Gene loci information

Transcript annotation

  • This transcript has been annotated as hypothetical.

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 g6438 g6438.t3 TSS g6438.t3 17071575 17071575
chr_2 g6438 g6438.t3 isoform g6438.t3 17072288 17073145
chr_2 g6438 g6438.t3 exon g6438.t3.exon1 17072288 17072291
chr_2 g6438 g6438.t3 cds g6438.t3.CDS1 17072288 17072291
chr_2 g6438 g6438.t3 exon g6438.t3.exon2 17072353 17072526
chr_2 g6438 g6438.t3 cds g6438.t3.CDS2 17072353 17072526
chr_2 g6438 g6438.t3 exon g6438.t3.exon3 17072581 17072739
chr_2 g6438 g6438.t3 cds g6438.t3.CDS3 17072581 17072739
chr_2 g6438 g6438.t3 exon g6438.t3.exon4 17072861 17072942
chr_2 g6438 g6438.t3 cds g6438.t3.CDS4 17072861 17072942
chr_2 g6438 g6438.t3 exon g6438.t3.exon5 17073132 17073145
chr_2 g6438 g6438.t3 cds g6438.t3.CDS5 17073132 17073144
chr_2 g6438 g6438.t3 TTS g6438.t3 17073340 17073340

Sequences

>g6438.t3 Gene=g6438 Length=433
ATGGATCCAAATCAAAAAACTCCTTATCCACAAGCTTACCCTTCAATGCCTATGCCTGGT
CAACCACAGAATAATCCCATGCAATCACATTCAGGCTATCCACAACATAATCAAGGAATG
CCGCCACCTACTTATGATTATCAACCAACACCAACACCAGTCATAACTCAACAACCAACT
ACAACTGTAATTGTGCAACAAGCATCTTTTGGACCAAATCCACAGCCAATGACATGTCCA
CAATGTAGAGCAAATATTGTAACAACTGTTAATAATGAGCCATCAACTAAAACACATTTG
ATTGCACTTGTAATTTGTCTTGTTGGAGGTTGGGCAGGTTGCTGTCTTATACCTTATTGT
ACTTCTTCTTGCCAGGCTCAAACACACAAATGTCCAAATTGTGGAAACTTCTTGGGTCTG
TACCCACAACTAA

>g6438.t3 Gene=g6438 Length=144
MDPNQKTPYPQAYPSMPMPGQPQNNPMQSHSGYPQHNQGMPPPTYDYQPTPTPVITQQPT
TTVIVQQASFGPNPQPMTCPQCRANIVTTVNNEPSTKTHLIALVICLVGGWAGCCLIPYC
TSSCQAQTHKCPNCGNFLGLYPQL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g6438.t3 MobiDBLite mobidb-lite consensus disorder prediction 1 43 -
6 g6438.t3 MobiDBLite mobidb-lite consensus disorder prediction 22 43 -
2 g6438.t3 PANTHER PTHR23292:SF14 FI16615P1-RELATED 10 142 4.6E-31
3 g6438.t3 PANTHER PTHR23292 LIPOPOLYSACCHARIDE-INDUCED TUMOR NECROSIS FACTOR-ALPHA FACTOR 10 142 4.6E-31
1 g6438.t3 Pfam PF10601 LITAF-like zinc ribbon domain 73 141 2.1E-22
9 g6438.t3 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 99 -
11 g6438.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 100 119 -
10 g6438.t3 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 120 144 -
8 g6438.t3 ProSiteProfiles PS51837 LITAF domain profile. 59 143 19.441
5 g6438.t3 SMART SM00714 litaf 74 143 2.2E-20
4 g6438.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 98 120 -

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

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