General information for g2967.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as U5 small nuclear ribonucleoprotein 40 kDa protein.
Parent gene
- The parent gene g2967 is located on chr_3: 21622217..21623088 (+ 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 | g2967 | g2967.t1 | TSS | g2967.t1 | 21621293 | 21621293 |
| chr_3 | g2967 | g2967.t1 | isoform | g2967.t1 | 21621361 | 21622594 |
| chr_3 | g2967 | g2967.t1 | exon | g2967.t1.exon1 | 21621361 | 21621589 |
| chr_3 | g2967 | g2967.t1 | cds | g2967.t1.CDS1 | 21621361 | 21621589 |
| chr_3 | g2967 | g2967.t1 | exon | g2967.t1.exon2 | 21621756 | 21622594 |
| chr_3 | g2967 | g2967.t1 | cds | g2967.t1.CDS2 | 21621756 | 21622594 |
| chr_3 | g2967 | g2967.t1 | TTS | g2967.t1 | 21623081 | 21623081 |
Sequences
>g2967.t1 Gene=g2967 Length=1068
ATGATTTCGAGTGCCCAAAAGAGACCTGGTGATAATCTGAGTCTAGTTGCTGTTCAACAG
AATACTAAAAGAGCTCGAAATGATGAATTGGTGGCGACTTTTAAAGATAAACAACTTATG
GAAAAAGGAATTAACAGAACATCAAATCTTTATGCACCTATAATGAAACTAGAAGGGCAT
GAAGGAGAAATATTCTCTTGTGAATTTCATCCAGAAGGCGAGTTACTTGCATCAGCCGGT
GTTGAAAGAAAAATATTCTTATGGACTGTATATGATGAGGAATGTCAAAATATTGCAGTC
ATGAGTGGACATAAAGGAGTTATTACCGAAATGCATTTTAGTCCTGATGGAACTTCAATT
TATAGCTGCAGTACTGATAAGTTTGTGAGTGTATTTAATACTGAAACAGCACAGCGAGTT
CGTAAAATGAAAGGACATACGAATTTTATCAATTCTATTAGTAACGCAAGAAGAGGGGTT
GAGACTTTAGTAACAGGAAGTGATGATAACACGATTAAAATTTGGGATGCACGTAAAAAA
CTTGTATGTCACACCCTCGAAAGCAATTATCAAGTAACTGCTGTTTGCTTAAATGACACA
GCTGAACAAGTGATAGCAGGCGGTATTGATAATGATATCAAAATTTATGACATTAGAAAG
AACGAAATATTGTTTAAAATGCAAGGTCACACTGATACAATTACTGGTTTAAAATTATCT
CCATGTGGTTCATATGTTCTTTCAAATTCGATGGATAACACTTGCAGAATTTGGGACATT
AGACCATATTGTTCACAAGATCGATGTAAATCAGTTTTTCAGGGACATTCCCATAATTTT
GAGAAAAATCTTTTAAGATGTGCATGGAGTTCAGATGGCACAATGATTTCAGCTGGATCG
GCGGATAGATTTGTTTATATTTGGGACGTTAATTCTAAGAAGATTCTATACAAACTCCCT
GGTCATTTAGGAGCTGTAAATGATGTTGATTTTTCACCAAAAGAAGAAATTATTCTCAGT
GGTTCTTCAGATAAGACTCTATACATGGGTGAATTACTAGAAAATTAG
>g2967.t1 Gene=g2967 Length=355
MISSAQKRPGDNLSLVAVQQNTKRARNDELVATFKDKQLMEKGINRTSNLYAPIMKLEGH
EGEIFSCEFHPEGELLASAGVERKIFLWTVYDEECQNIAVMSGHKGVITEMHFSPDGTSI
YSCSTDKFVSVFNTETAQRVRKMKGHTNFINSISNARRGVETLVTGSDDNTIKIWDARKK
LVCHTLESNYQVTAVCLNDTAEQVIAGGIDNDIKIYDIRKNEILFKMQGHTDTITGLKLS
PCGSYVLSNSMDNTCRIWDIRPYCSQDRCKSVFQGHSHNFEKNLLRCAWSSDGTMISAGS
ADRFVYIWDVNSKKILYKLPGHLGAVNDVDFSPKEEIILSGSSDKTLYMGELLEN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 13 | g2967.t1 | CDD | cd00200 | WD40 | 57 | 347 | 7.47394E-68 |
| 12 | g2967.t1 | Gene3D | G3DSA:2.130.10.10 | - | 53 | 353 | 8.0E-99 |
| 7 | g2967.t1 | PANTHER | PTHR44006 | U5 SMALL NUCLEAR RIBONUCLEOPROTEIN 40 KDA PROTEIN | 29 | 352 | 2.0E-135 |
| 10 | g2967.t1 | PRINTS | PR00320 | G protein beta WD-40 repeat signature | 163 | 177 | 9.8E-8 |
| 8 | g2967.t1 | PRINTS | PR00320 | G protein beta WD-40 repeat signature | 246 | 260 | 9.8E-8 |
| 9 | g2967.t1 | PRINTS | PR00320 | G protein beta WD-40 repeat signature | 296 | 310 | 9.8E-8 |
| 6 | g2967.t1 | Pfam | PF00400 | WD domain, G-beta repeat | 53 | 88 | 9.2E-4 |
| 5 | g2967.t1 | Pfam | PF00400 | WD domain, G-beta repeat | 96 | 133 | 2.7E-4 |
| 1 | g2967.t1 | Pfam | PF00400 | WD domain, G-beta repeat | 139 | 176 | 9.0E-6 |
| 4 | g2967.t1 | Pfam | PF00400 | WD domain, G-beta repeat | 224 | 259 | 1.7E-6 |
| 3 | g2967.t1 | Pfam | PF00400 | WD domain, G-beta repeat | 268 | 309 | 1.1E-5 |
| 2 | g2967.t1 | Pfam | PF00400 | WD domain, G-beta repeat | 315 | 348 | 3.0E-4 |
| 15 | g2967.t1 | ProSitePatterns | PS00678 | Trp-Asp (WD) repeats signature. | 163 | 177 | - |
| 14 | g2967.t1 | ProSitePatterns | PS00678 | Trp-Asp (WD) repeats signature. | 296 | 310 | - |
| 23 | g2967.t1 | ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 57 | 355 | 52.15 |
| 28 | g2967.t1 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 57 | 98 | 12.413 |
| 26 | g2967.t1 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 101 | 142 | 11.344 |
| 24 | g2967.t1 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 143 | 176 | 12.413 |
| 29 | g2967.t1 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 227 | 261 | 14.352 |
| 27 | g2967.t1 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 288 | 318 | 10.676 |
| 25 | g2967.t1 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 319 | 355 | 11.143 |
| 22 | g2967.t1 | SMART | SM00320 | WD40_4 | 50 | 89 | 2.1E-6 |
| 17 | g2967.t1 | SMART | SM00320 | WD40_4 | 94 | 133 | 1.3E-5 |
| 16 | g2967.t1 | SMART | SM00320 | WD40_4 | 136 | 176 | 3.4E-7 |
| 19 | g2967.t1 | SMART | SM00320 | WD40_4 | 179 | 217 | 0.045 |
| 18 | g2967.t1 | SMART | SM00320 | WD40_4 | 220 | 259 | 2.8E-8 |
| 21 | g2967.t1 | SMART | SM00320 | WD40_4 | 266 | 309 | 3.4E-6 |
| 20 | g2967.t1 | SMART | SM00320 | WD40_4 | 312 | 351 | 3.6E-5 |
| 11 | g2967.t1 | SUPERFAMILY | SSF50978 | WD40 repeat-like | 53 | 348 | 2.2E-79 |
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 transcript has been annotated with K12857 (Prp8 binding protein)
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.
