General information for g4141.t8
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative NPC intracellular cholesterol transporter 2 homolog a.
Parent gene
- The parent gene g4141 is located on chr_3: 30907395..30909809 (+ strand)
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.t8 | TSS | g4141.t8 | 30907144 | 30907144 |
| chr_3 | g4141 | g4141.t8 | isoform | g4141.t8 | 30907395 | 30907946 |
| chr_3 | g4141 | g4141.t8 | exon | g4141.t8.exon1 | 30907395 | 30907512 |
| chr_3 | g4141 | g4141.t8 | cds | g4141.t8.CDS1 | 30907395 | 30907512 |
| chr_3 | g4141 | g4141.t8 | exon | g4141.t8.exon2 | 30907618 | 30907668 |
| chr_3 | g4141 | g4141.t8 | cds | g4141.t8.CDS2 | 30907618 | 30907668 |
| chr_3 | g4141 | g4141.t8 | exon | g4141.t8.exon3 | 30907735 | 30907946 |
| chr_3 | g4141 | g4141.t8 | cds | g4141.t8.CDS3 | 30907735 | 30907946 |
| chr_3 | g4141 | g4141.t8 | TTS | g4141.t8 | 30908070 | 30908070 |
Sequences
>g4141.t8 Gene=g4141 Length=381
GATACAGAAGCAGAGGGTAAATTTACACGTGTGACTGTGACTGATTGTGACGAAAGTCAG
GAAAGATGTATTTTAAAAAAAGGAACAAACGCCACAATTACAATAGATTTTGAATTGGAC
GTTGAGACGGAAAATGAGGTCAAGGCAGTTTGTTTCGGTAAATTAGGAGCTCTTGAAGTT
CCATTTAAATTACCAAATCCAAATGCTTGTAAAGACTCAGGACTGGAGTGTCCATTAAAA
AAGAATGTTGCATATACATATGAAGCATCGTTTCCGATCCTAAAAGTCTACCCCAAAGTC
AACGTTGATGTGAAATATGAGTTGAAAAATAAAGAAAATAAGAATATCGTTTGTGTCCTC
GTACCAGTTAAAATTGTTTAA
>g4141.t8 Gene=g4141 Length=126
DTEAEGKFTRVTVTDCDESQERCILKKGTNATITIDFELDVETENEVKAVCFGKLGALEV
PFKLPNPNACKDSGLECPLKKNVAYTYEASFPILKVYPKVNVDVKYELKNKENKNIVCVL
VPVKIV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g4141.t8 | CDD | cd00916 | Npc2_like | 5 | 123 | 0 |
| 6 | g4141.t8 | Gene3D | G3DSA:2.60.40.770 | - | 2 | 126 | 0 |
| 2 | g4141.t8 | PANTHER | PTHR11306 | NIEMANN PICK TYPE C2 PROTEIN NPC2-RELATED | 4 | 126 | 0 |
| 3 | g4141.t8 | PANTHER | PTHR11306:SF30 | NPC INTRACELLULAR CHOLESTEROL TRANSPORTER 2 | 4 | 126 | 0 |
| 1 | g4141.t8 | Pfam | PF02221 | ML domain | 6 | 125 | 0 |
| 5 | g4141.t8 | SMART | SM00737 | pgtp_13 | 1 | 123 | 0 |
| 4 | g4141.t8 | SUPERFAMILY | SSF81296 | E set domains | 7 | 126 | 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
- This transcript has been annotated with K13443 (Niemann-Pick C2 protein)
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.
