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.t1 TSS g6669.t1 18014147 18014147
chr_2 g6669 g6669.t1 isoform g6669.t1 18014191 18017019
chr_2 g6669 g6669.t1 exon g6669.t1.exon1 18014191 18014242
chr_2 g6669 g6669.t1 cds g6669.t1.CDS1 18014191 18014242
chr_2 g6669 g6669.t1 exon g6669.t1.exon2 18014312 18014407
chr_2 g6669 g6669.t1 cds g6669.t1.CDS2 18014312 18014407
chr_2 g6669 g6669.t1 exon g6669.t1.exon3 18015026 18016928
chr_2 g6669 g6669.t1 cds g6669.t1.CDS3 18015026 18016928
chr_2 g6669 g6669.t1 exon g6669.t1.exon4 18016995 18017019
chr_2 g6669 g6669.t1 cds g6669.t1.CDS4 18016995 18017019
chr_2 g6669 g6669.t1 TTS g6669.t1 18017083 18017083

Sequences

>g6669.t1 Gene=g6669 Length=2076
ATGATCAAAATTAAATTAATTTTGCTTAATATTGTAATTTTAGTTAATACAGTATATTGT
GATCGAACAAAAGATAAAATTTATGAAAATATAAGTGGGCATATGTGCTTCAGACGGCTT
AATGCAACACATCAGACTGGATGTTCATCTGCAGGAAAATCAAGAGGATCTGTAGGAGTT
CTACATTTAATTAGCAGTGAAGACGATATAAATTTTATCATTAACGATCCACCTTCTCCG
CCATACGCTCCGATTATTTTACCAAATCATTTCACTCGAGAAAATATAATTAAGCTAAGA
GATTCAAATTATGTGTCAGCTATAGTACTTGTTAATGACACAAGTGATTTAGACAACTTT
TCTCAAGAATCAAAATGTCCTAATCAATTTTTTAGACACGCTAAACAGCCTGTATGTGAT
TCGAAAAATCAAAATACAGTTTGGAATCCTTTCGGAACTGGACTATTACACGAAAACTTT
GACATTCCAATCATCTTCTTGGCGAAGAAAGAAGAATCAGATAAAGTGATCAAATGCTAT
AATGATTTCAACAAAGCATCATCACGTAAATCATTATGTAGCATAGAAATTAATTCATTT
ATGGCTGCATCAGGCAATTCGGAAATATGTATAAGGAGATCAAGAAGTTTGGCAATAATT
CGTCAACTAACTTTTTGTGATCCTTTACAAGGCAAAAATGTTTATGGAACTTTGTATCCC
CGAGAAATTGTCAATCCAATTAATCGAACAAATGACATAGACGAGAAATTCATTATTGTT
TCTGCTCACTTCGATACAACATCAATGTTTGATGGAATAGCTTTAGGTGCAATGGAATTT
AGTTCAGTTGCAACACTCATTAGCTCAGCACATTTTTTGAAAAAGATTATCAAAAAAGAT
AAGAAAAGCAAGTATAACATTCTCTTTATGTTATTTAATGGTGAATCATATGATTATATT
GGATCACAAAGATTTATCTATGATTTAAAGAAAAATGATTCATTTCCTTCACCATCATCA
TATACTCGACCACTAACATTAGACAATATTGTTATGATGATTGATATTGGTGCCCTTGAT
GATTTTGATAGTGTTTCAATATACCATCTAAATGAATCGGAATCTTTTGCATCTAAATTT
ACATCTGCAATAAATAGCTACAATAATAAATTAAAACTTAATGTCAATATCAATGCAGTA
AATTCTAACAATTTGCCTCCTGTTTCTGCGCAAATGTTTTTAAGAGAAAATCCAAACTTT
CCAACTTTAATTTTTGCATCGAAAAAGCCAAAAAACAAATTTTATCATTCAGTATATGAT
GATGTAAAAAATATGAAATTTTCATATTATAATACAAGTGAAGATTTTGATCAACTTGAT
GACTCAACAAAAATAACTCATTTTCCATCTGACTCTATTCAAATAAAAATTCGTAATGTT
GCCACACTAATATCACTCGGTCTGTACAATCTACTTAACGAAGATAACAAGTATGCAGAG
AATTTAATTGCAAGTTCAACGTTAGTTGATGAATTTTTATATTGCTACTTAAAAGCAACT
AAATGTCGTTTATTTGACTCTATATTTGTCTTTTCAAATGATTTTAATGGTCTTGATTAT
CCACCACAACGATACGTGAGTGTACAAGCTGCAATTACATTAGAAGCTACTGGATGGGCA
TATAGAGTTTTAGGATTTGTTCTCAGTCAAAAAATTGAGAATATTCAAAAAGAAAATTGC
ACAGTGTTACCATATTATTGGATTCCAGGAAGTTTAAAAACTGGTGAATGTCGTCTTACT
ACTCAAAATTTAAGTTATGCATTAAGCCCAGCATTTGAAGAAGAAGGATACAACTACAAA
AGCAACTTATATTCCACTTGGACTGAATCAACATGGAATGATCTCTCAGCACGCATATTT
TTACAACCATCAACAGCACATGAATCTCTCACCTTTATTATTGGTTTAATTATGCTGATT
TTATCTTTTATATTGGTTTATTTTATAAATTCAAAGGCTGAAATTTTATTCAATGATATC
AACACAGAACATGTAGCGTTACCTGCTCAGTGCTAA

>g6669.t1 Gene=g6669 Length=691
MIKIKLILLNIVILVNTVYCDRTKDKIYENISGHMCFRRLNATHQTGCSSAGKSRGSVGV
LHLISSEDDINFIINDPPSPPYAPIILPNHFTRENIIKLRDSNYVSAIVLVNDTSDLDNF
SQESKCPNQFFRHAKQPVCDSKNQNTVWNPFGTGLLHENFDIPIIFLAKKEESDKVIKCY
NDFNKASSRKSLCSIEINSFMAASGNSEICIRRSRSLAIIRQLTFCDPLQGKNVYGTLYP
REIVNPINRTNDIDEKFIIVSAHFDTTSMFDGIALGAMEFSSVATLISSAHFLKKIIKKD
KKSKYNILFMLFNGESYDYIGSQRFIYDLKKNDSFPSPSSYTRPLTLDNIVMMIDIGALD
DFDSVSIYHLNESESFASKFTSAINSYNNKLKLNVNINAVNSNNLPPVSAQMFLRENPNF
PTLIFASKKPKNKFYHSVYDDVKNMKFSYYNTSEDFDQLDDSTKITHFPSDSIQIKIRNV
ATLISLGLYNLLNEDNKYAENLIASSTLVDEFLYCYLKATKCRLFDSIFVFSNDFNGLDY
PPQRYVSVQAAITLEATGWAYRVLGFVLSQKIENIQKENCTVLPYYWIPGSLKTGECRLT
TQNLSYALSPAFEEEGYNYKSNLYSTWTESTWNDLSARIFLQPSTAHESLTFIIGLIMLI
LSFILVYFINSKAEILFNDINTEHVALPAQC

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g6669.t1 Gene3D G3DSA:3.40.630.10 Zn peptidases 189 460 2.4E-20
3 g6669.t1 PANTHER PTHR21092 NICASTRIN 9 676 1.5E-138
2 g6669.t1 Pfam PF18266 Nicastrin small lobe 36 203 4.7E-47
1 g6669.t1 Pfam PF05450 Nicastrin 256 489 2.0E-57
10 g6669.t1 Phobius SIGNAL_PEPTIDE Signal peptide region 1 20 -
11 g6669.t1 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 5 -
12 g6669.t1 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 6 15 -
14 g6669.t1 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 16 20 -
9 g6669.t1 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 21 649 -
13 g6669.t1 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 650 669 -
8 g6669.t1 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 670 691 -
5 g6669.t1 SUPERFAMILY SSF53187 Zn-dependent exopeptidases 224 453 1.48E-16
6 g6669.t1 SignalP_EUK SignalP-noTM SignalP-noTM 1 20 -
4 g6669.t1 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 649 671 -

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

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.

Raw TPM values