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.t7 TSS g4141.t7 30907144 30907144
chr_3 g4141 g4141.t7 isoform g4141.t7 30907213 30909809
chr_3 g4141 g4141.t7 exon g4141.t7.exon1 30907213 30907291
chr_3 g4141 g4141.t7 cds g4141.t7.CDS1 30907213 30907291
chr_3 g4141 g4141.t7 exon g4141.t7.exon2 30907396 30907512
chr_3 g4141 g4141.t7 cds g4141.t7.CDS2 30907396 30907512
chr_3 g4141 g4141.t7 exon g4141.t7.exon3 30907618 30907668
chr_3 g4141 g4141.t7 cds g4141.t7.CDS3 30907618 30907668
chr_3 g4141 g4141.t7 exon g4141.t7.exon4 30907735 30908374
chr_3 g4141 g4141.t7 cds g4141.t7.CDS4 30907735 30907946
chr_3 g4141 g4141.t7 exon g4141.t7.exon5 30908837 30908886
chr_3 g4141 g4141.t7 exon g4141.t7.exon6 30909605 30909809
chr_3 g4141 g4141.t7 TTS g4141.t7 NA NA

Sequences

>g4141.t7 Gene=g4141 Length=1142
ATGAAATTGTCTGCCGTAGTTATTGTTCTTATCAGCGGTTTTTTGTGTGTAGCCTATTGT
GCAGAGATTAAAAATTGCGATACAGAAGCAGAGGGTAAATTTACACGTGTGACTGTGACT
GATTGTGACGAAAGTCAGGAAAGATGTATTTTAAAAAAAGGAACAAACGCCACAATTACA
ATAGATTTTGAATTGGACGTTGAGACGGAAAATGAGGTCAAGGCAGTTTGTTTCGGTAAA
TTAGGAGCTCTTGAAGTTCCATTTAAATTACCAAATCCAAATGCTTGTAAAGACTCAGGA
CTGGAGTGTCCATTAAAAAAGAATGTTGCATATACATATGAAGCATCGTTTCCGATCCTA
AAAGTCTACCCCAAAGTCAACGTTGATGTGAAATATGAGTTGAAAAATAAAGAAAATAAG
AATATCGTTTGTGTCCTCGTACCAGTTAAAATTGTTTAAAAACAAAAAAAAATCAAAAGA
AAATCATGACTTTGTGTTTGTGATATCATTAAAAACAAAAGTAGAAGAATATCAAGCATT
GTATTACACATTTAATAAAAAATAATATTACTAAGAAATAAACAAAAAATTTATCTCTTA
GCTCGTATTTCTTTAACTTTATTTTATTAAATAAATAATGTTGACTAATGGATTTTCTAA
ATAAATACATGTATAATGCAATCATAGCACAGTGATCCAAAATTTAAAAAATCAGTAATA
TTAACCGTCAGTGACGTGTTAAAAGCGCATTTTCCTGCAACAAATTAGTTTTGTTTCCAA
ATTCATTGAAAGTTTCAAAAAAAAAAAAGCTTTTTACAGCCTTTTTGAAGTCTGTACAGC
CTAAAACATACACTTGGGTCCAAATGTCCAGAAATCACTTCTGACATACTAGTTACGAAG
ACAGACAGACGGACAAAGTGGGCACAATAGCGCCTTTTTTCTAAATATGATGGAAAATGC
GCTAAAAATTGTTCACTTTTACAAATGTGCGCAGTTTTTGTAAATGTTGCACACCAACAT
AAAAAATTTTTCAAAATACAAAATGTCGTTTATATCAAATTTTTATTTCAACTGATTAAT
GAATTTTAAACATTTTATTTACACTGTAAGTTCTTCTAACAAATAAAACACTTCTCAATG
AT

>g4141.t7 Gene=g4141 Length=152
MKLSAVVIVLISGFLCVAYCAEIKNCDTEAEGKFTRVTVTDCDESQERCILKKGTNATIT
IDFELDVETENEVKAVCFGKLGALEVPFKLPNPNACKDSGLECPLKKNVAYTYEASFPIL
KVYPKVNVDVKYELKNKENKNIVCVLVPVKIV

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g4141.t7 CDD cd00916 Npc2_like 31 149 9.45988E-36
7 g4141.t7 Gene3D G3DSA:2.60.40.770 - 22 152 6.5E-41
2 g4141.t7 PANTHER PTHR11306 NIEMANN PICK TYPE C2 PROTEIN NPC2-RELATED 3 152 9.8E-34
3 g4141.t7 PANTHER PTHR11306:SF30 NPC INTRACELLULAR CHOLESTEROL TRANSPORTER 2 3 152 9.8E-34
1 g4141.t7 Pfam PF02221 ML domain 23 151 1.6E-26
9 g4141.t7 Phobius SIGNAL_PEPTIDE Signal peptide region 1 20 -
10 g4141.t7 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 2 -
11 g4141.t7 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 3 15 -
12 g4141.t7 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 16 20 -
8 g4141.t7 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 21 152 -
15 g4141.t7 SMART SM00737 pgtp_13 23 149 2.5E-26
4 g4141.t7 SUPERFAMILY SSF81296 E set domains 22 152 5.6E-30
6 g4141.t7 SignalP_EUK SignalP-noTM SignalP-noTM 1 20 -
14 g4141.t7 SignalP_GRAM_NEGATIVE SignalP-noTM SignalP-noTM 1 20 -
5 g4141.t7 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.

Raw TPM values