General information for g9954.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as U3 small nucleolar RNA-associated protein 4-like protein.
Parent gene
- The parent gene g9954 is located on chr_1: 6182205..6184148 (+ 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_1 | g9954 | g9954.t1 | TSS | g9954.t1 | 6179926 | 6179926 |
| chr_1 | g9954 | g9954.t1 | isoform | g9954.t1 | 6179971 | 6182205 |
| chr_1 | g9954 | g9954.t1 | exon | g9954.t1.exon1 | 6179971 | 6180077 |
| chr_1 | g9954 | g9954.t1 | cds | g9954.t1.CDS1 | 6179971 | 6180077 |
| chr_1 | g9954 | g9954.t1 | exon | g9954.t1.exon2 | 6180141 | 6182016 |
| chr_1 | g9954 | g9954.t1 | cds | g9954.t1.CDS2 | 6180141 | 6182016 |
| chr_1 | g9954 | g9954.t1 | exon | g9954.t1.exon3 | 6182086 | 6182205 |
| chr_1 | g9954 | g9954.t1 | cds | g9954.t1.CDS3 | 6182086 | 6182205 |
| chr_1 | g9954 | g9954.t1 | TTS | g9954.t1 | 6182255 | 6182255 |
Sequences
>g9954.t1 Gene=g9954 Length=2103
ATGGTGAGAGAAATAAAATTACATGGAATTAAATGCTACAATATATTAGCAAGAGGTATT
AAGCATTTAGCTTATTCAAAAGAGCTCAGTAAATTAGCTGTTCTTCGAAATGATTTTAGT
ATAGAAATATGGAATTTTACTAATGCTCCTTTTATTGAGCGTGTTATACCTGGTACAATT
GATTGTGCTCTTGAACAAGTCTGTTGGATAGACAAAAGATTATTTTCTATCTCAATATCT
GGTTTTGGTTTGATTGAATGGGATCTTAAAACATTGAGCGTTAAAAGAAAATTGATGCTA
ACAGGAGATAAAGGAATATGCATTGACTATCATAAAAAAACACAAAGAATTGCAGTTGGA
ACTGAAGAAGGATTTATAAATATCTTCGATGTAAGTGATGATGATTTGCAATATGTGAAA
ATTTTAGATCGTCAAGATAATAGAATTGTTTGTTGTAAATTCAATGAGTCCGGTGATAGT
ATTGTATCGGGGTCAACAGATGCTGTAAAAATATGGAGTATCAAAACTGGACATGTAATT
CATAAAATGAGCACAGGGAGAGTTGATAAATTTCAAGAAACCATTGTTTGGTGTGTTCAA
GTTCTAAAAGATTTTACAATTATAACTGGCGATTCAAGAGGAAGAGTCACATTTTGGGAT
GGTAATATTGGAACGCAAATTGATTGGGTTCAAGCATCGAATGAGGATATCATGTGTCTT
ACAGTGTCTGAAGATCAAAATTCCTTTTTCTGTTCTGGTGTTGAACAAGTTGTAAGAAAG
TATGTGAAAATCACAAACACAAGAGATAACCAGAAGTTTGATCAGTGGATTCGAAATGCA
AAGCGATACAAATTACATACACATGATATTTTGACATTAACTATGATATCAGATTATCAA
ATTGTTTCTGCTGGAATTGATGGTTTCCTATCTATTGCTTCAAATGAATTAAAAATAATT
GAAAGAATTGGTCCCTTTTTGAAACATCCATTTGCTGTAACAGCTGATGAAGCTAGATTA
ATGCTTTTGATGTACACAAATTATATTGAAGTTTGGAAGTTAGCTGAAGCTAAGGATGAA
ATGGAAGAAAAACTTCTACGGCAGCAATCTAATGAAGAAACTGATTTAGAAGAAGACGAT
GATGGAATATTAAAACCTGCTGTAACCAATACAACAAGTCAATATTACAAGATGTCAGTT
TTTCCAGAGAAATATCTTGAATTGAGGAGTAAAGGAGATGAGACTGTTTTGTGTGCAACA
ATTTCAACAAATGGTAAATGGATTGCATATTCGACATTAACAACGATGCGTCTATTTCAT
TTTGACCTTGAAAACAATAAGCCACAATTGATTCGAATCAAAAATATACCAGACGATTTG
TCAACTTGTATACAAATGAAATTTTCGTGCGATTCCAATTCACTGATTACTGTAGATTCA
AAAAGAATTTGCAAAATTTTTGATTTATGTTCAAATGAATTAGAGCATCGACAAACAATT
GAATTGAATGAATATCATAATGACATAATCCATCACTTGACTATATCAAATTGTTCAAAA
TATTTAATTTTTGCTAGTTTATACAATAATGTCAGTGTATGGACTTTGAAGAAGAAAAAG
TACACACATGTTAAAAATTTACCTAAACATATTTGTCCAGCGACTGCGTTAAAACTTCAC
AATAGTAAACCATATTTATTAGTTGCTTATGCAAATAATAGAATTATTGAATTCAATCTC
GAGGAACTTTATATTCAATTTTCACCTTATCTCGCAGAAGATTCATCAAGACATGCTATA
TTAGACATTTGTATTGATCCAGAAAATCCTGATGCCATAATTTTTTCACAAAAAAATTCG
ATAAACATTATTAAAAGAGGAGATGGAGAAAATGATGCAAAAAAATCAGTGAAGAAAAAG
AAATTACAGACTGATGAAGAAAAGTTAAAATATACGCATAGAATCGTTAAAAAGTTTGAC
ACTTATCTTATTCATCTTGAATGGCTTGGAGAGAGCGAACTTTTAGCATTAGAAATGAAT
CCTGTTTCACTTATGGAAAATTTACCGGCACCTCTGAGAAGAAAAGTTTTTGGTACTATG
TAA
>g9954.t1 Gene=g9954 Length=700
MVREIKLHGIKCYNILARGIKHLAYSKELSKLAVLRNDFSIEIWNFTNAPFIERVIPGTI
DCALEQVCWIDKRLFSISISGFGLIEWDLKTLSVKRKLMLTGDKGICIDYHKKTQRIAVG
TEEGFINIFDVSDDDLQYVKILDRQDNRIVCCKFNESGDSIVSGSTDAVKIWSIKTGHVI
HKMSTGRVDKFQETIVWCVQVLKDFTIITGDSRGRVTFWDGNIGTQIDWVQASNEDIMCL
TVSEDQNSFFCSGVEQVVRKYVKITNTRDNQKFDQWIRNAKRYKLHTHDILTLTMISDYQ
IVSAGIDGFLSIASNELKIIERIGPFLKHPFAVTADEARLMLLMYTNYIEVWKLAEAKDE
MEEKLLRQQSNEETDLEEDDDGILKPAVTNTTSQYYKMSVFPEKYLELRSKGDETVLCAT
ISTNGKWIAYSTLTTMRLFHFDLENNKPQLIRIKNIPDDLSTCIQMKFSCDSNSLITVDS
KRICKIFDLCSNELEHRQTIELNEYHNDIIHHLTISNCSKYLIFASLYNNVSVWTLKKKK
YTHVKNLPKHICPATALKLHNSKPYLLVAYANNRIIEFNLEELYIQFSPYLAEDSSRHAI
LDICIDPENPDAIIFSQKNSINIIKRGDGENDAKKSVKKKKLQTDEEKLKYTHRIVKKFD
TYLIHLEWLGESELLALEMNPVSLMENLPAPLRRKVFGTM
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 14 | g9954.t1 | Coils | Coil | Coil | 354 | 374 | - |
| 13 | g9954.t1 | Gene3D | G3DSA:2.130.10.10 | - | 104 | 401 | 3.3E-24 |
| 12 | g9954.t1 | Gene3D | G3DSA:2.130.10.10 | - | 405 | 667 | 2.9E-17 |
| 1 | g9954.t1 | PANTHER | PTHR44163 | U3 SMALL NUCLEOLAR RNA-ASSOCIATED PROTEIN 4 HOMOLOG | 4 | 699 | 2.2E-134 |
| 7 | g9954.t1 | SMART | SM00320 | WD40_4 | 9 | 45 | 180.0 |
| 11 | g9954.t1 | SMART | SM00320 | WD40_4 | 93 | 130 | 7.1 |
| 8 | g9954.t1 | SMART | SM00320 | WD40_4 | 135 | 173 | 0.0049 |
| 4 | g9954.t1 | SMART | SM00320 | WD40_4 | 176 | 220 | 14.0 |
| 3 | g9954.t1 | SMART | SM00320 | WD40_4 | 223 | 262 | 200.0 |
| 5 | g9954.t1 | SMART | SM00320 | WD40_4 | 270 | 314 | 110.0 |
| 9 | g9954.t1 | SMART | SM00320 | WD40_4 | 449 | 488 | 24.0 |
| 6 | g9954.t1 | SMART | SM00320 | WD40_4 | 495 | 535 | 21.0 |
| 10 | g9954.t1 | SMART | SM00320 | WD40_4 | 540 | 579 | 25.0 |
| 2 | g9954.t1 | SUPERFAMILY | SSF50998 | Quinoprotein alcohol dehydrogenase-like | 85 | 593 | 1.96E-31 |
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 K14548 (U3 small nucleolar RNA-associated protein 4)
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.
