General information for g2380.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Brix domain-containing protein ZK795.3.
Parent gene
- The parent gene g2380 is located on chr_3: 17469321..17470289 (+ 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 | g2380 | g2380.t1 | TSS | g2380.t1 | 17469243 | 17469243 |
| chr_3 | g2380 | g2380.t1 | isoform | g2380.t1 | 17469321 | 17470289 |
| chr_3 | g2380 | g2380.t1 | exon | g2380.t1.exon1 | 17469321 | 17469792 |
| chr_3 | g2380 | g2380.t1 | cds | g2380.t1.CDS1 | 17469321 | 17469792 |
| chr_3 | g2380 | g2380.t1 | exon | g2380.t1.exon2 | 17469853 | 17470289 |
| chr_3 | g2380 | g2380.t1 | cds | g2380.t1.CDS2 | 17469853 | 17470289 |
| chr_3 | g2380 | g2380.t1 | TTS | g2380.t1 | 17470325 | 17470325 |
Sequences
>g2380.t1 Gene=g2380 Length=909
ATGTTAAGAAGACAAGCTAGATTGAGAAGAGAATATCTTTATCGAAAGACAGCTGAAATA
AAACATAAAACATTGCAAGATAAAAAGGAAAGGATTAAAAAGAGTTTAGAAGAGCATACA
ACAATTCATGGTGATTTAAGAAGAGAGGCACTTGAACTTCAAAAGAAACAAAAATATACT
GAAACTTCAGAAGAAGCGACAAAGACAAGTTCGCAAGATGATGAGTATCGATTTGCAGGA
TGTGAGGACCCAAAAGTTTTCATTACAACTTCACATAATCCATCAACAACATTAAAGCAA
TTTGTAAAAGAATTTCGATTACTTATTCCTAATGCTCAACGTGTCAACAGAGGTAATTAC
GATATGAAGCAACTAGTTCATGCGAGTCGTGCAAATGATGCTACTGATTTAATTATCATA
CACGAAACACGGGGTGTTCCAACAAATTTAGTCATATGTCATTTACCTTATGGACCTACT
GCAAAATTCAACATCTCTTCAATTGTAACGAGACATGAAATTCCAGATATAGAGAACATG
CCAGAAGCAAAACCTCATCTGATCTTTCACAATTTCACAACAAAACTCGGCGAAAGAACA
ATGTCCATCCTAAAATATCTTTTTCCAGTACCAAAAGAAGATTCAAAACGAGTGATAACT
TTTGCAAATCATGATGACTACATCAGTTTTAGACATCATTCATATCGTTATATAGATGGA
AATCTCGAACTTAATGAACTTGGTCCGCGCTTTCAGTTGAAATTGTATCATATTCTTTTA
GGCACCGTTGATGAAGAAAAATCTGCAGATACTGAGTGGATACATCGCCCATACATGAAT
ACTGCTGCAAAAAGACGATTCCTTTCTGAACAAGACGGTTGGAAAGAAGATGATGTTGAA
GCAGAATAA
>g2380.t1 Gene=g2380 Length=302
MLRRQARLRREYLYRKTAEIKHKTLQDKKERIKKSLEEHTTIHGDLRREALELQKKQKYT
ETSEEATKTSSQDDEYRFAGCEDPKVFITTSHNPSTTLKQFVKEFRLLIPNAQRVNRGNY
DMKQLVHASRANDATDLIIIHETRGVPTNLVICHLPYGPTAKFNISSIVTRHEIPDIENM
PEAKPHLIFHNFTTKLGERTMSILKYLFPVPKEDSKRVITFANHDDYISFRHHSYRYIDG
NLELNELGPRFQLKLYHILLGTVDEEKSADTEWIHRPYMNTAAKRRFLSEQDGWKEDDVE
AE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g2380.t1 | Coils | Coil | Coil | 15 | 35 | - |
| 6 | g2380.t1 | Gene3D | G3DSA:3.40.50.10480 | - | 84 | 231 | 9.6E-26 |
| 2 | g2380.t1 | PANTHER | PTHR22734:SF2 | U3 SMALL NUCLEOLAR RIBONUCLEOPROTEIN PROTEIN IMP4 | 1 | 287 | 4.8E-124 |
| 3 | g2380.t1 | PANTHER | PTHR22734 | U3 SMALL NUCLEOLAR RIBONUCLEOPROTEIN PROTEIN IMP4 | 1 | 287 | 4.8E-124 |
| 1 | g2380.t1 | Pfam | PF04427 | Brix domain | 92 | 256 | 6.7E-30 |
| 8 | g2380.t1 | ProSiteProfiles | PS50833 | Brix domain profile. | 84 | 264 | 45.388 |
| 5 | g2380.t1 | SMART | SM00879 | Brix_2 | 87 | 258 | 7.2E-57 |
| 4 | g2380.t1 | SUPERFAMILY | SSF52954 | Class II aaRS ABD-related | 83 | 261 | 5.59E-59 |
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:0042134 | rRNA primary transcript binding | MF |
| GO:0006364 | rRNA processing | BP |
| GO:0019843 | rRNA binding | MF |
KEGG
Orthology
- This transcript has been annotated with K14561 (U3 small nucleolar ribonucleoprotein protein IMP4)
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.
