3.CDS1 | 20093200 | 20093217 |
| chr_2 | g6946 | g6946.t3 | exon | g6946.t3.exon2 | 20093277 | 20093389 |
| chr_2 | g6946 | g6946.t3 | cds | g6946.t3.CDS2 | 20093277 | 20093389 |
| chr_2 | g6946 | g6946.t3 | exon | g6946.t3.exon3 | 20093447 | 20093670 |
| chr_2 | g6946 | g6946.t3 | cds | g6946.t3.CDS3 | 20093447 | 20093670 |
| chr_2 | g6946 | g6946.t3 | exon | g6946.t3.exon4 | 20093734 | 20094259 |
| chr_2 | g6946 | g6946.t3 | cds | g6946.t3.CDS4 | 20093734 | 20094257 |
| chr_2 | g6946 | g6946.t3 | TTS | g6946.t3 | NA | NA |
Sequences
>g6946.t3 Gene=g6946 Length=881
ATGAAGTTTGCGTATAAGTTTAACAACTTATTAGGAACTGTTTACCGAAAAGGAAATTTA
ATTTTCAGTGCAGATGGAAATTCGGTCATTAGTCCAGTTGGAAATCGATTAACAATCTTT
GATTTAAAAAATAATAAATCAAATACATTAGCTATACAAAGTAGTTACAACATTACGGCT
CTTGATTTGTCACCAAATGGTTGTCTGATTGTAGCTTCAAATGAAAATGGAGAGACTTAT
ATGATTAGTACTCTTAGTCAAACAGTTATTCATACATATAAATTTCATAGAGAACCAAAA
TGTATAAGATTTAGTCCAAATGGAAAACTCTTTGCAATATGTATTGAAGAATGTGTGTAT
ATTTTCAAAACACCTGGCATTATCACAGGTCAGTTCAATTCTTTTGTAATTGAACGAATC
TTCAAAGACACTCACGGCGAAAAGATTCATGTTGACTGGTCATATGATTCTCGATTTTTG
GTAGTAGGATCTCGTGATAACACAACAAGAATTTATTCGGTAAAACTTCTTGAAAACTTC
AAATCAGTAGTTTTAAGCGGACATTCTGATTCGGTTGTAACTTGTGCATTTGAGGATAAT
TCATTGAATATTATTATCGTTAGTCGTAATGGACATTTGACTAAATGGGAATGTAGTATG
AAATCCGAAGAAATGTATGAGTTGGAGTATGTTAGAGATGAAGAGCCAACTAATAAAAGA
CAAAAGGAAACTGATTCAGATGAAGAAGAGGATAATTTAAGTGAAGAAGAAGAAAATGCA
GAAAAAATTCAAGAAGATGATTCTGAAAGAGATAAGCAAGGTAAAGTTATACCAGAGACA
GCAGAAAAACCACGTTTTTACTATAAGAAACTTGTTCGCCA
>g6946.t3 Gene=g6946 Length=293
MKFAYKFNNLLGTVYRKGNLIFSADGNSVISPVGNRLTIFDLKNNKSNTLAIQSSYNITA
LDLSPNGCLIVASNENGETYMISTLSQTVIHTYKFHREPKCIRFSPNGKLFAICIEECVY
IFKTPGIITGQFNSFVIERIFKDTHGEKIHVDWSYDSRFLVVGSRDNTTRIYSVKLLENF
KSVVLSGHSDSVVTCAFEDNSLNIIIVSRNGHLTKWECSMKSEEMYELEYVRDEEPTNKR
QKETDSDEEEDNLSEEEENAEKIQEDDSERDKQGKVIPETAEKPRFYYKKLVR
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g6946.t3 | Coils | Coil | Coil | 239 | 266 | - |
| 4 | g6946.t3 | Gene3D | G3DSA:2.130.10.10 | - | 13 | 245 | 1.8E-21 |
| 10 | g6946.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 229 | 279 | - |
| 13 | g6946.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 229 | 247 | - |
| 12 | g6946.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 248 | 264 | - |
| 11 | g6946.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 265 | 279 | - |
| 2 | g6946.t3 | PANTHER | PTHR19858 | WD40 REPEAT PROTEIN | 1 | 262 | 1.3E-75 |
| 1 | g6946.t3 | Pfam | PF00400 | WD domain, G-beta repeat | 141 | 172 | 0.0074 |
| 14 | g6946.t3 | ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 141 | 226 | 11.128 |
| 7 | g6946.t3 | SMART | SM00320 | WD40_4 | 43 | 83 | 57.0 |
| 9 | g6946.t3 | SMART | SM00320 | WD40_4 | 86 | 123 | 2.2 |
| 8 | g6946.t3 | SMART | SM00320 | WD40_4 | 134 | 173 | 0.31 |
| 6 | g6946.t3 | SMART | SM00320 | WD40_4 | 178 | 217 | 2.1 |
| 3 | g6946.t3 | SUPERFAMILY | SSF50978 | WD40 repeat-like | 20 | 229 | 2.27E-28 |
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. There were no conditions that were differentially expressed