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.t2 TSS g4141.t2 30907144 30907144
chr_3 g4141 g4141.t2 isoform g4141.t2 30907213 30907946
chr_3 g4141 g4141.t2 exon g4141.t2.exon1 30907213 30907291
chr_3 g4141 g4141.t2 cds g4141.t2.CDS1 30907213 30907291
chr_3 g4141 g4141.t2 exon g4141.t2.exon2 30907396 30907512
chr_3 g4141 g4141.t2 cds g4141.t2.CDS2 30907396 30907512
chr_3 g4141 g4141.t2 exon g4141.t2.exon3 30907612 30907668
chr_3 g4141 g4141.t2 cds g4141.t2.CDS3 30907612 30907668
chr_3 g4141 g4141.t2 exon g4141.t2.exon4 30907735 30907946
chr_3 g4141 g4141.t2 cds g4141.t2.CDS4 30907735 30907946
chr_3 g4141 g4141.t2 TTS g4141.t2 30908070 30908070

Sequences

>g4141.t2 Gene=g4141 Length=465
ATGAAATTGTCTGCCGTAGTTATTGTTCTTATCAGCGGTTTTTTGTGTGTAGCCTATTGT
GCAGAGATTAAAAATTGCGATACAGAAGCAGAGGGTAAATTTACACGTGTGACTGTGACT
GATTGTGACGAAAGTCAGGAAAGATGTATTTTAAAAAAAGGAACAAACGCCACAATTACA
ATAGATTTTGAATTGGATTTAGACGTTGAGACGGAAAATGAGGTCAAGGCAGTTTGTTTC
GGTAAATTAGGAGCTCTTGAAGTTCCATTTAAATTACCAAATCCAAATGCTTGTAAAGAC
TCAGGACTGGAGTGTCCATTAAAAAAGAATGTTGCATATACATATGAAGCATCGTTTCCG
ATCCTAAAAGTCTACCCCAAAGTCAACGTTGATGTGAAATATGAGTTGAAAAATAAAGAA
AATAAGAATATCGTTTGTGTCCTCGTACCAGTTAAAATTGTTTAA

>g4141.t2 Gene=g4141 Length=154
MKLSAVVIVLISGFLCVAYCAEIKNCDTEAEGKFTRVTVTDCDESQERCILKKGTNATIT
IDFELDLDVETENEVKAVCFGKLGALEVPFKLPNPNACKDSGLECPLKKNVAYTYEASFP
ILKVYPKVNVDVKYELKNKENKNIVCVLVPVKIV

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g4141.t2 CDD cd00916 Npc2_like 31 151 1.04862E-35
7 g4141.t2 Gene3D G3DSA:2.60.40.770 - 22 154 1.5E-40
2 g4141.t2 PANTHER PTHR11306 NIEMANN PICK TYPE C2 PROTEIN NPC2-RELATED 3 154 4.5E-33
3 g4141.t2 PANTHER PTHR11306:SF30 NPC INTRACELLULAR CHOLESTEROL TRANSPORTER 2 3 154 4.5E-33
1 g4141.t2 Pfam PF02221 ML domain 23 153 1.2E-24
9 g4141.t2 Phobius SIGNAL_PEPTIDE Signal peptide region 1 20 -
10 g4141.t2 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 2 -
11 g4141.t2 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 3 15 -
12 g4141.t2 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 16 20 -
8 g4141.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 21 154 -
14 g4141.t2 SMART SM00737 pgtp_13 23 151 1.4E-23
4 g4141.t2 SUPERFAMILY SSF81296 E set domains 22 154 2.29E-29
6 g4141.t2 SignalP_EUK SignalP-noTM SignalP-noTM 1 20 -
5 g4141.t2 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM 1 20 -

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