General information for g9954.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative 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.t3 | TSS | g9954.t3 | 6179926 | 6179926 |
| chr_1 | g9954 | g9954.t3 | isoform | g9954.t3 | 6179971 | 6182205 |
| chr_1 | g9954 | g9954.t3 | exon | g9954.t3.exon1 | 6179971 | 6182016 |
| chr_1 | g9954 | g9954.t3 | cds | g9954.t3.CDS1 | 6180328 | 6182016 |
| chr_1 | g9954 | g9954.t3 | exon | g9954.t3.exon2 | 6182086 | 6182205 |
| chr_1 | g9954 | g9954.t3 | cds | g9954.t3.CDS2 | 6182086 | 6182205 |
| chr_1 | g9954 | g9954.t3 | TTS | g9954.t3 | 6182255 | 6182255 |
Sequences
>g9954.t3 Gene=g9954 Length=2166
ATGGTGAGAGAAATAAAATTACATGGAATTAAATGCTACAATATATTAGCAAGAGGTATT
AAGCATTTAGCTTATTCAAAAGAGCTCAGTAAATTAGCTGTTCTTCGGTAAGTAAAAATA
TTTCAAATTTTTATCCGGATCAATATTTTAAAAAAAAAATATTTTTGTAGAAATGATTTT
AGTATAGAAATATGGAATTTTACTAATGCTCCTTTTATTGAGCGTGTTATACCTGGTACA
ATTGATTGTGCTCTTGAACAAGTCTGTTGGATAGACAAAAGATTATTTTCTATCTCAATA
TCTGGTTTTGGTTTGATTGAATGGGATCTTAAAACATTGAGCGTTAAAAGAAAATTGATG
CTAACAGGAGATAAAGGAATATGCATTGACTATCATAAAAAAACACAAAGAATTGCAGTT
GGAACTGAAGAAGGATTTATAAATATCTTCGATGTAAGTGATGATGATTTGCAATATGTG
AAAATTTTAGATCGTCAAGATAATAGAATTGTTTGTTGTAAATTCAATGAGTCCGGTGAT
AGTATTGTATCGGGGTCAACAGATGCTGTAAAAATATGGAGTATCAAAACTGGACATGTA
ATTCATAAAATGAGCACAGGGAGAGTTGATAAATTTCAAGAAACCATTGTTTGGTGTGTT
CAAGTTCTAAAAGATTTTACAATTATAACTGGCGATTCAAGAGGAAGAGTCACATTTTGG
GATGGTAATATTGGAACGCAAATTGATTGGGTTCAAGCATCGAATGAGGATATCATGTGT
CTTACAGTGTCTGAAGATCAAAATTCCTTTTTCTGTTCTGGTGTTGAACAAGTTGTAAGA
AAGTATGTGAAAATCACAAACACAAGAGATAACCAGAAGTTTGATCAGTGGATTCGAAAT
GCAAAGCGATACAAATTACATACACATGATATTTTGACATTAACTATGATATCAGATTAT
CAAATTGTTTCTGCTGGAATTGATGGTTTCCTATCTATTGCTTCAAATGAATTAAAAATA
ATTGAAAGAATTGGTCCCTTTTTGAAACATCCATTTGCTGTAACAGCTGATGAAGCTAGA
TTAATGCTTTTGATGTACACAAATTATATTGAAGTTTGGAAGTTAGCTGAAGCTAAGGAT
GAAATGGAAGAAAAACTTCTACGGCAGCAATCTAATGAAGAAACTGATTTAGAAGAAGAC
GATGATGGAATATTAAAACCTGCTGTAACCAATACAACAAGTCAATATTACAAGATGTCA
GTTTTTCCAGAGAAATATCTTGAATTGAGGAGTAAAGGAGATGAGACTGTTTTGTGTGCA
ACAATTTCAACAAATGGTAAATGGATTGCATATTCGACATTAACAACGATGCGTCTATTT
CATTTTGACCTTGAAAACAATAAGCCACAATTGATTCGAATCAAAAATATACCAGACGAT
TTGTCAACTTGTATACAAATGAAATTTTCGTGCGATTCCAATTCACTGATTACTGTAGAT
TCAAAAAGAATTTGCAAAATTTTTGATTTATGTTCAAATGAATTAGAGCATCGACAAACA
ATTGAATTGAATGAATATCATAATGACATAATCCATCACTTGACTATATCAAATTGTTCA
AAATATTTAATTTTTGCTAGTTTATACAATAATGTCAGTGTATGGACTTTGAAGAAGAAA
AAGTACACACATGTTAAAAATTTACCTAAACATATTTGTCCAGCGACTGCGTTAAAACTT
CACAATAGTAAACCATATTTATTAGTTGCTTATGCAAATAATAGAATTATTGAATTCAAT
CTCGAGGAACTTTATATTCAATTTTCACCTTATCTCGCAGAAGATTCATCAAGACATGCT
ATATTAGACATTTGTATTGATCCAGAAAATCCTGATGCCATAATTTTTTCACAAAAAAAT
TCGATAAACATTATTAAAAGAGGAGATGGAGAAAATGATGCAAAAAAATCAGTGAAGAAA
AAGAAATTACAGACTGATGAAGAAAAGTTAAAATATACGCATAGAATCGTTAAAAAGTTT
GACACTTATCTTATTCATCTTGAATGGCTTGGAGAGAGCGAACTTTTAGCATTAGAAATG
AATCCTGTTTCACTTATGGAAAATTTACCGGCACCTCTGAGAAGAAAAGTTTTTGGTACT
ATGTAA
>g9954.t3 Gene=g9954 Length=602
MLTGDKGICIDYHKKTQRIAVGTEEGFINIFDVSDDDLQYVKILDRQDNRIVCCKFNESG
DSIVSGSTDAVKIWSIKTGHVIHKMSTGRVDKFQETIVWCVQVLKDFTIITGDSRGRVTF
WDGNIGTQIDWVQASNEDIMCLTVSEDQNSFFCSGVEQVVRKYVKITNTRDNQKFDQWIR
NAKRYKLHTHDILTLTMISDYQIVSAGIDGFLSIASNELKIIERIGPFLKHPFAVTADEA
RLMLLMYTNYIEVWKLAEAKDEMEEKLLRQQSNEETDLEEDDDGILKPAVTNTTSQYYKM
SVFPEKYLELRSKGDETVLCATISTNGKWIAYSTLTTMRLFHFDLENNKPQLIRIKNIPD
DLSTCIQMKFSCDSNSLITVDSKRICKIFDLCSNELEHRQTIELNEYHNDIIHHLTISNC
SKYLIFASLYNNVSVWTLKKKKYTHVKNLPKHICPATALKLHNSKPYLLVAYANNRIIEF
NLEELYIQFSPYLAEDSSRHAILDICIDPENPDAIIFSQKNSINIIKRGDGENDAKKSVK
KKKLQTDEEKLKYTHRIVKKFDTYLIHLEWLGESELLALEMNPVSLMENLPAPLRRKVFG
TM
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 13 | g9954.t3 | Coils | Coil | Coil | 256 | 276 | - |
| 12 | g9954.t3 | Coils | Coil | Coil | 602 | 602 | - |
| 10 | g9954.t3 | Gene3D | G3DSA:2.130.10.10 | - | 7 | 302 | 2.1E-24 |
| 11 | g9954.t3 | Gene3D | G3DSA:2.130.10.10 | - | 307 | 569 | 2.1E-17 |
| 1 | g9954.t3 | PANTHER | PTHR44163 | U3 SMALL NUCLEOLAR RNA-ASSOCIATED PROTEIN 4 HOMOLOG | 8 | 601 | 8.0E-109 |
| 4 | g9954.t3 | SMART | SM00320 | WD40_4 | 37 | 75 | 0.0049 |
| 8 | g9954.t3 | SMART | SM00320 | WD40_4 | 78 | 122 | 14.0 |
| 3 | g9954.t3 | SMART | SM00320 | WD40_4 | 125 | 164 | 200.0 |
| 7 | g9954.t3 | SMART | SM00320 | WD40_4 | 172 | 216 | 110.0 |
| 5 | g9954.t3 | SMART | SM00320 | WD40_4 | 351 | 390 | 24.0 |
| 9 | g9954.t3 | SMART | SM00320 | WD40_4 | 397 | 437 | 21.0 |
| 6 | g9954.t3 | SMART | SM00320 | WD40_4 | 442 | 481 | 25.0 |
| 2 | g9954.t3 | SUPERFAMILY | SSF50998 | Quinoprotein alcohol dehydrogenase-like | 8 | 471 | 1.33E-33 |
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 gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).
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.
