Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative 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.t4 TSS g6669.t4 18014147 18014147
chr_2 g6669 g6669.t4 isoform g6669.t4 18014191 18016170
chr_2 g6669 g6669.t4 exon g6669.t4.exon1 18014191 18014242
chr_2 g6669 g6669.t4 exon g6669.t4.exon2 18014312 18014407
chr_2 g6669 g6669.t4 exon g6669.t4.exon3 18015032 18016170
chr_2 g6669 g6669.t4 cds g6669.t4.CDS1 18015478 18016170
chr_2 g6669 g6669.t4 TTS g6669.t4 18017083 18017083

Sequences

>g6669.t4 Gene=g6669 Length=1287
ATGATCAAAATTAAATTAATTTTGCTTAATATTGTAATTTTAGTTAATACAGTATATTGT
GATCGAACAAAAGATAAAATTTATGAAAATATAAGTGGGCATATGTGCTTCAGACGGCTT
AATGCAACACATCAGACTGGATGTTCATGAAAATCAAGAGGATCTGTAGGAGTTCTACAT
TTAATTAGCAGTGAAGACGATATAAATTTTATCATTAACGATCCACCTTCTCCGCCATAC
GCTCCGATTATTTTACCAAATCATTTCACTCGAGAAAATATAATTAAGCTAAGAGATTCA
AATTATGTGTCAGCTATAGTACTTGTTAATGACACAAGTGATTTAGACAACTTTTCTCAA
GAATCAAAATGTCCTAATCAATTTTTTAGACACGCTAAACAGCCTGTATGTGATTCGAAA
AATCAAAATACAGTTTGGAATCCTTTCGGAACTGGACTATTACACGAAAACTTTGACATT
CCAATCATCTTCTTGGCGAAGAAAGAAGAATCAGATAAAGTGATCAAATGCTATAATGAT
TTCAACAAAGCATCATCACGTAAATCATTATGTAGCATAGAAATTAATTCATTTATGGCT
GCATCAGGCAATTCGGAAATATGTATAAGGAGATCAAGAAGTTTGGCAATAATTCGTCAA
CTAACTTTTTGTGATCCTTTACAAGGCAAAAATGTTTATGGAACTTTGTATCCCCGAGAA
ATTGTCAATCCAATTAATCGAACAAATGACATAGACGAGAAATTCATTATTGTTTCTGCT
CACTTCGATACAACATCAATGTTTGATGGAATAGCTTTAGGTGCAATGGAATTTAGTTCA
GTTGCAACACTCATTAGCTCAGCACATTTTTTGAAAAAGATTATCAAAAAAGATAAGAAA
AGCAAGTATAACATTCTCTTTATGTTATTTAATGGTGAATCATATGATTATATTGGATCA
CAAAGATTTATCTATGATTTAAAGAAAAATGATTCATTTCCTTCACCATCATCATATACT
CGACCACTAACATTAGACAATATTGTTATGATGATTGATATTGGTGCCCTTGATGATTTT
GATAGTGTTTCAATATACCATCTAAATGAATCGGAATCTTTTGCATCTAAATTTACATCT
GCAATAAATAGCTACAATAATAAATTAAAACTTAATGTCAATATCAATGCAGTAAATTCT
AACAATTTGCCTCCTGTTTCTGCGCAAATGTTTTTAAGAGAAAATCCAAACTTTCCAACT
TTAATTTTTGCATCGAAAAAGCCAAAA

>g6669.t4 Gene=g6669 Length=231
MAASGNSEICIRRSRSLAIIRQLTFCDPLQGKNVYGTLYPREIVNPINRTNDIDEKFIIV
SAHFDTTSMFDGIALGAMEFSSVATLISSAHFLKKIIKKDKKSKYNILFMLFNGESYDYI
GSQRFIYDLKKNDSFPSPSSYTRPLTLDNIVMMIDIGALDDFDSVSIYHLNESESFASKF
TSAINSYNNKLKLNVNINAVNSNNLPPVSAQMFLRENPNFPTLIFASKKPK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
4 g6669.t4 Gene3D G3DSA:3.40.630.10 Zn peptidases 17 228 1.1E-15
2 g6669.t4 PANTHER PTHR21092 NICASTRIN 1 226 3.7E-43
1 g6669.t4 Pfam PF05450 Nicastrin 56 228 2.9E-45
6 g6669.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 72 -
7 g6669.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 73 93 -
5 g6669.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 94 231 -
3 g6669.t4 SUPERFAMILY SSF53187 Zn-dependent exopeptidases 24 225 1.69E-13

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