General information for g6333.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Nucleolar protein 56.
Parent gene
- The parent gene g6333 is located on chr_2: 16218412..16219478 (- 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_2 | g6333 | g6333.t4 | isoform | g6333.t4 | 16217523 | 16219478 |
| chr_2 | g6333 | g6333.t4 | exon | g6333.t4.exon1 | 16217523 | 16217909 |
| chr_2 | g6333 | g6333.t4 | cds | g6333.t4.CDS1 | 16217523 | 16217909 |
| chr_2 | g6333 | g6333.t4 | exon | g6333.t4.exon2 | 16217971 | 16218089 |
| chr_2 | g6333 | g6333.t4 | cds | g6333.t4.CDS2 | 16217971 | 16218089 |
| chr_2 | g6333 | g6333.t4 | exon | g6333.t4.exon3 | 16218146 | 16218354 |
| chr_2 | g6333 | g6333.t4 | cds | g6333.t4.CDS3 | 16218146 | 16218354 |
| chr_2 | g6333 | g6333.t4 | exon | g6333.t4.exon4 | 16218407 | 16219350 |
| chr_2 | g6333 | g6333.t4 | cds | g6333.t4.CDS4 | 16218407 | 16219278 |
| chr_2 | g6333 | g6333.t4 | exon | g6333.t4.exon5 | 16219472 | 16219478 |
| chr_2 | g6333 | g6333.t4 | TSS | g6333.t4 | 16219586 | 16219586 |
| chr_2 | g6333 | g6333.t4 | TTS | g6333.t4 | NA | NA |
Sequences
>g6333.t4 Gene=g6333 Length=1666
ATGGTAAGCTTTGCATGTTTTATATGAGCATGCATCGGGTTATGCTTTGTTCAAGGTGAA
AGAATTTGAAGATGTTGGGATGTTAATACCACAAGTTCAAGAATCACATGCTGATGTTTC
AAGATTTCAATCAATTGTGAGTCTAGCAGGTTTTTCACCTTTCAAAACAGCAGTAGCTGC
ATTAGAAAATGTAAACGCTGTATCAGAAGGAATCGTTACCGAAGATTTGACAGTATTCCT
CGATACTACATTACCATCAAAAAAGAAAAAGTTGACATTAGGTGTTGCTGATGCCAAATT
AGGTGCCGCGATTGCTGAAGCTCTAAATATTCAATGCTCACATATTGGTGCTGTACCTGA
AATTTTACGAGGTATTCGTATGCATTTTCCAAATTTGGTAAAAGGATTCACACCAAAGAG
TGCTGCAATTGCTCAACTTGGTCTTGGTCATAGCTATTCAAGAGCTAAAGTTAAATTCAA
TGTAAACAGAGCTGACAACATGATTATTCAATCGATAGCTTTACTTGATCAATTGGACAA
AGACATTAACACATTTGCCATGCGTATTCGTGAATGGTATTCTTATCACTTTCCAGAATT
GGTCAAAATTGTTCCCGACAATTACATGTATGCAAAAGTTGCTCAATTCATTAAAGATCG
TAGCAGTTTATCAGATGAAAGCATTCCAGAATTGGAAGAAATTTTAATGGATTCGGGTAA
AGCAGCTTCAATTGTTGAAGCATCAAAAATGTCAATGGGCATGGATATTTCTGAAATTGA
CTTGATGAACATTGAAATGTTTGCTAAACGTGTTGTCAATTTATCAGAATATCGTAAACA
ACTTTCAGAATATCTTCATTCAAAAATGAATCAAGTTGCACCTAATCTTCAATCACTCAT
TGGTGATCAAGTTGGAGCTCGTCTGATTTCCAAAGCAGGCAGTTTAACAAATTTGGCAAA
ATATCCAGCATCAACAGTTCAAATTTTGGGTGCTGAAAAGGCATTGTTCCGTGCATTGAA
AACTCGCAGTAATACACCAAAATATGGTTTGCTCTTCCATTCTTCATTCATTGCTAAAGC
AGGATCAAAAAATAAAGGACGAATTTCAAGATTCTTAGCAAATAAATGTTCAGTTGCTTC
AAGAATTGATTGCTTCACTGAAACACCAACACATGTTTTTGGCGATTATCTAAAGCAACA
AGTTGAAGATCGATTGAAATTCTATGAATCTGGTGATGCTCCACGAAAGAATTTGGATGT
GATGAAAGAAGCCATTCAAGTTGCAGGAAATCAAGCATCAGAAGAAAGTAAGAAGAAAAA
GAAGAAGAAGGATAAGAAACGCAAATCAGAAAATGGTGCCACTATAGCGGATGAGAGTTT
AATGGAAACATCAGCAGTTGTTGAAGAAGAAACTCCCTCAAAGAAAAAGAAGAAGAAATC
AAAACAGAATGGAAATGATGCTGATGTAAATGTCTCACAAGAAGAGGATGTTGCTGTTGA
AGAACCACCGAAAAAGAAGAAGAAAAAGAATGGGACAGCAAATGCCGATGAAACTTTGAA
TGATGACTCGCAGCTTAATGCAACACAAGAAGAAGAGACAAATGGCGAAGAAAAGAAGAA
AAAAAAGAAAAAGAAGAAGAGTTTAGTGGCAATGGATGAAGATTAA
>g6333.t4 Gene=g6333 Length=528
MLIPQVQESHADVSRFQSIVSLAGFSPFKTAVAALENVNAVSEGIVTEDLTVFLDTTLPS
KKKKLTLGVADAKLGAAIAEALNIQCSHIGAVPEILRGIRMHFPNLVKGFTPKSAAIAQL
GLGHSYSRAKVKFNVNRADNMIIQSIALLDQLDKDINTFAMRIREWYSYHFPELVKIVPD
NYMYAKVAQFIKDRSSLSDESIPELEEILMDSGKAASIVEASKMSMGMDISEIDLMNIEM
FAKRVVNLSEYRKQLSEYLHSKMNQVAPNLQSLIGDQVGARLISKAGSLTNLAKYPASTV
QILGAEKALFRALKTRSNTPKYGLLFHSSFIAKAGSKNKGRISRFLANKCSVASRIDCFT
ETPTHVFGDYLKQQVEDRLKFYESGDAPRKNLDVMKEAIQVAGNQASEESKKKKKKKDKK
RKSENGATIADESLMETSAVVEEETPSKKKKKKSKQNGNDADVNVSQEEDVAVEEPPKKK
KKKNGTANADETLNDDSQLNATQEEETNGEEKKKKKKKKKSLVAMDED
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 13 | g6333.t4 | Gene3D | G3DSA:1.10.287.660 | Helix hairpin bin | 142 | 257 | 1.5E-50 |
| 12 | g6333.t4 | Gene3D | G3DSA:1.10.150.460 | - | 172 | 226 | 1.5E-50 |
| 11 | g6333.t4 | Gene3D | G3DSA:1.10.246.90 | - | 258 | 384 | 1.9E-52 |
| 10 | g6333.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 401 | 528 | - |
| 9 | g6333.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 442 | 458 | - |
| 8 | g6333.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 471 | 489 | - |
| 7 | g6333.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 490 | 504 | - |
| 3 | g6333.t4 | PANTHER | PTHR10894 | NUCLEOLAR PROTEIN 5 NUCLEOLAR PROTEIN NOP5 NOP58 | 2 | 519 | 2.8E-220 |
| 4 | g6333.t4 | PANTHER | PTHR10894:SF0 | NUCLEOLAR PROTEIN 56 | 2 | 519 | 2.8E-220 |
| 1 | g6333.t4 | Pfam | PF08156 | NOP5NT (NUC127) domain | 4 | 44 | 3.1E-9 |
| 2 | g6333.t4 | Pfam | PF01798 | snoRNA binding domain, fibrillarin | 148 | 380 | 5.4E-84 |
| 14 | g6333.t4 | ProSiteProfiles | PS51358 | Nop domain profile. | 266 | 384 | 38.13 |
| 6 | g6333.t4 | SMART | SM00931 | NOSIC_2 | 141 | 193 | 3.5E-32 |
| 5 | g6333.t4 | SUPERFAMILY | SSF89124 | Nop domain | 134 | 383 | 5.23E-92 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
There are no GO annotations for this transcript.
KEGG
Orthology
- This transcript has been annotated with K14564 (nucleolar protein 56)
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. There were no conditions that were differentially expressed