General information for g12952.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 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.t3 | isoform | g12952.t3 | 27110942 | 27113085 |
| chr_1 | g12952 | g12952.t3 | exon | g12952.t3.exon1 | 27110942 | 27111383 |
| chr_1 | g12952 | g12952.t3 | cds | g12952.t3.CDS1 | 27110944 | 27111383 |
| chr_1 | g12952 | g12952.t3 | exon | g12952.t3.exon2 | 27111446 | 27111770 |
| chr_1 | g12952 | g12952.t3 | cds | g12952.t3.CDS2 | 27111446 | 27111770 |
| chr_1 | g12952 | g12952.t3 | exon | g12952.t3.exon3 | 27112240 | 27112541 |
| chr_1 | g12952 | g12952.t3 | cds | g12952.t3.CDS3 | 27112240 | 27112541 |
| chr_1 | g12952 | g12952.t3 | exon | g12952.t3.exon4 | 27112597 | 27112756 |
| chr_1 | g12952 | g12952.t3 | cds | g12952.t3.CDS4 | 27112597 | 27112693 |
| chr_1 | g12952 | g12952.t3 | exon | g12952.t3.exon5 | 27112854 | 27113085 |
| chr_1 | g12952 | g12952.t3 | TSS | g12952.t3 | NA | NA |
| chr_1 | g12952 | g12952.t3 | TTS | g12952.t3 | NA | NA |
Sequences
>g12952.t3 Gene=g12952 Length=1461
AACATTGCTTGGTCAAAGGTTAGTGAAATGTGATGTGAAGCAAAGTAATAGTTGTGTGTG
GTATGGAATTTGTGATCGAGTTAAGGAGTACAATTCAGTGAAAATTAAAAATTGTGCTTA
TGATGGTCCACCTAAAAAATTAGATTCAAATGGAGTTTTTGCATTGAATGAATGGTGCTC
ACATTTACGAGAGGATGACGATGATGTTTACACTTGTTGTGATAATGAACAGCTTTATGC
ACTAAACGAAAACATCAAACAAGCTTCAAATCTTCTAAATCGTTGCCCAGCTTGCATGAA
AAATTTTGCAAAACATATTTGTGATTATATTTGTAGCCCACGTCATGGTGAATTCATTAA
TGTTTTAAAGAAAAAACAAAGCATATCAAAACCAAATAAAGAATATATCGATGAAATTGA
TTTGTTTGTTACTGAAGATTATTTAAATGGAACTTATGATTCTTGTAAAAATGTTTTAAT
GCCATCGACTGGTCAAAAAGTGATGGATATGATGTGTGGTGGTTTTCCTGCATCAAAATG
TTCACCAATGAGATGGTTTCAACATATGGGTGATGTGAATGTCGCACAAATTCCATTTCA
AATCAATTATATTCCACAAAAATCATTGATGACTTCTGACAATAAATTTAAACCAATGAA
TCCAAAAATTATTCCATGCAATGAAAGTTTTAATAATGATCCACCATGTTCATGCGTCGA
TTGTATTTCATCATGTCCAATAGCACAGGAAGTAAAAAAGAATTCTGAAAACTTTAAAAT
TCTCAACTATGACGGCTATATTTTCATAATTATGCTCATATTCTTCATTGGCAGTTTAAT
GTTTACGGTGTTTGCAAACAGAAAAGTTCCGAGTAAAGAAATGAATCACATAAAGAACAA
GAATTTTGAATTGAGTATGTCAGAACAATATGCTCAAAAAGTTGAAAAGTTTTTACAGGA
AATATTTACTAATTGGGGAAAATTTTGTGCAACTCATCCATTGAAAGTTATTTTTATAAG
TTTGTTATTAGTCGCATGTTTTGCTTATGGAACACGATTTTCACAAGTAACTGTCGATCC
AATTGAATTATGGGCTTCATCAACTTCTCAATCACGCATTCAAAAAGATTTTTTTGATTC
AAAATTTGATCCATTTTATCGAGTTGAGCAAGTAATCATTACAGCCAAAGGTTATCAGGA
TATCATTCACAATACATCAAATGGGGTCATTAATTTTGGACCAGCTTTTAACAAAGAATT
TCTTTTAAAAGTGCTAGAAATTCAACAATCAATTGAAAATATTGACAATGGAGTTTTAAA
GGACATTTGTTTTGCACCATTAAGATCTGCAAATTTACCAAAAGATGAATATGAAGTGAC
TGATTGCCTTGTACAGAGTATTTGGGGCTATTTCCAAAATAGAAAAAAAGAAATTACCGA
TCCAAAAAGGAATAATAGAAA
>g12952.t3 Gene=g12952 Length=388
MKNFAKHICDYICSPRHGEFINVLKKKQSISKPNKEYIDEIDLFVTEDYLNGTYDSCKNV
LMPSTGQKVMDMMCGGFPASKCSPMRWFQHMGDVNVAQIPFQINYIPQKSLMTSDNKFKP
MNPKIIPCNESFNNDPPCSCVDCISSCPIAQEVKKNSENFKILNYDGYIFIIMLIFFIGS
LMFTVFANRKVPSKEMNHIKNKNFELSMSEQYAQKVEKFLQEIFTNWGKFCATHPLKVIF
ISLLLVACFAYGTRFSQVTVDPIELWASSTSQSRIQKDFFDSKFDPFYRVEQVIITAKGY
QDIIHNTSNGVINFGPAFNKEFLLKVLEIQQSIENIDNGVLKDICFAPLRSANLPKDEYE
VTDCLVQSIWGYFQNRKKEITDPKRNNR
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g12952.t3 | PANTHER | PTHR45727 | NPC INTRACELLULAR CHOLESTEROL TRANSPORTER 1 | 2 | 383 | 1.4E-93 |
| 1 | g12952.t3 | Pfam | PF16414 | Niemann-Pick C1 N terminus | 1 | 166 | 3.0E-46 |
| 6 | g12952.t3 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 166 | - |
| 8 | g12952.t3 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 167 | 187 | - |
| 5 | g12952.t3 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 188 | 235 | - |
| 9 | g12952.t3 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 236 | 253 | - |
| 7 | g12952.t3 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 254 | 388 | - |
| 3 | g12952.t3 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 165 | 187 | - |
| 4 | g12952.t3 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 230 | 252 | - |
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