General information for g5064.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Nuclear pore complex protein Nup75.
Parent gene
- The parent gene g5064 is located on chr_2: 6721272..6722028 (- 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 | g5064 | g5064.t1 | isoform | g5064.t1 | 6721272 | 6722028 |
| chr_2 | g5064 | g5064.t1 | exon | g5064.t1.exon1 | 6721272 | 6721394 |
| chr_2 | g5064 | g5064.t1 | cds | g5064.t1.CDS1 | 6721272 | 6721394 |
| chr_2 | g5064 | g5064.t1 | exon | g5064.t1.exon2 | 6721459 | 6721935 |
| chr_2 | g5064 | g5064.t1 | cds | g5064.t1.CDS2 | 6721459 | 6721935 |
| chr_2 | g5064 | g5064.t1 | exon | g5064.t1.exon3 | 6721999 | 6722028 |
| chr_2 | g5064 | g5064.t1 | cds | g5064.t1.CDS3 | 6721999 | 6722028 |
| chr_2 | g5064 | g5064.t1 | TSS | g5064.t1 | 6722140 | 6722140 |
| chr_2 | g5064 | g5064.t1 | TTS | g5064.t1 | NA | NA |
Sequences
>g5064.t1 Gene=g5064 Length=630
ATGTCATCAATTGATTCAACAGTTCGTTTGGTATATGATAAATTAAGCGCTAAAACAGGA
TTTTGTGGCAAATTTGTAACAAATGAAGTACTATCCTTATATCCATCTCAACCAACTCTT
AGTTCATCAGAAAAAGGTGTATCTAAATATGCAAATACAACTGATTCAGTGAATGTTATT
CATGTCACAGAAAATTTCATTCTGGATGATCATATTGTAAGAAGTTTAGTTGCAGAAGCC
TGCAGTATCTTTTATAATCTTCAGATTGCAAAAGAAAAAACAAATGATGTGTTCCTTCAA
ACTTCTCGAGTATATCGCTCAACAATAAGGGCAGCGTTGAATAAATTACAAGAAGCAGTC
ACTGAAGAAACCATAACTCAAGAAGAATTGCAAAAATACGAAAATTTCATTACAATTTTT
TACTCAATTGAATGTTTATGGCATCTTGTTGAATTTCTTTTGATTGATCGATCAACTTTA
TCTGTTGTTCCAAATATACTTGAATGGACAAAATTTCATTTTCCATCTGCGAGTCAAGCA
GCTGCAGATATGCTAATTAACAAAGATCGAGATTTAGATTTCAGAGGCAGTTATTGGGGC
ACAATTAAAGGATTGATTCTTCAAGGATAA
>g5064.t1 Gene=g5064 Length=209
MSSIDSTVRLVYDKLSAKTGFCGKFVTNEVLSLYPSQPTLSSSEKGVSKYANTTDSVNVI
HVTENFILDDHIVRSLVAEACSIFYNLQIAKEKTNDVFLQTSRVYRSTIRAALNKLQEAV
TEETITQEELQKYENFITIFYSIECLWHLVEFLLIDRSTLSVVPNILEWTKFHFPSASQA
AADMLINKDRDLDFRGSYWGTIKGLILQG
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g5064.t1 | PANTHER | PTHR13373 | FROUNT PROTEIN-RELATED | 46 | 209 | 0 |
| 1 | g5064.t1 | Pfam | PF07575 | Nup85 Nucleoporin | 59 | 209 | 0 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5064/g5064.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5064.t1.fa.iupred3.txt does not exist
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.
