General information for g6669.t7
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Nicastrin.
Parent gene
- The parent gene g6669 is located on chr_2: 18016934..18018147 (+ 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 | g6669 | g6669.t7 | isoform | g6669.t7 | 18016107 | 18017019 |
| chr_2 | g6669 | g6669.t7 | exon | g6669.t7.exon1 | 18016107 | 18016928 |
| chr_2 | g6669 | g6669.t7 | cds | g6669.t7.CDS1 | 18016111 | 18016928 |
| chr_2 | g6669 | g6669.t7 | exon | g6669.t7.exon2 | 18016995 | 18017019 |
| chr_2 | g6669 | g6669.t7 | cds | g6669.t7.CDS2 | 18016995 | 18017019 |
| chr_2 | g6669 | g6669.t7 | TTS | g6669.t7 | 18017083 | 18017083 |
| chr_2 | g6669 | g6669.t7 | TSS | g6669.t7 | NA | NA |
Sequences
>g6669.t7 Gene=g6669 Length=847
GCAAATGTTTTTAAGAGAAAATCCAAACTTTCCAACTTTAATTTTTGCATCGAAAAAGCC
AAAAAACAAATTTTATCATTCAGTATATGATGATGTAAAAAATATGAAATTTTCATATTA
TAATACAAGTGAAGATTTTGATCAACTTGATGACTCAACAAAAATAACTCATTTTCCATC
TGACTCTATTCAAATAAAAATTCGTAATGTTGCCACACTAATATCACTCGGTCTGTACAA
TCTACTTAACGAAGATAACAAGTATGCAGAGAATTTAATTGCAAGTTCAACGTTAGTTGA
TGAATTTTTATATTGCTACTTAAAAGCAACTAAATGTCGTTTATTTGACTCTATATTTGT
CTTTTCAAATGATTTTAATGGTCTTGATTATCCACCACAACGATACGTGAGTGTACAAGC
TGCAATTACATTAGAAGCTACTGGATGGGCATATAGAGTTTTAGGATTTGTTCTCAGTCA
AAAAATTGAGAATATTCAAAAAGAAAATTGCACAGTGTTACCATATTATTGGATTCCAGG
AAGTTTAAAAACTGGTGAATGTCGTCTTACTACTCAAAATTTAAGTTATGCATTAAGCCC
AGCATTTGAAGAAGAAGGATACAACTACAAAAGCAACTTATATTCCACTTGGACTGAATC
AACATGGAATGATCTCTCAGCACGCATATTTTTACAACCATCAACAGCACATGAATCTCT
CACCTTTATTATTGGTTTAATTATGCTGATTTTATCTTTTATATTGGTTTATTTTATAAA
TTCAAAGGCTGAAATTTTATTCAATGATATCAACACAGAACATGTAGCGTTACCTGCTCA
GTGCTAA
>g6669.t7 Gene=g6669 Length=280
MFLRENPNFPTLIFASKKPKNKFYHSVYDDVKNMKFSYYNTSEDFDQLDDSTKITHFPSD
SIQIKIRNVATLISLGLYNLLNEDNKYAENLIASSTLVDEFLYCYLKATKCRLFDSIFVF
SNDFNGLDYPPQRYVSVQAAITLEATGWAYRVLGFVLSQKIENIQKENCTVLPYYWIPGS
LKTGECRLTTQNLSYALSPAFEEEGYNYKSNLYSTWTESTWNDLSARIFLQPSTAHESLT
FIIGLIMLILSFILVYFINSKAEILFNDINTEHVALPAQC
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g6669.t7 | PANTHER | PTHR21092 | NICASTRIN | 2 | 265 | 4.6E-42 |
| 1 | g6669.t7 | Pfam | PF05450 | Nicastrin | 2 | 78 | 8.7E-13 |
| 5 | g6669.t7 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 238 | - |
| 6 | g6669.t7 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 239 | 258 | - |
| 4 | g6669.t7 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 259 | 280 | - |
| 3 | g6669.t7 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 238 | 260 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0016485 | protein processing | BP |
| GO:0016021 | integral component of membrane | CC |
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.
