General information for g12952.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative NPC intracellular cholesterol transporter 1 homolog 1b.
Parent gene
- The parent gene g12952 is located on chr_1: 27111772..27114877 (- 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_1 | g12952 | g12952.t2 | isoform | g12952.t2 | 27110942 | 27112242 |
| chr_1 | g12952 | g12952.t2 | exon | g12952.t2.exon1 | 27110942 | 27111383 |
| chr_1 | g12952 | g12952.t2 | cds | g12952.t2.CDS1 | 27110944 | 27111383 |
| chr_1 | g12952 | g12952.t2 | exon | g12952.t2.exon2 | 27111446 | 27112242 |
| chr_1 | g12952 | g12952.t2 | cds | g12952.t2.CDS2 | 27111446 | 27111584 |
| chr_1 | g12952 | g12952.t2 | TSS | g12952.t2 | NA | NA |
| chr_1 | g12952 | g12952.t2 | TTS | g12952.t2 | NA | NA |
Sequences
>g12952.t2 Gene=g12952 Length=1239
AATGTAAGTTTACATTTGTCAAAAAGTAATCTGCAAAGATTTTCAATTCTAAGATTTTTC
GCATTTTTATTTATTTCTACTTCTTGGTCAGGGAACAGGACCGTTATAATTCTTAATTTG
AATGGCGCGCATTTTTCTTTATCCTAAAAAGACGTTACAAATTTCGTTCCAAAAGTTTTA
ATTTCTTTGAAAATGACAAATTTTGTTTAAATACTTGTTAAATTCAATAGTAATTACTCA
ATGATGATTCATTATGGTGTTGTAATCAAGTTTTAAATCGTAATTATCATTAAAACTTTA
AAACTAAAAAATTTTTTTAGAAGAATTTTTGTTTCTTTGGATTGAAACGCGCTCATTCAA
TTTGAATTTGAAAAAATTAACTGCCAAATTTTTGTATCCGGTTCCCTTGACTTTTTGGAT
AAAATTTTTAGTTAATTTCATAACTCTAATTTTTATTTTTTATTTCTAACAGAATGATCC
ACCATGTTCATGCGTCGATTGTATTTCATCATGTCCAATAGCACAGGAAGTAAAAAAGAA
TTCTGAAAACTTTAAAATTCTCAACTATGACGGCTATATTTTCATAATTATGCTCATATT
CTTCATTGGCAGTTTAATGTTTACGGTGTTTGCAAACAGAAAAGTTCCGAGTAAAGAAAT
GAATCACATAAAGAACAAGAATTTTGAATTGAGTATGTCAGAACAATATGCTCAAAAAGT
TGAAAAGTTTTTACAGGAAATATTTACTAATTGGGGAAAATTTTGTGCAACTCATCCATT
GAAAGTTATTTTTATAAGTTTGTTATTAGTCGCATGTTTTGCTTATGGAACACGATTTTC
ACAAGTAACTGTCGATCCAATTGAATTATGGGCTTCATCAACTTCTCAATCACGCATTCA
AAAAGATTTTTTTGATTCAAAATTTGATCCATTTTATCGAGTTGAGCAAGTAATCATTAC
AGCCAAAGGTTATCAGGATATCATTCACAATACATCAAATGGGGTCATTAATTTTGGACC
AGCTTTTAACAAAGAATTTCTTTTAAAAGTGCTAGAAATTCAACAATCAATTGAAAATAT
TGACAATGGAGTTTTAAAGGACATTTGTTTTGCACCATTAAGATCTGCAAATTTACCAAA
AGATGAATATGAAGTGACTGATTGCCTTGTACAGAGTATTTGGGGCTATTTCCAAAATAG
AAAAAAAGAAATTACCGATCCAAAAAGGAATAATAGAAA
>g12952.t2 Gene=g12952 Length=193
MNHIKNKNFELSMSEQYAQKVEKFLQEIFTNWGKFCATHPLKVIFISLLLVACFAYGTRF
SQVTVDPIELWASSTSQSRIQKDFFDSKFDPFYRVEQVIITAKGYQDIIHNTSNGVINFG
PAFNKEFLLKVLEIQQSIENIDNGVLKDICFAPLRSANLPKDEYEVTDCLVQSIWGYFQN
RKKEITDPKRNNR
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value |
|---|---|---|---|---|---|---|
| g12952.t2 | PANTHER | PTHR45727 | NPC INTRACELLULAR CHOLESTEROL TRANSPORTER 1 | 20 | 185 | 0 |
| g12952.t2 | PANTHER | PTHR45727:SF6 | NPC INTRACELLULAR CHOLESTEROL TRANSPORTER 1 HOMOLOG 1B | 20 | 185 | 0 |
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. There were no conditions that were differentially expressed