Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative TBC1 domain family member 4.

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_1 g11880 g11880.t4 isoform g11880.t4 18948729 18950137
chr_1 g11880 g11880.t4 exon g11880.t4.exon1 18948729 18948732
chr_1 g11880 g11880.t4 cds g11880.t4.CDS1 18948731 18948732
chr_1 g11880 g11880.t4 exon g11880.t4.exon2 18948839 18949002
chr_1 g11880 g11880.t4 cds g11880.t4.CDS2 18948839 18949002
chr_1 g11880 g11880.t4 exon g11880.t4.exon3 18949062 18950137
chr_1 g11880 g11880.t4 cds g11880.t4.CDS3 18949062 18949888
chr_1 g11880 g11880.t4 TSS g11880.t4 18950637 18950637
chr_1 g11880 g11880.t4 TTS g11880.t4 NA NA

Sequences

>g11880.t4 Gene=g11880 Length=1244
AGTATTGAGGTGAATGGGAAACAAAATACAGACAGTCAACAGACGCCAGAAAATTCTCAA
AACGGATATGATAAAAAAATTGACGAGGAAAGCGATTCATCAAGCGTTAAGAGCAGTGAT
AGCAAAAGTCAGAGTGATGAAACAAACAAACAACAACCAAATTTTCATCGACTTGATTCA
ATAAAAGCTGAAGAAATACCAAAAAGAAATCGATCAGCTTCATTTAGTTCAATTGAACAA
AATCGTACAATGGTATACATTTTAGGAAGATCAGATTTGAGATTGATAAGTCCCGATCGA
AAACAAATTTTGCTTCATAAAAATTTTAATGATGTCGTTAATGCTGTTCAAGGAATTAAT
AGTGCTGAACATTTTGGAATTATTTGCAATGAAGTGAAAGATAATAAACAAGAATTTATT
GGTTATGTCTTTAAATGTCAATCTGCTGTCATTGCACATGATGTTGTCTCATCTATGTTG
AAATCTTTAGAGACACTTGAGCAAGATAAAAAATATTCAGATGAAAATTTTGAAGACTCA
AAAAAGATGTCAGGTTCTTTACAATGCGATCATTGTCCTTTAGTATGGTTCAATAAGCTT
CAAAATTCAGTTCAAGGTCTCAGCGAAAAAAAAATTTATAGTGTCATAATGAAACATATT
GAAGAATTGAATGCTGACGACTATGAAATATTAATGGAAAAATTCTTTGCTTCTGATAAA
GTCAATGATTATTCCCTCACAGAACGTAATAAATTTCTCATGGCACTAATTGAAGCACAT
TGTCAAATGCGTCAACAGCGACATGTGCACGATACAATTGAAAATCGATCAGAATTCTTA
AATTACTATCTAGGTGGCAGTACAATTTTAATGAAGGCAAAACGTTCTTTGTCAAGCTCG
TTTGATCAACTATTAAAAAGAAGAGGAAGTAAGGATTCAAATGAAAATAACCACATTACA
ATTCATGAAGAAGAGCAAAGAAAGTTCAAACCAATTAGATCAATATCGTTGACATCTCCT
TTAATATCACCTTGTGATAATAAACAACAATTATTGAATACATCTAAAATGGACATGTTT
ATGAAAGTGGGAAATACTTCAAAAGACAAAAATATGCACACAATTTCATGGCGTCAAAAA
ATCCTTAAAAACGTAATTTTAACAGAAAAAGAAGAACCAACTTCAAAAGCTTGCCTAAAT
GACGACTCTATAAAATTTCTTTCAAAAAGATCAAACAAGCGACA

>g11880.t4 Gene=g11880 Length=331
MVYILGRSDLRLISPDRKQILLHKNFNDVVNAVQGINSAEHFGIICNEVKDNKQEFIGYV
FKCQSAVIAHDVVSSMLKSLETLEQDKKYSDENFEDSKKMSGSLQCDHCPLVWFNKLQNS
VQGLSEKKIYSVIMKHIEELNADDYEILMEKFFASDKVNDYSLTERNKFLMALIEAHCQM
RQQRHVHDTIENRSEFLNYYLGGSTILMKAKRSLSSSFDQLLKRRGSKDSNENNHITIHE
EEQRKFKPIRSISLTSPLISPCDNKQQLLNTSKMDMFMKVGNTSKDKNMHTISWRQKILK
NVILTEKEEPTSKACLNDDSIKFLSKRSNKR

Protein features from InterProScan

Transcript Database ID Name Start End E.value
4 g11880.t4 Gene3D G3DSA:2.30.29.30 - 4 81 8.3e-06
1 g11880.t4 PANTHER PTHR11232 PHOSPHOTYROSINE INTERACTION DOMAIN-CONTAINING FAMILY MEMBER 1 187 0.0e+00
2 g11880.t4 PANTHER PTHR11232:SF67 - 1 187 0.0e+00
3 g11880.t4 SUPERFAMILY SSF50729 PH domain-like 5 75 0.0e+00

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