General information for g6669.t5
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.t5 | TSS | g6669.t5 | 18014147 | 18014147 |
| chr_2 | g6669 | g6669.t5 | isoform | g6669.t5 | 18014191 | 18017019 |
| chr_2 | g6669 | g6669.t5 | exon | g6669.t5.exon1 | 18014191 | 18014407 |
| chr_2 | g6669 | g6669.t5 | cds | g6669.t5.CDS1 | 18014362 | 18014407 |
| chr_2 | g6669 | g6669.t5 | exon | g6669.t5.exon2 | 18015026 | 18016928 |
| chr_2 | g6669 | g6669.t5 | cds | g6669.t5.CDS2 | 18015026 | 18016928 |
| chr_2 | g6669 | g6669.t5 | exon | g6669.t5.exon3 | 18016995 | 18017019 |
| chr_2 | g6669 | g6669.t5 | cds | g6669.t5.CDS3 | 18016995 | 18017019 |
| chr_2 | g6669 | g6669.t5 | TTS | g6669.t5 | 18017083 | 18017083 |
Sequences
>g6669.t5 Gene=g6669 Length=2145
ATGATCAAAATTAAATTAATTTTGCTTAATATTGTAATTTTAGTTAATACAGGTAGGTAA
CAAATAACAAAATTATTATTTTTGCATCATTCAAATAAAATATAAATTATCTTTATTACA
GTATATTGTGATCGAACAAAAGATAAAATTTATGAAAATATAAGTGGGCATATGTGCTTC
AGACGGCTTAATGCAACACATCAGACTGGATGTTCATCTGCAGGAAAATCAAGAGGATCT
GTAGGAGTTCTACATTTAATTAGCAGTGAAGACGATATAAATTTTATCATTAACGATCCA
CCTTCTCCGCCATACGCTCCGATTATTTTACCAAATCATTTCACTCGAGAAAATATAATT
AAGCTAAGAGATTCAAATTATGTGTCAGCTATAGTACTTGTTAATGACACAAGTGATTTA
GACAACTTTTCTCAAGAATCAAAATGTCCTAATCAATTTTTTAGACACGCTAAACAGCCT
GTATGTGATTCGAAAAATCAAAATACAGTTTGGAATCCTTTCGGAACTGGACTATTACAC
GAAAACTTTGACATTCCAATCATCTTCTTGGCGAAGAAAGAAGAATCAGATAAAGTGATC
AAATGCTATAATGATTTCAACAAAGCATCATCACGTAAATCATTATGTAGCATAGAAATT
AATTCATTTATGGCTGCATCAGGCAATTCGGAAATATGTATAAGGAGATCAAGAAGTTTG
GCAATAATTCGTCAACTAACTTTTTGTGATCCTTTACAAGGCAAAAATGTTTATGGAACT
TTGTATCCCCGAGAAATTGTCAATCCAATTAATCGAACAAATGACATAGACGAGAAATTC
ATTATTGTTTCTGCTCACTTCGATACAACATCAATGTTTGATGGAATAGCTTTAGGTGCA
ATGGAATTTAGTTCAGTTGCAACACTCATTAGCTCAGCACATTTTTTGAAAAAGATTATC
AAAAAAGATAAGAAAAGCAAGTATAACATTCTCTTTATGTTATTTAATGGTGAATCATAT
GATTATATTGGATCACAAAGATTTATCTATGATTTAAAGAAAAATGATTCATTTCCTTCA
CCATCATCATATACTCGACCACTAACATTAGACAATATTGTTATGATGATTGATATTGGT
GCCCTTGATGATTTTGATAGTGTTTCAATATACCATCTAAATGAATCGGAATCTTTTGCA
TCTAAATTTACATCTGCAATAAATAGCTACAATAATAAATTAAAACTTAATGTCAATATC
AATGCAGTAAATTCTAACAATTTGCCTCCTGTTTCTGCGCAAATGTTTTTAAGAGAAAAT
CCAAACTTTCCAACTTTAATTTTTGCATCGAAAAAGCCAAAAAACAAATTTTATCATTCA
GTATATGATGATGTAAAAAATATGAAATTTTCATATTATAATACAAGTGAAGATTTTGAT
CAACTTGATGACTCAACAAAAATAACTCATTTTCCATCTGACTCTATTCAAATAAAAATT
CGTAATGTTGCCACACTAATATCACTCGGTCTGTACAATCTACTTAACGAAGATAACAAG
TATGCAGAGAATTTAATTGCAAGTTCAACGTTAGTTGATGAATTTTTATATTGCTACTTA
AAAGCAACTAAATGTCGTTTATTTGACTCTATATTTGTCTTTTCAAATGATTTTAATGGT
CTTGATTATCCACCACAACGATACGTGAGTGTACAAGCTGCAATTACATTAGAAGCTACT
GGATGGGCATATAGAGTTTTAGGATTTGTTCTCAGTCAAAAAATTGAGAATATTCAAAAA
GAAAATTGCACAGTGTTACCATATTATTGGATTCCAGGAAGTTTAAAAACTGGTGAATGT
CGTCTTACTACTCAAAATTTAAGTTATGCATTAAGCCCAGCATTTGAAGAAGAAGGATAC
AACTACAAAAGCAACTTATATTCCACTTGGACTGAATCAACATGGAATGATCTCTCAGCA
CGCATATTTTTACAACCATCAACAGCACATGAATCTCTCACCTTTATTATTGGTTTAATT
ATGCTGATTTTATCTTTTATATTGGTTTATTTTATAAATTCAAAGGCTGAAATTTTATTC
AATGATATCAACACAGAACATGTAGCGTTACCTGCTCAGTGCTAA
>g6669.t5 Gene=g6669 Length=657
MCFRRLNATHQTGCSSAGKSRGSVGVLHLISSEDDINFIINDPPSPPYAPIILPNHFTRE
NIIKLRDSNYVSAIVLVNDTSDLDNFSQESKCPNQFFRHAKQPVCDSKNQNTVWNPFGTG
LLHENFDIPIIFLAKKEESDKVIKCYNDFNKASSRKSLCSIEINSFMAASGNSEICIRRS
RSLAIIRQLTFCDPLQGKNVYGTLYPREIVNPINRTNDIDEKFIIVSAHFDTTSMFDGIA
LGAMEFSSVATLISSAHFLKKIIKKDKKSKYNILFMLFNGESYDYIGSQRFIYDLKKNDS
FPSPSSYTRPLTLDNIVMMIDIGALDDFDSVSIYHLNESESFASKFTSAINSYNNKLKLN
VNINAVNSNNLPPVSAQMFLRENPNFPTLIFASKKPKNKFYHSVYDDVKNMKFSYYNTSE
DFDQLDDSTKITHFPSDSIQIKIRNVATLISLGLYNLLNEDNKYAENLIASSTLVDEFLY
CYLKATKCRLFDSIFVFSNDFNGLDYPPQRYVSVQAAITLEATGWAYRVLGFVLSQKIEN
IQKENCTVLPYYWIPGSLKTGECRLTTQNLSYALSPAFEEEGYNYKSNLYSTWTESTWND
LSARIFLQPSTAHESLTFIIGLIMLILSFILVYFINSKAEILFNDINTEHVALPAQC
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g6669.t5 | Gene3D | G3DSA:3.40.630.10 | Zn peptidases | 155 | 426 | 2.1E-20 |
| 3 | g6669.t5 | PANTHER | PTHR21092 | NICASTRIN | 2 | 642 | 1.5E-133 |
| 2 | g6669.t5 | Pfam | PF18266 | Nicastrin small lobe | 2 | 169 | 4.3E-47 |
| 1 | g6669.t5 | Pfam | PF05450 | Nicastrin | 222 | 455 | 1.8E-57 |
| 8 | g6669.t5 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 615 | - |
| 9 | g6669.t5 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 616 | 635 | - |
| 7 | g6669.t5 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 636 | 657 | - |
| 5 | g6669.t5 | SUPERFAMILY | SSF53187 | Zn-dependent exopeptidases | 190 | 419 | 1.3E-16 |
| 4 | g6669.t5 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 615 | 637 | - |
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 transcript has been annotated with K06171 (nicastrin)
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.
