General information for g2987.t6
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Puff-specific protein Bx42.
Parent gene
- The parent gene g2987 is located on chr_3: 21747441..21748541 (- 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 | g2987 | g2987.t6 | TTS | g2987.t6 | 21746740 | 21746740 |
| chr_3 | g2987 | g2987.t6 | isoform | g2987.t6 | 21747441 | 21748394 |
| chr_3 | g2987 | g2987.t6 | exon | g2987.t6.exon1 | 21747441 | 21748394 |
| chr_3 | g2987 | g2987.t6 | cds | g2987.t6.CDS1 | 21747442 | 21748254 |
| chr_3 | g2987 | g2987.t6 | TSS | g2987.t6 | NA | NA |
Sequences
>g2987.t6 Gene=g2987 Length=954
TGAATTTAGGTGTTTTACAGCAAGCAAAAAGCTCAGCACCACCATATGGCGCAAGAAGAG
GCTTCATACCGAGAACAGAATCAGATTATGGTGATGGCGGCGCATATCCAGAAATTCATG
TTGCTCAATATCCCTTAAACATGGGACGACCTAATTCAAGCAAAAAATCAAACGCACTCG
CATTACAAACAGATTCTACTGGAAAAGTGAAATATGATATAATAGCAAAACAAGGACATG
GAAAAGATAAAATTGTATATTCAAATATTAATCAATTACTTCCAGCTGAAGTATTATCAG
AGGATGCACCAGAATTACAGAGACCATCAGAAGAAGAAATCAATGATATTACTGAGAATA
CTAGAAAAGCTTTGGAAAAATTGACAAATCAGAAAATTGCAGCCGCAATGCCAGTAAGAG
CTGCAGAAAAACAAGCAGCAGCTCAATATATTCGTTATAAACCTTCTCAACAAGCAATGC
AATTCAATTCTGGTGCAAAGGAACGAATAATTCGAATGGTTGAAGCTCAAGTTGATCCAA
TGGAACCGCCAAAATTTAAAATTAACAAAAAAATTCCACGAGCACCACCTTCACCACCAG
CTCCTGTCCTTCACTCGCCTAGTCGAAAAGTATCTGTAAAAGAGCAAAAAGATTGGAAAG
TGCCCCCATGTATTAGTAATTGGAAAAACGCTAAAGGTTATACAATTCCACTCGATAAAC
GTCTTGCTGCTGATGGTCGAGGATTGCAACAAGTGCATATTAATGAAAAATTTGCAAAAA
TGGCAGAAGCATTGTATATTGCTGATCGAAAAGCACGAGAAGCTGTAGAAGCTCGTGCAC
AGCTTGAAAAGAAATTGGCACAGAAAGAAAAAGATAAGAAGGAAGAACAATTGCGTCAAA
TGGCTCAACGTGCACGTGAAGAAAGAGCAGGTATCAGTAGATACACAGGAAATG
>g2987.t6 Gene=g2987 Length=271
MGRPNSSKKSNALALQTDSTGKVKYDIIAKQGHGKDKIVYSNINQLLPAEVLSEDAPELQ
RPSEEEINDITENTRKALEKLTNQKIAAAMPVRAAEKQAAAQYIRYKPSQQAMQFNSGAK
ERIIRMVEAQVDPMEPPKFKINKKIPRAPPSPPAPVLHSPSRKVSVKEQKDWKVPPCISN
WKNAKGYTIPLDKRLAADGRGLQQVHINEKFAKMAEALYIADRKAREAVEARAQLEKKLA
QKEKDKKEEQLRQMAQRAREERAGISRYTGN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g2987.t6 | Coils | Coil | Coil | 221 | 264 | - |
| 4 | g2987.t6 | MobiDBLite | mobidb-lite | consensus disorder prediction | 239 | 271 | - |
| 5 | g2987.t6 | MobiDBLite | mobidb-lite | consensus disorder prediction | 239 | 264 | - |
| 2 | g2987.t6 | PANTHER | PTHR12096 | NUCLEAR PROTEIN SKIP-RELATED | 1 | 266 | 2.3E-127 |
| 3 | g2987.t6 | PANTHER | PTHR12096:SF0 | SNW DOMAIN-CONTAINING PROTEIN 1 | 1 | 266 | 2.3E-127 |
| 1 | g2987.t6 | Pfam | PF02731 | SKIP/SNW domain | 102 | 262 | 3.5E-72 |
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:0005681 | spliceosomal complex | CC |
| GO:0000398 | mRNA splicing, via spliceosome | BP |
KEGG
Orthology
- This transcript has been annotated with K06063 (SNW domain-containing protein 1)
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.
