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.t6 isoform g12300.t6 22260646 22261649
chr_1 g12300 g12300.t6 exon g12300.t6.exon1 22260646 22261288
chr_1 g12300 g12300.t6 cds g12300.t6.CDS1 22260977 22261288
chr_1 g12300 g12300.t6 exon g12300.t6.exon2 22261363 22261649
chr_1 g12300 g12300.t6 cds g12300.t6.CDS2 22261363 22261539
chr_1 g12300 g12300.t6 TSS g12300.t6 NA NA
chr_1 g12300 g12300.t6 TTS g12300.t6 NA NA

Sequences

>g12300.t6 Gene=g12300 Length=930
CATATGTAGATGAGATAGACATTTACATAACAGAAAAATATTTCAATGGAACATATGACT
CATGTAAAAATGTCATCTATCCGTCGAGTGGACAACTTGCACTTGATTTAATGTGCGGAT
CGTGGGGTGCATCAAAATGTTCGCCTGCTAGATGGTTCGGTTATATGGGAGACGCTGTCA
ATAATCCATTTGTTCCATTTCAAATTAACTATTTGCCTCAAGATTCATCGAGTAGGAATG
ATGATATAAAGCCATTAGACTCAAAAGTCGTACCATGCAATCAGCCTGATAAAACACCAG
CCTGTTCATGTGTTGATTGCCAAGCATCATGCCCTAAGCCTCCACCACCAGATCCTGTTG
TACGACCTTTTATAATTTGGGGTTTTGACGGATATGCGGTCGTTATGTTTTTCATATTTC
TTCTGGGAAGTTTAATATTCATCATGGGTGCAGGATGCTGCTCAACTTCCGAAACTGGTG
AGCTTTTTCGACAATCATTTATTTTTCTTATTCAAATATTGTATACGAATAGAGTGATTA
TTTTTATAAAATCCCCCCGTTTCCTTCTCCCATATCATAAATTCTCCCCTTTTCAATAAG
AAAAATTTTCCATTGAAAATGAAGCAATAAAAAGTTTTCTTTTTCTCTTATTGCTTTAAT
CTGAATAAACTCTTCTTTCATTCTCGTTTTAATGAGGTTTTTGCAACTAACGAGCAACCT
TCATTAATGCGCTTTAAGTTTTTTTTGAAGGAAATTTATTTAACCCAGACTTTGTAAAAT
TCTAAGAAAAAAGTTGAAGCAATGATTAATATCGCTACAAAAATGAAGAAAAATGACGAA
TTTTGTGTACACAGGTGTTTTTTAGTGCAGTGGTGCGATAATAGGAATTTCTTATCAATT
TTTGTTTATGCTCGATTGATATCTATAAAG

>g12300.t6 Gene=g12300 Length=162
MCGSWGASKCSPARWFGYMGDAVNNPFVPFQINYLPQDSSSRNDDIKPLDSKVVPCNQPD
KTPACSCVDCQASCPKPPPPDPVVRPFIIWGFDGYAVVMFFIFLLGSLIFIMGAGCCSTS
ETGELFRQSFIFLIQILYTNRVIIFIKSPRFLLPYHKFSPFQ

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g12300.t6 PANTHER PTHR45727 NPC INTRACELLULAR CHOLESTEROL TRANSPORTER 1 1 111 2.1E-22
3 g12300.t6 PANTHER PTHR45727:SF3 NPC1-LIKE INTRACELLULAR CHOLESTEROL TRANSPORTER 1 1 111 2.1E-22
1 g12300.t6 Pfam PF16414 Niemann-Pick C1 N terminus 1 93 1.5E-22
7 g12300.t6 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 86 -
9 g12300.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 87 113 -
6 g12300.t6 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 114 124 -
10 g12300.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 125 146 -
8 g12300.t6 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 147 162 -
4 g12300.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 95 117 -
5 g12300.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 130 152 -

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.

Raw TPM values