Gene loci information

Transcript annotation

  • This transcript has been annotated as Trafficking protein particle complex subunit 3.

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_2 g7211 g7211.t7 TSS g7211.t7 22105961 22105961
chr_2 g7211 g7211.t7 isoform g7211.t7 22106107 22108622
chr_2 g7211 g7211.t7 exon g7211.t7.exon1 22106107 22106405
chr_2 g7211 g7211.t7 cds g7211.t7.CDS1 22106370 22106405
chr_2 g7211 g7211.t7 exon g7211.t7.exon2 22108070 22108275
chr_2 g7211 g7211.t7 cds g7211.t7.CDS2 22108070 22108275
chr_2 g7211 g7211.t7 exon g7211.t7.exon3 22108334 22108622
chr_2 g7211 g7211.t7 cds g7211.t7.CDS3 22108334 22108622
chr_2 g7211 g7211.t7 TTS g7211.t7 22108657 22108657

Sequences

>g7211.t7 Gene=g7211 Length=794
TGTGAGTGTCTTAAATAATTTAAAAATATTGAAAAATTAATTTTGATATTGTGTATGTTT
TTGATGGATACATTTCATTATGAACGCTCATTCGGGAGAGAGAGAAAGAAAGAGAACACA
CTCGTCCCTAATACATGTCTGTTAATTTTTTCCTTAGCCAATCGACATTACATTTTTCAA
CCAATAGATTTTCTGGACAAATCACCATCAATATCAAATCAAGGATCAAAATAAAGTTAA
ATCTTAAGAACTGATTGCCTAAAATGTCTCGACAAAGCCGTTTTGAAGTGAAAAAAGTGA
ATTCCGAATTGTTGACACTCACTTATGGAGCACTTGTTACTCAGATGCTGAGAGATTTTG
AAAATGTGGAAGATGTTAATAAGCAATTAGAACGACTTGGTTATAATATGGGAATGAGAC
TAATTGAAGACTATCTCTCAAAAACTAATTCATCGCGATGTTTAGATATGCGCGACACTG
CTGAAAAAATTCAATCAGCATTTCGGATGTATTTAAATGTGCAGCCAACTATAACCAATT
GGGCTCCCTCAGCAGACGAGTTTTCGCTTGTTTTTGATAATAATCCTTTAACAGAATTCG
TTGAATTACCATCGGACTTGAACACTAGTCTGCGTTATTGCGGAATCATAAACGGTTGCA
TTCGAGGTGCTCTCGAAATGGTACAACTAGAAGTTCAATGTTGGTTTGTTCAAGATCAAT
TAAAAGGAGATTCTACAACAGAGATTCGAGTAAAATTTATCCGAAAAATGGATGATACAT
TACCAGAAGATTAA

>g7211.t7 Gene=g7211 Length=176
MSRQSRFEVKKVNSELLTLTYGALVTQMLRDFENVEDVNKQLERLGYNMGMRLIEDYLSK
TNSSRCLDMRDTAEKIQSAFRMYLNVQPTITNWAPSADEFSLVFDNNPLTEFVELPSDLN
TSLRYCGIINGCIRGALEMVQLEVQCWFVQDQLKGDSTTEIRVKFIRKMDDTLPED

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g7211.t7 CDD cd14942 TRAPPC3_bet3 13 167 5.9741E-95
6 g7211.t7 Coils Coil Coil 25 45 -
5 g7211.t7 Gene3D G3DSA:3.30.1380.20 Trafficking protein particle complex subunit 3 2 176 5.6E-70
2 g7211.t7 PANTHER PTHR13048 TRAFFICKING PROTEIN PARTICLE COMPLEX SUBUNIT 3 8 175 3.8E-67
3 g7211.t7 PANTHER PTHR13048:SF0 TRAFFICKING PROTEIN PARTICLE COMPLEX SUBUNIT 8 175 3.8E-67
7 g7211.t7 PIRSF PIRSF018293 TRAPP_1_Bet3 1 176 9.0E-78
1 g7211.t7 Pfam PF04051 Transport protein particle (TRAPP) component 18 164 3.1E-32
4 g7211.t7 SUPERFAMILY SSF111126 Ligand-binding domain in the NO signalling and Golgi transport 10 167 2.49E-49

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:0048193 Golgi vesicle transport BP
GO:0030008 TRAPP complex CC

KEGG

Orthology

Pathway

This gene does not belong to any 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