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 g7197 g7197.t4 TTS g7197.t4 22048930 22048930
chr_2 g7197 g7197.t4 isoform g7197.t4 22049269 22053499
chr_2 g7197 g7197.t4 exon g7197.t4.exon1 22049269 22049577
chr_2 g7197 g7197.t4 cds g7197.t4.CDS1 22049269 22049577
chr_2 g7197 g7197.t4 exon g7197.t4.exon2 22049639 22049790
chr_2 g7197 g7197.t4 cds g7197.t4.CDS2 22049639 22049790
chr_2 g7197 g7197.t4 exon g7197.t4.exon3 22049843 22049929
chr_2 g7197 g7197.t4 cds g7197.t4.CDS3 22049843 22049929
chr_2 g7197 g7197.t4 exon g7197.t4.exon4 22050029 22050248
chr_2 g7197 g7197.t4 cds g7197.t4.CDS4 22050029 22050197
chr_2 g7197 g7197.t4 exon g7197.t4.exon5 22053425 22053499
chr_2 g7197 g7197.t4 TSS g7197.t4 22053531 22053531

Sequences

>g7197.t4 Gene=g7197 Length=843
TCTTTTTTAGTCTCTTAATGTACCGGCATTTCCATGGTGGATCAATTACTATAAAATCAA
ATTTTTCACTTTCTGAAGTACAATGATTCAACGCCAATACCTATTCAGACACGTCAATCA
CGAGTTATGCATTTTGAGGACAAGAATAAAGCCTTCAGGCAAGTTGTCAACAAGGATCAA
TTAGCAAAATTAAAAGAGCAACGTCTTCCACCAATTGAACATGTTCAAATGATAAATGGT
GTTAGAAGAAGAATTTATCAAAATATGCCACTCCGAAAAAATCTCGAAATGAAAAATGCT
AAGAGAATGAAAATTACTGCTGTTCATTACGATGGGGACACAACTAGACTTGAAGGAACC
GGTCACCAAAGTTACAAAGGTAGTAACGGAAAAGTGATATTGGATAAAAATGAGTACATG
CATTGGAAACAAGCGGATTGGGTTCCTGATCATGGCATGGAGAGATTTTTCCATATGGAT
TCTACAGGCACTCTTACTGTAAAAGATCATGGATTGTTTTTGATTTACGCGCAAGTATAT
TACAGCGACAATCACGATTTAAATGGCTATGAAATTGTTCATAACAATCATGTAAAATAT
CAGTGCACAACAATGACACATGGTTCTCATGGCGAACCCAAAACAAACAGTTGCTACACC
AGTGGCCTCATTCATTTGAGAAATGGTGATAAAATTCGTTTGCGTGATGTCGGTAATCAT
CGATATGTATTGATGCAGCCAAATAAAAGCTTTTTCGGTTTAATTAAAATCAATCTATTG
CCATCAGTTGCATCAGATAGCAGTAGCAGTACAGATATCGAACAATACGAATCAATTAAA
TAA

>g7197.t4 Gene=g7197 Length=238
MHFEDKNKAFRQVVNKDQLAKLKEQRLPPIEHVQMINGVRRRIYQNMPLRKNLEMKNAKR
MKITAVHYDGDTTRLEGTGHQSYKGSNGKVILDKNEYMHWKQADWVPDHGMERFFHMDST
GTLTVKDHGLFLIYAQVYYSDNHDLNGYEIVHNNHVKYQCTTMTHGSHGEPKTNSCYTSG
LIHLRNGDKIRLRDVGNHRYVLMQPNKSFFGLIKINLLPSVASDSSSSTDIEQYESIK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
5 g7197.t4 Gene3D G3DSA:2.60.120.40 - 80 220 0.000
2 g7197.t4 PANTHER PTHR15151 PROTEIN EIGER 52 216 0.000
3 g7197.t4 PANTHER PTHR15151:SF24 PROTEIN EIGER 52 216 0.000
1 g7197.t4 Pfam PF00229 TNF(Tumour Necrosis Factor) family 119 215 0.000
6 g7197.t4 ProSiteProfiles PS50049 TNF family profile. 65 215 13.665
4 g7197.t4 SUPERFAMILY SSF49842 TNF-like 98 217 0.000

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:0016020 membrane CC
GO:0005164 tumor necrosis factor receptor binding MF
GO:0005515 protein binding MF
GO:0006955 immune response 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