Gene loci information

Transcript annotation

  • This transcript has been annotated as hypothetical.

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_1 g12300 g12300.t5 isoform g12300.t5 22258132 22261649
chr_1 g12300 g12300.t5 exon g12300.t5.exon1 22258132 22258314
chr_1 g12300 g12300.t5 cds g12300.t5.CDS1 22258133 22258314
chr_1 g12300 g12300.t5 exon g12300.t5.exon2 22259041 22259160
chr_1 g12300 g12300.t5 cds g12300.t5.CDS2 22259041 22259160
chr_1 g12300 g12300.t5 exon g12300.t5.exon3 22261099 22261288
chr_1 g12300 g12300.t5 cds g12300.t5.CDS3 22261099 22261288
chr_1 g12300 g12300.t5 exon g12300.t5.exon4 22261357 22261427
chr_1 g12300 g12300.t5 cds g12300.t5.CDS4 22261357 22261427
chr_1 g12300 g12300.t5 exon g12300.t5.exon5 22261512 22261649
chr_1 g12300 g12300.t5 cds g12300.t5.CDS5 22261512 22261539
chr_1 g12300 g12300.t5 TSS g12300.t5 NA NA
chr_1 g12300 g12300.t5 TTS g12300.t5 NA NA

Sequences

>g12300.t5 Gene=g12300 Length=702
CATATGTAGATGAGATAGACATTTACATAACAGAAAAATATTTCAATGGAACATATGACT
CATGTAAAAATGTCATCTATCCGTCGAGTGGACAACTTGCACTTGATTTAATGTGCGGAT
CGTGGGGTGCATCAAAATATTCATCGAGTAGGAATGATGATATAAAGCCATTAGACTCAA
AAGTCGTACCATGCAATCAGCCTGTGGATGATAAAACACCAGCCTGTTCATGTGTTGATT
GCCAAGCATCATGCCCTAAGCCTCCACCACCAGATCCTGTTGTACGACCTTTTATAATTT
GGGGTTTTGACGGATATGCGGTCGTTATGTTTTTCATATTTCTTCTGGGAAGTTTAATAT
TCATCATGGGTGCAGGATGCTGCTCAACTTCCGAAACTGATGTGCAAGATGAACCATATT
TGCATCAGCAGATTGGCAGAAGTTTGGCTGACGATAGATTATCGTCTAGTGACATTGCAA
CCGATCGAGAAGATTCTCCATTGCAGAGTAAACGTTCGAGCCAATCGTCTGAAAACGATC
AAGAATTAACAACACATCCGTCAGCAATTGTTGATAATGAACTTGGAGAGGAAAGTGGAT
ATTTCGAGAAGCTCGGAGCTAAAACAGAGCATGTTCTTGAACAATTTTTCACAGCGTGGG
GAACGTGGTGTGCAAACAATCCATGGAAAGTTTTATTACTCG

>g12300.t5 Gene=g12300 Length=197
MCGSWGASKYSSSRNDDIKPLDSKVVPCNQPVDDKTPACSCVDCQASCPKPPPPDPVVRP
FIIWGFDGYAVVMFFIFLLGSLIFIMGAGCCSTSETDVQDEPYLHQQIGRSLADDRLSSS
DIATDREDSPLQSKRSSQSSENDQELTTHPSAIVDNELGEESGYFEKLGAKTEHVLEQFF
TAWGTWCANNPWKVLLL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
5 g12300.t5 MobiDBLite mobidb-lite consensus disorder prediction 115 151 -
4 g12300.t5 MobiDBLite mobidb-lite consensus disorder prediction 133 151 -
2 g12300.t5 PANTHER PTHR45727 NPC INTRACELLULAR CHOLESTEROL TRANSPORTER 1 12 196 3.4E-19
1 g12300.t5 Pfam PF16414 Niemann-Pick C1 N terminus 11 67 1.4E-10
7 g12300.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 60 -
8 g12300.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 61 85 -
6 g12300.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 86 197 -
3 g12300.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 62 84 -

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

There are no GO annotations for this transcript.

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. There were no conditions that were differentially expressed