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.t4 TSS g6438.t4 17071575 17071575
chr_2 g6438 g6438.t4 isoform g6438.t4 17072288 17073145
chr_2 g6438 g6438.t4 exon g6438.t4.exon1 17072288 17072291
chr_2 g6438 g6438.t4 cds g6438.t4.CDS1 17072288 17072291
chr_2 g6438 g6438.t4 exon g6438.t4.exon2 17072353 17072526
chr_2 g6438 g6438.t4 cds g6438.t4.CDS2 17072353 17072526
chr_2 g6438 g6438.t4 exon g6438.t4.exon3 17072581 17072739
chr_2 g6438 g6438.t4 cds g6438.t4.CDS3 17072581 17072739
chr_2 g6438 g6438.t4 exon g6438.t4.exon4 17072861 17073145
chr_2 g6438 g6438.t4 cds g6438.t4.CDS4 17072861 17072964
chr_2 g6438 g6438.t4 TTS g6438.t4 17073340 17073340

Sequences

>g6438.t4 Gene=g6438 Length=622
ATGGATCCAAATCAAAAAACTCCTTATCCACAAGCTTACCCTTCAATGCCTATGCCTGGT
CAACCACAGAATAATCCCATGCAATCACATTCAGGCTATCCACAACATAATCAAGGAATG
CCGCCACCTACTTATGATTATCAACCAACACCAACACCAGTCATAACTCAACAACCAACT
ACAACTGTAATTGTGCAACAAGCATCTTTTGGACCAAATCCACAGCCAATGACATGTCCA
CAATGTAGAGCAAATATTGTAACAACTGTTAATAATGAGCCATCAACTAAAACACATTTG
ATTGCACTTGTAATTTGTCTTGTTGGAGGTTGGGCAGGTTGCTGTCTTATACCTTATTGT
ACTTCTTCTTGCCAGGCTCAAACACACAAATGTCCAAATTGTGGAAACTTCTTGGGTCTG
TACTTAAAAAATTTTGATTAAATATTTCACATTATTGATAAAGATGGAAACATTTTATGA
TTGTATTTTGTGACTCATCTCTTTTATGCTAAATTTATTATTAATCATTAAATGTTTTTC
ATCTTGATTTTATAAATTATAGATTCAATATAAAATTTCATACTTAAAAATATATCTTTA
AATTTTAGGTACCCACAACTAA

>g6438.t4 Gene=g6438 Length=146
MDPNQKTPYPQAYPSMPMPGQPQNNPMQSHSGYPQHNQGMPPPTYDYQPTPTPVITQQPT
TTVIVQQASFGPNPQPMTCPQCRANIVTTVNNEPSTKTHLIALVICLVGGWAGCCLIPYC
TSSCQAQTHKCPNCGNFLGLYLKNFD

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g6438.t4 MobiDBLite mobidb-lite consensus disorder prediction 1 43 -
6 g6438.t4 MobiDBLite mobidb-lite consensus disorder prediction 22 43 -
2 g6438.t4 PANTHER PTHR23292:SF14 FI16615P1-RELATED 10 142 2.0E-31
3 g6438.t4 PANTHER PTHR23292 LIPOPOLYSACCHARIDE-INDUCED TUMOR NECROSIS FACTOR-ALPHA FACTOR 10 142 2.0E-31
1 g6438.t4 Pfam PF10601 LITAF-like zinc ribbon domain 73 141 2.4E-22
9 g6438.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 99 -
11 g6438.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 100 119 -
10 g6438.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 120 146 -
8 g6438.t4 ProSiteProfiles PS51837 LITAF domain profile. 59 143 19.395
5 g6438.t4 SMART SM00714 litaf 74 143 2.4E-19
4 g6438.t4 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

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