General information for g6333.t7
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.t7 | TTS | g6333.t7 | 16217679 | 16217679 |
| chr_2 | g6333 | g6333.t7 | isoform | g6333.t7 | 16218077 | 16219478 |
| chr_2 | g6333 | g6333.t7 | exon | g6333.t7.exon1 | 16218077 | 16218089 |
| chr_2 | g6333 | g6333.t7 | cds | g6333.t7.CDS1 | 16218079 | 16218089 |
| chr_2 | g6333 | g6333.t7 | exon | g6333.t7.exon2 | 16218146 | 16218354 |
| chr_2 | g6333 | g6333.t7 | cds | g6333.t7.CDS2 | 16218146 | 16218354 |
| chr_2 | g6333 | g6333.t7 | exon | g6333.t7.exon3 | 16218407 | 16219350 |
| chr_2 | g6333 | g6333.t7 | cds | g6333.t7.CDS3 | 16218407 | 16219350 |
| chr_2 | g6333 | g6333.t7 | exon | g6333.t7.exon4 | 16219476 | 16219478 |
| chr_2 | g6333 | g6333.t7 | cds | g6333.t7.CDS4 | 16219476 | 16219478 |
| chr_2 | g6333 | g6333.t7 | TSS | g6333.t7 | 16219586 | 16219586 |
Sequences
>g6333.t7 Gene=g6333 Length=1169
ATGGCTTTGCATGTTTTATATGAGCATGCATCGGGTTATGCTTTGTTCAAGGTGAAAGAA
TTTGAAGATGTTGGGATGTTAATACCACAAGTTCAAGAATCACATGCTGATGTTTCAAGA
TTTCAATCAATTGTGAGTCTAGCAGGTTTTTCACCTTTCAAAACAGCAGTAGCTGCATTA
GAAAATGTAAACGCTGTATCAGAAGGAATCGTTACCGAAGATTTGACAGTATTCCTCGAT
ACTACATTACCATCAAAAAAGAAAAAGTTGACATTAGGTGTTGCTGATGCCAAATTAGGT
GCCGCGATTGCTGAAGCTCTAAATATTCAATGCTCACATATTGGTGCTGTACCTGAAATT
TTACGAGGTATTCGTATGCATTTTCCAAATTTGGTAAAAGGATTCACACCAAAGAGTGCT
GCAATTGCTCAACTTGGTCTTGGTCATAGCTATTCAAGAGCTAAAGTTAAATTCAATGTA
AACAGAGCTGACAACATGATTATTCAATCGATAGCTTTACTTGATCAATTGGACAAAGAC
ATTAACACATTTGCCATGCGTATTCGTGAATGGTATTCTTATCACTTTCCAGAATTGGTC
AAAATTGTTCCCGACAATTACATGTATGCAAAAGTTGCTCAATTCATTAAAGATCGTAGC
AGTTTATCAGATGAAAGCATTCCAGAATTGGAAGAAATTTTAATGGATTCGGGTAAAGCA
GCTTCAATTGTTGAAGCATCAAAAATGTCAATGGGCATGGATATTTCTGAAATTGACTTG
ATGAACATTGAAATGTTTGCTAAACGTGTTGTCAATTTATCAGAATATCGTAAACAACTT
TCAGAATATCTTCATTCAAAAATGAATCAAGTTGCACCTAATCTTCAATCACTCATTGGT
GATCAAGTTGGAGCTCGTCTGATTTCCAAAGCAGGCAGTTTAACAAATTTGGCAAAATAT
CCAGCATCAACAGTTCAAATTTTGGGTGCTGAAAAGGCATTGTTCCGTGCATTGAAAACT
CGCAGTAATACACCAAAATATGGTTTGCTCTTCCATTCTTCATTCATTGCTAAAGCAGGA
TCAAAAAATAAAGGACGAATTTCAAGATTCTTAGCAAATAAATGTTCAGTTGCTTCAAGA
ATTGATTGCTTCACTGAAACACCAACACA
>g6333.t7 Gene=g6333 Length=389
MALHVLYEHASGYALFKVKEFEDVGMLIPQVQESHADVSRFQSIVSLAGFSPFKTAVAAL
ENVNAVSEGIVTEDLTVFLDTTLPSKKKKLTLGVADAKLGAAIAEALNIQCSHIGAVPEI
LRGIRMHFPNLVKGFTPKSAAIAQLGLGHSYSRAKVKFNVNRADNMIIQSIALLDQLDKD
INTFAMRIREWYSYHFPELVKIVPDNYMYAKVAQFIKDRSSLSDESIPELEEILMDSGKA
ASIVEASKMSMGMDISEIDLMNIEMFAKRVVNLSEYRKQLSEYLHSKMNQVAPNLQSLIG
DQVGARLISKAGSLTNLAKYPASTVQILGAEKALFRALKTRSNTPKYGLLFHSSFIAKAG
SKNKGRISRFLANKCSVASRIDCFTETPT
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g6333.t7 | Gene3D | G3DSA:1.10.287.660 | Helix hairpin bin | 167 | 282 | 0.000 |
| 8 | g6333.t7 | Gene3D | G3DSA:1.10.150.460 | - | 197 | 251 | 0.000 |
| 7 | g6333.t7 | Gene3D | G3DSA:1.10.246.90 | - | 283 | 389 | 0.000 |
| 3 | g6333.t7 | PANTHER | PTHR10894 | NUCLEOLAR PROTEIN 5 NUCLEOLAR PROTEIN NOP5 NOP58 | 1 | 389 | 0.000 |
| 4 | g6333.t7 | PANTHER | PTHR10894:SF0 | NUCLEOLAR PROTEIN 56 | 1 | 389 | 0.000 |
| 1 | g6333.t7 | Pfam | PF08156 | NOP5NT (NUC127) domain | 4 | 69 | 0.000 |
| 2 | g6333.t7 | Pfam | PF01798 | snoRNA binding domain, fibrillarin | 173 | 387 | 0.000 |
| 10 | g6333.t7 | ProSiteProfiles | PS51358 | Nop domain profile. | 291 | 389 | 35.733 |
| 6 | g6333.t7 | SMART | SM00931 | NOSIC_2 | 166 | 218 | 0.000 |
| 5 | g6333.t7 | SUPERFAMILY | SSF89124 | Nop domain | 159 | 388 | 0.000 |
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.
