Gene loci information

Transcript annotation

  • This transcript has been annotated as Nicastrin.

Parent gene

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.t6 TSS g6669.t6 18015025 18015025
chr_2 g6669 g6669.t6 isoform g6669.t6 18015773 18016928
chr_2 g6669 g6669.t6 exon g6669.t6.exon1 18015773 18016928
chr_2 g6669 g6669.t6 cds g6669.t6.CDS1 18015805 18016926
chr_2 g6669 g6669.t6 TTS g6669.t6 18017083 18017083

Sequences

>g6669.t6 Gene=g6669 Length=1156
AAGATAAGAAAAGCAAGTATAACATTCTCTTTATGTTATTTAATGGTGAATCATATGATT
ATATTGGATCACAAAGATTTATCTATGATTTAAAGAAAAATGATTCATTTCCTTCACCAT
CATCATATACTCGACCACTAACATTAGACAATATTGTTATGATGATTGATATTGGTGCCC
TTGATGATTTTGATAGTGTTTCAATATACCATCTAAATGAATCGGAATCTTTTGCATCTA
AATTTACATCTGCAATAAATAGCTACAATAATAAATTAAAACTTAATGTCAATATCAATG
CAGTAAATTCTAACAATTTGCCTCCTGTTTCTGCGCAAATGTTTTTAAGAGAAAATCCAA
ACTTTCCAACTTTAATTTTTGCATCGAAAAAGCCAAAAAACAAATTTTATCATTCAGTAT
ATGATGATGTAAAAAATATGAAATTTTCATATTATAATACAAGTGAAGATTTTGATCAAC
TTGATGACTCAACAAAAATAACTCATTTTCCATCTGACTCTATTCAAATAAAAATTCGTA
ATGTTGCCACACTAATATCACTCGGTCTGTACAATCTACTTAACGAAGATAACAAGTATG
CAGAGAATTTAATTGCAAGTTCAACGTTAGTTGATGAATTTTTATATTGCTACTTAAAAG
CAACTAAATGTCGTTTATTTGACTCTATATTTGTCTTTTCAAATGATTTTAATGGTCTTG
ATTATCCACCACAACGATACGTGAGTGTACAAGCTGCAATTACATTAGAAGCTACTGGAT
GGGCATATAGAGTTTTAGGATTTGTTCTCAGTCAAAAAATTGAGAATATTCAAAAAGAAA
ATTGCACAGTGTTACCATATTATTGGATTCCAGGAAGTTTAAAAACTGGTGAATGTCGTC
TTACTACTCAAAATTTAAGTTATGCATTAAGCCCAGCATTTGAAGAAGAAGGATACAACT
ACAAAAGCAACTTATATTCCACTTGGACTGAATCAACATGGAATGATCTCTCAGCACGCA
TATTTTTACAACCATCAACAGCACATGAATCTCTCACCTTTATTATTGGTTTAATTATGC
TGATTTTATCTTTTATATTGGTTTATTTTATAAATTCAAAGGCTGAAATTTTATTCAATG
ATATCAACACAGAACA

>g6669.t6 Gene=g6669 Length=374
MLFNGESYDYIGSQRFIYDLKKNDSFPSPSSYTRPLTLDNIVMMIDIGALDDFDSVSIYH
LNESESFASKFTSAINSYNNKLKLNVNINAVNSNNLPPVSAQMFLRENPNFPTLIFASKK
PKNKFYHSVYDDVKNMKFSYYNTSEDFDQLDDSTKITHFPSDSIQIKIRNVATLISLGLY
NLLNEDNKYAENLIASSTLVDEFLYCYLKATKCRLFDSIFVFSNDFNGLDYPPQRYVSVQ
AAITLEATGWAYRVLGFVLSQKIENIQKENCTVLPYYWIPGSLKTGECRLTTQNLSYALS
PAFEEEGYNYKSNLYSTWTESTWNDLSARIFLQPSTAHESLTFIIGLIMLILSFILVYFI
NSKAEILFNDINTE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
5 g6669.t6 Gene3D G3DSA:3.40.630.10 Zn peptidases 1 154 2.5E-7
2 g6669.t6 PANTHER PTHR21092 NICASTRIN 2 367 1.8E-65
1 g6669.t6 Pfam PF05450 Nicastrin 2 180 2.4E-41
7 g6669.t6 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 340 -
8 g6669.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 341 360 -
6 g6669.t6 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 361 374 -
4 g6669.t6 SUPERFAMILY SSF53187 Zn-dependent exopeptidases 2 144 7.69E-5
3 g6669.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 340 362 -

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

## Warning: Removed 1 row(s) containing missing values (geom_path).

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.

Raw TPM values