General information for g3401.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as U3 small nucleolar RNA-associated protein 15-like protein.
Parent gene
- The parent gene g3401 is located on chr_3: 25199393..25200511 (- 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 | g3401 | g3401.t1 | TTS | g3401.t1 | 25198766 | 25198766 |
| chr_3 | g3401 | g3401.t1 | isoform | g3401.t1 | 25198879 | 25200511 |
| chr_3 | g3401 | g3401.t1 | exon | g3401.t1.exon1 | 25198879 | 25200363 |
| chr_3 | g3401 | g3401.t1 | cds | g3401.t1.CDS1 | 25198879 | 25200363 |
| chr_3 | g3401 | g3401.t1 | exon | g3401.t1.exon2 | 25200422 | 25200511 |
| chr_3 | g3401 | g3401.t1 | cds | g3401.t1.CDS2 | 25200422 | 25200511 |
| chr_3 | g3401 | g3401.t1 | TSS | g3401.t1 | 25200569 | 25200569 |
Sequences
>g3401.t1 Gene=g3401 Length=1575
ATGAATAATTTTAAGAAAACTACAGTTCAGAATTTTACAAAAGCATCAATAGTGACAAGT
GAAGAGTGCAAATATTGGAAACAACTTGGGACACCAGTATTTATTAAGGAATTTGGCGCT
ATAGATTATATTGATTTTAGTCCAATTGAACCATATAACTTTGCTGCAACCTGTTCACTA
CGCGTACAAATTTATAATCCACTTACAAAACTTGTTTTAAAAAATATTACAACATTTCAA
AAAGAAGCATTCGGCGCAACATACAGAAATGACGGTAAATTAATTGCAGCGGGTGATGAT
GAAGGAAAAGTAAGACTTTTTGATGCAAACACAAAAACAATATTGAGAATATTTTCTGGT
CATCGAGCTGCAGTGCATAGAACATATTTTGTCTCTGATTTACATCATCTTGCTAGTTTT
TCTGATGATAGAACAGTGAAATTATGGGATGTTGGTACTGAAAAAATTGTATATACTTTT
CGAGAACATAATGATTATATCAGAGCTGGAGCAGTGAATCGTGCAAGTCCTCACACACTT
ATAAGCGGTGGTTACGATCATGTTATAAATATGTATGATACACGATCTGAAAAACGTGTA
ATGTCAGTCAATCATGGTAATCCAATAGAAGCACTCGTCTTTCATCCAAGTGGAGGTATC
TTCATTTCAGCTGGCGGTAATGAAATCAAATTTTGGGATGCTGTGGCAGGTGGACGTCTT
TTAGGAACAATTTCTCAACATACCAAGACAGTTACATGTCTTTCAGTTAGTTCTGATGGC
CGTCATTTAATTTCTGGTAGTCTCGATAGACATGTCAAGTTTTTCAACACGTCAAACTAT
CAAATGATTCATAACATTAATTACACAAATTCAATTCTAAGCGTTGGAATTGCAAAAGAT
GGAAATACTTTAGCAGTTGGTCATGTTGATGGAACATTGGCAATTCACAGACGAGAAGAA
AATTTCGATGATGATAAAATAGAACGAATTGAAAGAGAAAAACGGAGAAAAGAGCGAACT
TATCAAATTGCTGATGAAGTGATTGAGAAGCCAGAACGAAAACATTTGAAGGGATATGAT
ATGAGTTTAAGGAAATTTGAATATTCAAAAGCATTAGATCAAGTGATGAATCGTTTTTGT
GTTACAAAAACTCCAGAAGTAACTGTTGCAATCATTCATGAACTGATAAGACGTAATGGA
TTAAGACAGGCATTCGCAAATCGTGAACAAGATTCAATTGCAAAAATTTTAACATTTTTC
AATAAATACATCGGTGATGGACGATTCACTCGAGTTCTCGTTGACGCCATTAATATTTTT
CTTGATGTATATGAACCCAATTTCATGTCATTAGCACCTGATGTTCAAAGACTGATTGTC
GAATTAAATCGACGCATTCAAGTGGAAGAAAACATGACTTTGGAATTTCTCAAACTGCAA
GGAGCATTGGACATTATAACGAATGCCACAGAGTTGGCTAATGAAACGCAAAATGATACA
ATCGATTTAACAGTACCATCATCAAAAATGCAACCGAGTGCTGATGCAATGAAAGCATTT
ATTATAAATGTATAA
>g3401.t1 Gene=g3401 Length=524
MNNFKKTTVQNFTKASIVTSEECKYWKQLGTPVFIKEFGAIDYIDFSPIEPYNFAATCSL
RVQIYNPLTKLVLKNITTFQKEAFGATYRNDGKLIAAGDDEGKVRLFDANTKTILRIFSG
HRAAVHRTYFVSDLHHLASFSDDRTVKLWDVGTEKIVYTFREHNDYIRAGAVNRASPHTL
ISGGYDHVINMYDTRSEKRVMSVNHGNPIEALVFHPSGGIFISAGGNEIKFWDAVAGGRL
LGTISQHTKTVTCLSVSSDGRHLISGSLDRHVKFFNTSNYQMIHNINYTNSILSVGIAKD
GNTLAVGHVDGTLAIHRREENFDDDKIERIEREKRRKERTYQIADEVIEKPERKHLKGYD
MSLRKFEYSKALDQVMNRFCVTKTPEVTVAIIHELIRRNGLRQAFANREQDSIAKILTFF
NKYIGDGRFTRVLVDAINIFLDVYEPNFMSLAPDVQRLIVELNRRIQVEENMTLEFLKLQ
GALDIITNATELANETQNDTIDLTVPSSKMQPSADAMKAFIINV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g3401.t1 | CDD | cd00200 | WD40 | 44 | 315 | 1.14511E-48 |
| 10 | g3401.t1 | Coils | Coil | Coil | 327 | 347 | - |
| 9 | g3401.t1 | Gene3D | G3DSA:2.130.10.10 | - | 18 | 178 | 7.1E-24 |
| 8 | g3401.t1 | Gene3D | G3DSA:2.130.10.10 | - | 179 | 334 | 3.7E-30 |
| 5 | g3401.t1 | PANTHER | PTHR19924 | UTP15 U3 SMALL NUCLEOLAR RNA-ASSOCIATED PROTEIN 15 FAMILY MEMBER | 1 | 490 | 6.1E-137 |
| 6 | g3401.t1 | PANTHER | PTHR19924:SF30 | U3 SMALL NUCLEOLAR RNA-ASSOCIATED PROTEIN 15 HOMOLOG | 1 | 490 | 6.1E-137 |
| 4 | g3401.t1 | Pfam | PF00400 | WD domain, G-beta repeat | 114 | 150 | 0.0012 |
| 3 | g3401.t1 | Pfam | PF00400 | WD domain, G-beta repeat | 204 | 233 | 0.15 |
| 2 | g3401.t1 | Pfam | PF00400 | WD domain, G-beta repeat | 239 | 276 | 1.6E-6 |
| 1 | g3401.t1 | Pfam | PF09384 | UTP15 C terminal | 342 | 486 | 8.5E-42 |
| 18 | g3401.t1 | ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 76 | 285 | 27.342 |
| 19 | g3401.t1 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 118 | 159 | 13.249 |
| 20 | g3401.t1 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 244 | 285 | 11.478 |
| 12 | g3401.t1 | SMART | SM00320 | WD40_4 | 69 | 108 | 1.5 |
| 13 | g3401.t1 | SMART | SM00320 | WD40_4 | 111 | 150 | 8.5E-5 |
| 15 | g3401.t1 | SMART | SM00320 | WD40_4 | 153 | 193 | 2.1E-4 |
| 14 | g3401.t1 | SMART | SM00320 | WD40_4 | 196 | 233 | 0.0011 |
| 16 | g3401.t1 | SMART | SM00320 | WD40_4 | 237 | 276 | 2.8E-8 |
| 17 | g3401.t1 | SMART | SM00320 | WD40_4 | 279 | 317 | 0.62 |
| 7 | g3401.t1 | SUPERFAMILY | SSF50978 | WD40 repeat-like | 37 | 317 | 9.57E-60 |
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:0005730 | nucleolus | CC |
| GO:0005515 | protein binding | MF |
| GO:0006364 | rRNA processing | BP |
KEGG
Orthology
- This transcript has been annotated with K14549 (U3 small nucleolar RNA-associated protein 15)
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.
