General information for g6669.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative 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.t3 | TSS | g6669.t3 | 18014147 | 18014147 |
| chr_2 | g6669 | g6669.t3 | isoform | g6669.t3 | 18014191 | 18015773 |
| chr_2 | g6669 | g6669.t3 | exon | g6669.t3.exon1 | 18014191 | 18014242 |
| chr_2 | g6669 | g6669.t3 | exon | g6669.t3.exon2 | 18014312 | 18014411 |
| chr_2 | g6669 | g6669.t3 | cds | g6669.t3.CDS1 | 18014381 | 18014411 |
| chr_2 | g6669 | g6669.t3 | exon | g6669.t3.exon3 | 18015026 | 18015773 |
| chr_2 | g6669 | g6669.t3 | cds | g6669.t3.CDS2 | 18015026 | 18015771 |
| chr_2 | g6669 | g6669.t3 | TTS | g6669.t3 | 18015766 | 18015766 |
Sequences
>g6669.t3 Gene=g6669 Length=900
ATGATCAAAATTAAATTAATTTTGCTTAATATTGTAATTTTAGTTAATACAGTATATTGT
GATCGAACAAAAGATAAAATTTATGAAAATATAAGTGGGCATATGTGCTTCAGACGGCTT
AATGCAACACATCAGACTGGATGTTCATGTAACTGCAGGAAAATCAAGAGGATCTGTAGG
AGTTCTACATTTAATTAGCAGTGAAGACGATATAAATTTTATCATTAACGATCCACCTTC
TCCGCCATACGCTCCGATTATTTTACCAAATCATTTCACTCGAGAAAATATAATTAAGCT
AAGAGATTCAAATTATGTGTCAGCTATAGTACTTGTTAATGACACAAGTGATTTAGACAA
CTTTTCTCAAGAATCAAAATGTCCTAATCAATTTTTTAGACACGCTAAACAGCCTGTATG
TGATTCGAAAAATCAAAATACAGTTTGGAATCCTTTCGGAACTGGACTATTACACGAAAA
CTTTGACATTCCAATCATCTTCTTGGCGAAGAAAGAAGAATCAGATAAAGTGATCAAATG
CTATAATGATTTCAACAAAGCATCATCACGTAAATCATTATGTAGCATAGAAATTAATTC
ATTTATGGCTGCATCAGGCAATTCGGAAATATGTATAAGGAGATCAAGAAGTTTGGCAAT
AATTCGTCAACTAACTTTTTGTGATCCTTTACAAGGCAAAAATGTTTATGGAACTTTGTA
TCCCCGAGAAATTGTCAATCCAATTAATCGAACAAATGACATAGACGAGAAATTCATTAT
TGTTTCTGCTCACTTCGATACAACATCAATGTTTGATGGAATAGCTTTAGGTGCAATGGA
ATTTAGTTCAGTTGCAACACTCATTAGCTCAGCACATTTTTTGAAAAAGATTATCAAAAA
>g6669.t3 Gene=g6669 Length=259
MQHIRLDVHVTAGKSRGSVGVLHLISSEDDINFIINDPPSPPYAPIILPNHFTRENIIKL
RDSNYVSAIVLVNDTSDLDNFSQESKCPNQFFRHAKQPVCDSKNQNTVWNPFGTGLLHEN
FDIPIIFLAKKEESDKVIKCYNDFNKASSRKSLCSIEINSFMAASGNSEICIRRSRSLAI
IRQLTFCDPLQGKNVYGTLYPREIVNPINRTNDIDEKFIIVSAHFDTTSMFDGIALGAME
FSSVATLISSAHFLKKIIK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 3 | g6669.t3 | PANTHER | PTHR21092 | NICASTRIN | 14 | 257 | 0.0e+00 |
| 2 | g6669.t3 | Pfam | PF18266 | Nicastrin small lobe | 15 | 164 | 0.0e+00 |
| 1 | g6669.t3 | Pfam | PF05450 | Nicastrin | 217 | 257 | 5.1e-06 |
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.
