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.t3 TSS g4141.t3 30907144 30907144
chr_3 g4141 g4141.t3 isoform g4141.t3 30907213 30907946
chr_3 g4141 g4141.t3 exon g4141.t3.exon1 30907213 30907291
chr_3 g4141 g4141.t3 cds g4141.t3.CDS1 30907213 30907291
chr_3 g4141 g4141.t3 exon g4141.t3.exon2 30907402 30907512
chr_3 g4141 g4141.t3 cds g4141.t3.CDS2 30907402 30907512
chr_3 g4141 g4141.t3 exon g4141.t3.exon3 30907618 30907668
chr_3 g4141 g4141.t3 cds g4141.t3.CDS3 30907618 30907668
chr_3 g4141 g4141.t3 exon g4141.t3.exon4 30907735 30907946
chr_3 g4141 g4141.t3 cds g4141.t3.CDS4 30907735 30907946
chr_3 g4141 g4141.t3 TTS g4141.t3 30908070 30908070

Sequences

>g4141.t3 Gene=g4141 Length=453
ATGAAATTGTCTGCCGTAGTTATTGTTCTTATCAGCGGTTTTTTGTGTGTAGCCTATTGT
GCAGAGATTAAAAATTGCGAAGCAGAGGGTAAATTTACACGTGTGACTGTGACTGATTGT
GACGAAAGTCAGGAAAGATGTATTTTAAAAAAAGGAACAAACGCCACAATTACAATAGAT
TTTGAATTGGACGTTGAGACGGAAAATGAGGTCAAGGCAGTTTGTTTCGGTAAATTAGGA
GCTCTTGAAGTTCCATTTAAATTACCAAATCCAAATGCTTGTAAAGACTCAGGACTGGAG
TGTCCATTAAAAAAGAATGTTGCATATACATATGAAGCATCGTTTCCGATCCTAAAAGTC
TACCCCAAAGTCAACGTTGATGTGAAATATGAGTTGAAAAATAAAGAAAATAAGAATATC
GTTTGTGTCCTCGTACCAGTTAAAATTGTTTAA

>g4141.t3 Gene=g4141 Length=150
MKLSAVVIVLISGFLCVAYCAEIKNCEAEGKFTRVTVTDCDESQERCILKKGTNATITID
FELDVETENEVKAVCFGKLGALEVPFKLPNPNACKDSGLECPLKKNVAYTYEASFPILKV
YPKVNVDVKYELKNKENKNIVCVLVPVKIV

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g4141.t3 CDD cd00916 Npc2_like 23 147 6.28687E-36
7 g4141.t3 Gene3D G3DSA:2.60.40.770 - 22 150 1.2E-40
2 g4141.t3 PANTHER PTHR11306 NIEMANN PICK TYPE C2 PROTEIN NPC2-RELATED 3 150 4.9E-33
3 g4141.t3 PANTHER PTHR11306:SF30 NPC INTRACELLULAR CHOLESTEROL TRANSPORTER 2 3 150 4.9E-33
1 g4141.t3 Pfam PF02221 ML domain 23 149 8.0E-26
9 g4141.t3 Phobius SIGNAL_PEPTIDE Signal peptide region 1 20 -
10 g4141.t3 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 2 -
11 g4141.t3 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 3 15 -
12 g4141.t3 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 16 20 -
8 g4141.t3 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 21 150 -
14 g4141.t3 SMART SM00737 pgtp_13 23 147 1.1E-25
4 g4141.t3 SUPERFAMILY SSF81296 E set domains 22 150 4.53E-30
6 g4141.t3 SignalP_EUK SignalP-noTM SignalP-noTM 1 20 -
5 g4141.t3 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