Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative NPC intracellular cholesterol transporter 2 homolog a.

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_3 g4141 g4141.t5 TSS g4141.t5 30907144 30907144
chr_3 g4141 g4141.t5 isoform g4141.t5 30907213 30907946
chr_3 g4141 g4141.t5 exon g4141.t5.exon1 30907213 30907270
chr_3 g4141 g4141.t5 cds g4141.t5.CDS1 30907215 30907270
chr_3 g4141 g4141.t5 exon g4141.t5.exon2 30907370 30907512
chr_3 g4141 g4141.t5 cds g4141.t5.CDS2 30907370 30907512
chr_3 g4141 g4141.t5 exon g4141.t5.exon3 30907618 30907668
chr_3 g4141 g4141.t5 cds g4141.t5.CDS3 30907618 30907668
chr_3 g4141 g4141.t5 exon g4141.t5.exon4 30907735 30907946
chr_3 g4141 g4141.t5 cds g4141.t5.CDS4 30907735 30907946
chr_3 g4141 g4141.t5 TTS g4141.t5 30908070 30908070

Sequences

>g4141.t5 Gene=g4141 Length=464
ATGAAATTGTCTGCCGTAGTTATTGTTCTTATCAGCGGTTTTTTGTGTGTAGCCTATTTT
TTAAAATCCATTCGAACAATGCAGATACAGAAGCAGAGGGTAAATTTACACGTGTGACTG
TGACTGATTGTGACGAAAGTCAGGAAAGATGTATTTTAAAAAAAGGAACAAACGCCACAA
TTACAATAGATTTTGAATTGGACGTTGAGACGGAAAATGAGGTCAAGGCAGTTTGTTTCG
GTAAATTAGGAGCTCTTGAAGTTCCATTTAAATTACCAAATCCAAATGCTTGTAAAGACT
CAGGACTGGAGTGTCCATTAAAAAAGAATGTTGCATATACATATGAAGCATCGTTTCCGA
TCCTAAAAGTCTACCCCAAAGTCAACGTTGATGTGAAATATGAGTTGAAAAATAAAGAAA
ATAAGAATATCGTTTGTGTCCTCGTACCAGTTAAAATTGTTTAA

>g4141.t5 Gene=g4141 Length=153
EIVCRSYCSYQRFFVCSLFFKIHSNNADTEAEGKFTRVTVTDCDESQERCILKKGTNATI
TIDFELDVETENEVKAVCFGKLGALEVPFKLPNPNACKDSGLECPLKKNVAYTYEASFPI
LKVYPKVNVDVKYELKNKENKNIVCVLVPVKIV

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g4141.t5 CDD cd00916 Npc2_like 32 150 0
6 g4141.t5 Gene3D G3DSA:2.60.40.770 - 25 153 0
2 g4141.t5 PANTHER PTHR11306 NIEMANN PICK TYPE C2 PROTEIN NPC2-RELATED 29 153 0
3 g4141.t5 PANTHER PTHR11306:SF30 NPC INTRACELLULAR CHOLESTEROL TRANSPORTER 2 29 153 0
1 g4141.t5 Pfam PF02221 ML domain 33 152 0
5 g4141.t5 SMART SM00737 pgtp_13 13 150 0
4 g4141.t5 SUPERFAMILY SSF81296 E set domains 33 153 0

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:0032367 intracellular cholesterol transport BP

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. There were no conditions that were differentially expressed