General information for g792.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Nucleoporin Ndc1.
Parent gene
- The parent gene g792 is located on chr_3: 6060682..6061380 (+ 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_3 | g792 | g792.t1 | TSS | g792.t1 | 6058649 | 6058649 |
| chr_3 | g792 | g792.t1 | isoform | g792.t1 | 6058841 | 6060682 |
| chr_3 | g792 | g792.t1 | exon | g792.t1.exon1 | 6058841 | 6058848 |
| chr_3 | g792 | g792.t1 | cds | g792.t1.CDS1 | 6058841 | 6058848 |
| chr_3 | g792 | g792.t1 | exon | g792.t1.exon2 | 6058909 | 6060682 |
| chr_3 | g792 | g792.t1 | cds | g792.t1.CDS2 | 6058909 | 6060682 |
| chr_3 | g792 | g792.t1 | TTS | g792.t1 | 6060724 | 6060724 |
Sequences
>g792.t1 Gene=g792 Length=1782
ATGCAAAGCCCAAATGTATCATTTGCTAATTCAACACAAATCTTCTCTAGTCCAATACAA
CATCAAATGCCAACATCGCCAATTCTATTGCAGAATCCTTCAATTAATTCAAACTCGCCT
GTTCAAAAGTCATTTTCTTATGAATCAGAATGTAAGAAGATCTGCCTTAATCGCTTCAAA
TATGTGCTATTCATAACAGCAACAATGCAATATTTGCTATTTATGATATTTTCAATTCCT
TTGAATTTGAAATATTTACATCCAATCGAGTGGTTTAAAGAGTTTTTTGTGATTCTAATC
TCACCTCTGACAATAATCAGTGTTATACATGGTATAAGTTGTCTCAACTTATTGCTCAAA
GAAAAGATCTATTATCCTACAAGAATATCAAGATTCATCAAAAGTTTTACTTATGAAGTA
CTAATGACTCTATTGAATTTCTTGATTGGTCTCTTCACTGCACGCATGTTTGTACGATAT
TTAGATGACTATTACAAATCACCAACTATCAAAAATGAAGACAAAATCGTTTTAAATGAG
TGTTACTCATTCCTTCTATTCTGCGGAGTGTTTATGAGATTATACTATCATTTTAAATAT
AGAGACCACGACTTTGAAGAACTCACTTTTCCAACAGTAAATCAATCAAAATTTTCACAA
ATCAAGCAAGAGTTTTTTACAAGCATTAAATCATCATTTGCTAAGTCACTCATGCCAACA
TTTCATTTTATCGGCTTTTATATTTTCTTCGGGAGCGGATTTTCATATTTCTTGCGAAAA
ATTTACATGTTGAATGCTAGTAATGCATCATTTTGGAGCACATTTGCCATTCTTTTCAAT
ATTCGATTGCTATTCTACTCATATATTTTGGCTGCCTTCATTTTAAGTAATATAAAAATT
ATGAAGAAGATTGTGAATATGTTTGCAACACAACCACATCAATTTTCAATAGCTGGAACT
AACACGTTGATACTCAGTAAAGCACTCGAGTTAAACAAAATTAAAATCACATTGCATCTT
GCGGCACAAGATTTATTCTTGCTAGCGGATAATGCTAATGATTCTAGAAGAAAAGAATTT
TATTCATTATCAATTCCTGGTGGTCATCCACATAATTGGAAGCAACTCGTTCAACAAATA
CTTATTTTAATTGACACATTTTCATCAGATTTGAAGGCAAACATAGAATATGTCGCTAAA
AATCGCAACAACAACACAAGTCCAAATAATCTCAATATAGCCATGTCAAGATTTTATGAA
CAAAAGAGAATGATTCGCGAAACAAATGAAATTAATGGAATTAGAAGTTTTGTAACAAGT
CCATTGAAAGTGACCAATGAACCCACTGTAGAAAAAAGATCACAATTTTTAATGAATGTC
AAGCAAAAGCTTATGAGCAATCATTTAATTGCATATCTTTTTGGAGAAGAGGAAAGTGGA
AAACTTAATTTCATTTTATCGCAAAATTCTCAAGTCATTATATGGGTTGTTCAAGGTGTA
TCAGCAATTGTAGCTCGTTCTGTAAAAGAAGATAATTTTGGAATAATTCAACATGATATA
AAAGCTATTCTTAAATCATTTATCAAATTAAAATCTGTTCTTGATAAAGCAGGAGCAATC
AATACAATTGCCAAGGATAGAAATTTGTATGCAGTGAAAGCAGCATTACGTCGATCTCTC
TATCGAATTGTTACCGAATTTTCAAGCTTTTTCGATGACATGATGTTGGATCCTGAGGAT
ATTCGAGCACTGCAAACATTTGTTAGTTTCAAAGAGTTATAA
>g792.t1 Gene=g792 Length=593
MQSPNVSFANSTQIFSSPIQHQMPTSPILLQNPSINSNSPVQKSFSYESECKKICLNRFK
YVLFITATMQYLLFMIFSIPLNLKYLHPIEWFKEFFVILISPLTIISVIHGISCLNLLLK
EKIYYPTRISRFIKSFTYEVLMTLLNFLIGLFTARMFVRYLDDYYKSPTIKNEDKIVLNE
CYSFLLFCGVFMRLYYHFKYRDHDFEELTFPTVNQSKFSQIKQEFFTSIKSSFAKSLMPT
FHFIGFYIFFGSGFSYFLRKIYMLNASNASFWSTFAILFNIRLLFYSYILAAFILSNIKI
MKKIVNMFATQPHQFSIAGTNTLILSKALELNKIKITLHLAAQDLFLLADNANDSRRKEF
YSLSIPGGHPHNWKQLVQQILILIDTFSSDLKANIEYVAKNRNNNTSPNNLNIAMSRFYE
QKRMIRETNEINGIRSFVTSPLKVTNEPTVEKRSQFLMNVKQKLMSNHLIAYLFGEEESG
KLNFILSQNSQVIIWVVQGVSAIVARSVKEDNFGIIQHDIKAILKSFIKLKSVLDKAGAI
NTIAKDRNLYAVKAALRRSLYRIVTEFSSFFDDMMLDPEDIRALQTFVSFKEL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g792.t1 | PANTHER | PTHR13269 | UNCHARACTERIZED | 60 | 591 | 2.5E-63 |
| 1 | g792.t1 | Pfam | PF09531 | Nucleoporin protein Ndc1-Nup | 53 | 585 | 2.7E-58 |
| 10 | g792.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 60 | - |
| 19 | g792.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 61 | 83 | - |
| 12 | g792.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 84 | 94 | - |
| 17 | g792.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 95 | 119 | - |
| 9 | g792.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 120 | 139 | - |
| 16 | g792.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 140 | 157 | - |
| 14 | g792.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 158 | 176 | - |
| 15 | g792.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 177 | 196 | - |
| 11 | g792.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 197 | 239 | - |
| 18 | g792.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 240 | 258 | - |
| 13 | g792.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 259 | 269 | - |
| 20 | g792.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 270 | 295 | - |
| 8 | g792.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 296 | 593 | - |
| 7 | g792.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 61 | 80 | - |
| 4 | g792.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 95 | 117 | - |
| 5 | g792.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 136 | 158 | - |
| 6 | g792.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 236 | 258 | - |
| 3 | g792.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 271 | 293 | - |
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 K14315 (nucleoporin NDC1)
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.
