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.t2 TSS g6669.t2 18014147 18014147
chr_2 g6669 g6669.t2 isoform g6669.t2 18014191 18015773
chr_2 g6669 g6669.t2 exon g6669.t2.exon1 18014191 18014242
chr_2 g6669 g6669.t2 cds g6669.t2.CDS1 18014191 18014242
chr_2 g6669 g6669.t2 exon g6669.t2.exon2 18014312 18014407
chr_2 g6669 g6669.t2 cds g6669.t2.CDS2 18014312 18014407
chr_2 g6669 g6669.t2 exon g6669.t2.exon3 18015026 18015773
chr_2 g6669 g6669.t2 cds g6669.t2.CDS3 18015026 18015771
chr_2 g6669 g6669.t2 TTS g6669.t2 18015766 18015766

Sequences

>g6669.t2 Gene=g6669 Length=896
ATGATCAAAATTAAATTAATTTTGCTTAATATTGTAATTTTAGTTAATACAGTATATTGT
GATCGAACAAAAGATAAAATTTATGAAAATATAAGTGGGCATATGTGCTTCAGACGGCTT
AATGCAACACATCAGACTGGATGTTCATCTGCAGGAAAATCAAGAGGATCTGTAGGAGTT
CTACATTTAATTAGCAGTGAAGACGATATAAATTTTATCATTAACGATCCACCTTCTCCG
CCATACGCTCCGATTATTTTACCAAATCATTTCACTCGAGAAAATATAATTAAGCTAAGA
GATTCAAATTATGTGTCAGCTATAGTACTTGTTAATGACACAAGTGATTTAGACAACTTT
TCTCAAGAATCAAAATGTCCTAATCAATTTTTTAGACACGCTAAACAGCCTGTATGTGAT
TCGAAAAATCAAAATACAGTTTGGAATCCTTTCGGAACTGGACTATTACACGAAAACTTT
GACATTCCAATCATCTTCTTGGCGAAGAAAGAAGAATCAGATAAAGTGATCAAATGCTAT
AATGATTTCAACAAAGCATCATCACGTAAATCATTATGTAGCATAGAAATTAATTCATTT
ATGGCTGCATCAGGCAATTCGGAAATATGTATAAGGAGATCAAGAAGTTTGGCAATAATT
CGTCAACTAACTTTTTGTGATCCTTTACAAGGCAAAAATGTTTATGGAACTTTGTATCCC
CGAGAAATTGTCAATCCAATTAATCGAACAAATGACATAGACGAGAAATTCATTATTGTT
TCTGCTCACTTCGATACAACATCAATGTTTGATGGAATAGCTTTAGGTGCAATGGAATTT
AGTTCAGTTGCAACACTCATTAGCTCAGCACATTTTTTGAAAAAGATTATCAAAAA

>g6669.t2 Gene=g6669 Length=298
MIKIKLILLNIVILVNTVYCDRTKDKIYENISGHMCFRRLNATHQTGCSSAGKSRGSVGV
LHLISSEDDINFIINDPPSPPYAPIILPNHFTRENIIKLRDSNYVSAIVLVNDTSDLDNF
SQESKCPNQFFRHAKQPVCDSKNQNTVWNPFGTGLLHENFDIPIIFLAKKEESDKVIKCY
NDFNKASSRKSLCSIEINSFMAASGNSEICIRRSRSLAIIRQLTFCDPLQGKNVYGTLYP
REIVNPINRTNDIDEKFIIVSAHFDTTSMFDGIALGAMEFSSVATLISSAHFLKKIIK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
3 g6669.t2 PANTHER PTHR21092 NICASTRIN 9 296 3.5E-61
2 g6669.t2 Pfam PF18266 Nicastrin small lobe 36 203 7.4E-48
1 g6669.t2 Pfam PF05450 Nicastrin 256 296 6.3E-6
6 g6669.t2 Phobius SIGNAL_PEPTIDE Signal peptide region 1 20 -
7 g6669.t2 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 5 -
8 g6669.t2 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 6 15 -
9 g6669.t2 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 16 20 -
5 g6669.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 21 298 -
4 g6669.t2 SignalP_EUK SignalP-noTM SignalP-noTM 1 20 -

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.

Raw TPM values