Gene loci information

Transcript annotation

  • This transcript has been annotated as Nucleolar protein 56.

Parent gene

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.t9 TTS g6333.t9 16217679 16217679
chr_2 g6333 g6333.t9 isoform g6333.t9 16218412 16219478
chr_2 g6333 g6333.t9 exon g6333.t9.exon1 16218412 16219350
chr_2 g6333 g6333.t9 cds g6333.t9.CDS1 16218412 16219350
chr_2 g6333 g6333.t9 exon g6333.t9.exon2 16219476 16219478
chr_2 g6333 g6333.t9 cds g6333.t9.CDS2 16219476 16219478
chr_2 g6333 g6333.t9 TSS g6333.t9 16219586 16219586

Sequences

>g6333.t9 Gene=g6333 Length=942
ATGGCTTTGCATGTTTTATATGAGCATGCATCGGGTTATGCTTTGTTCAAGGTGAAAGAA
TTTGAAGATGTTGGGATGTTAATACCACAAGTTCAAGAATCACATGCTGATGTTTCAAGA
TTTCAATCAATTGTGAGTCTAGCAGGTTTTTCACCTTTCAAAACAGCAGTAGCTGCATTA
GAAAATGTAAACGCTGTATCAGAAGGAATCGTTACCGAAGATTTGACAGTATTCCTCGAT
ACTACATTACCATCAAAAAAGAAAAAGTTGACATTAGGTGTTGCTGATGCCAAATTAGGT
GCCGCGATTGCTGAAGCTCTAAATATTCAATGCTCACATATTGGTGCTGTACCTGAAATT
TTACGAGGTATTCGTATGCATTTTCCAAATTTGGTAAAAGGATTCACACCAAAGAGTGCT
GCAATTGCTCAACTTGGTCTTGGTCATAGCTATTCAAGAGCTAAAGTTAAATTCAATGTA
AACAGAGCTGACAACATGATTATTCAATCGATAGCTTTACTTGATCAATTGGACAAAGAC
ATTAACACATTTGCCATGCGTATTCGTGAATGGTATTCTTATCACTTTCCAGAATTGGTC
AAAATTGTTCCCGACAATTACATGTATGCAAAAGTTGCTCAATTCATTAAAGATCGTAGC
AGTTTATCAGATGAAAGCATTCCAGAATTGGAAGAAATTTTAATGGATTCGGGTAAAGCA
GCTTCAATTGTTGAAGCATCAAAAATGTCAATGGGCATGGATATTTCTGAAATTGACTTG
ATGAACATTGAAATGTTTGCTAAACGTGTTGTCAATTTATCAGAATATCGTAAACAACTT
TCAGAATATCTTCATTCAAAAATGAATCAAGTTGCACCTAATCTTCAATCACTCATTGGT
GATCAAGTTGGAGCTCGTCTGATTTCCAAAGCAGGCAGTTTA

>g6333.t9 Gene=g6333 Length=314
MALHVLYEHASGYALFKVKEFEDVGMLIPQVQESHADVSRFQSIVSLAGFSPFKTAVAAL
ENVNAVSEGIVTEDLTVFLDTTLPSKKKKLTLGVADAKLGAAIAEALNIQCSHIGAVPEI
LRGIRMHFPNLVKGFTPKSAAIAQLGLGHSYSRAKVKFNVNRADNMIIQSIALLDQLDKD
INTFAMRIREWYSYHFPELVKIVPDNYMYAKVAQFIKDRSSLSDESIPELEEILMDSGKA
ASIVEASKMSMGMDISEIDLMNIEMFAKRVVNLSEYRKQLSEYLHSKMNQVAPNLQSLIG
DQVGARLISKAGSL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g6333.t9 Gene3D G3DSA:1.10.287.660 Helix hairpin bin 167 282 0.000
8 g6333.t9 Gene3D G3DSA:1.10.150.460 - 197 251 0.000
7 g6333.t9 Gene3D G3DSA:1.10.246.90 - 283 314 0.000
3 g6333.t9 PANTHER PTHR10894 NUCLEOLAR PROTEIN 5 NUCLEOLAR PROTEIN NOP5 NOP58 1 314 0.000
4 g6333.t9 PANTHER PTHR10894:SF0 NUCLEOLAR PROTEIN 56 1 314 0.000
1 g6333.t9 Pfam PF08156 NOP5NT (NUC127) domain 4 69 0.000
2 g6333.t9 Pfam PF01798 snoRNA binding domain, fibrillarin 173 314 0.000
10 g6333.t9 ProSiteProfiles PS51358 Nop domain profile. 291 314 12.423
6 g6333.t9 SMART SM00931 NOSIC_2 166 218 0.000
5 g6333.t9 SUPERFAMILY SSF89124 Nop domain 159 314 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 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. There were no conditions that were differentially expressed