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_3 g3146 g3146.t4 TTS g3146.t4 23195203 23195203
chr_3 g3146 g3146.t4 isoform g3146.t4 23195307 23196647
chr_3 g3146 g3146.t4 exon g3146.t4.exon1 23195307 23196060
chr_3 g3146 g3146.t4 cds g3146.t4.CDS1 23195309 23196060
chr_3 g3146 g3146.t4 exon g3146.t4.exon2 23196141 23196279
chr_3 g3146 g3146.t4 cds g3146.t4.CDS2 23196141 23196279
chr_3 g3146 g3146.t4 exon g3146.t4.exon3 23196588 23196647
chr_3 g3146 g3146.t4 cds g3146.t4.CDS3 23196588 23196647
chr_3 g3146 g3146.t4 TSS g3146.t4 23196756 23196756

Sequences

>g3146.t4 Gene=g3146 Length=953
ATGACCGATGTTGTCAATAGAAACAGTGCCGATGAAAGCGAAGAAAAGCAACGAACGATG
AGCTTAACAGAAAACTCGCCAACATCGGGTGGAATTGAGTCTGAATATGATACGGCGAGT
ACAAATTCAAGATCTGATAATGAAAGAGATGAATATGAAGACAGCGAAGAGGACAGTATG
GATGAGGAAGAAGCTACTGATGATGAAGATGAACCGCAAGATGATGAAAGAGAATCAGGT
GATGACGATGATGAAAATCAAGAAGAGCAAGAAAGTGAAGGTGGAACAAAGAAAAAAGTC
GATCATGATGAAGATCGAAGTAATCCACAATATATCCCAAAAAAGGGAACATTTTATGAA
CATGATGATCGTACAGCTGAAGACCTTGATGCAAATGAACCAGTAGAAAATTTGGAAAAT
GCAAATAATAGCACAGAAGGTTTAGCCGGTACTGGAAAAGTTTTATCAACACAAAATCAA
AAAGTCACACCGAAACAGGTAAAGAAAAAAGAGGCAGATCGTTGGACTCATGATCGTTTT
AATGAATATGAGCAAGCACCGAAATCAAAAGCAGAATTGGTCTCAGCCTATGGCTATGAT
ATCAGAAATGAAGATTGCCCACCAAGACCACGTCGTCAAAGACGCTATGGTCGTCATCAA
TCAAAATACTCGAGAAATTGGGAAGATGAAGAAGCTTATAAAAAGCAACAGTCGAGTGCA
AAACCACCAAGGCGTGTTCCTAAACCAGAAGATTTTCCAGCACTCGGTTCAACTCCTCGT
CCTACTTCATCATCAAAATCTCGCATTTCGCGATCTCGTCGTAATCATCAACAAGATGAA
AATGATCCACAATCATCACAGCAGCAACAACAACAACAGAATTATCGATCGCCAATAAGA
AATTCTCGTGAGCAAAGGTCACATCGTGAAGATCGTGGATCACGTGGTGATGG

>g3146.t4 Gene=g3146 Length=317
MTDVVNRNSADESEEKQRTMSLTENSPTSGGIESEYDTASTNSRSDNERDEYEDSEEDSM
DEEEATDDEDEPQDDERESGDDDDENQEEQESEGGTKKKVDHDEDRSNPQYIPKKGTFYE
HDDRTAEDLDANEPVENLENANNSTEGLAGTGKVLSTQNQKVTPKQVKKKEADRWTHDRF
NEYEQAPKSKAELVSAYGYDIRNEDCPPRPRRQRRYGRHQSKYSRNWEDEEAYKKQQSSA
KPPRRVPKPEDFPALGSTPRPTSSSKSRISRSRRNHQQDENDPQSSQQQQQQQNYRSPIR
NSREQRSHREDRGSRGD

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g3146.t4 MobiDBLite mobidb-lite consensus disorder prediction 1 317 -
4 g3146.t4 MobiDBLite mobidb-lite consensus disorder prediction 20 41 -
9 g3146.t4 MobiDBLite mobidb-lite consensus disorder prediction 50 90 -
7 g3146.t4 MobiDBLite mobidb-lite consensus disorder prediction 91 131 -
10 g3146.t4 MobiDBLite mobidb-lite consensus disorder prediction 136 163 -
6 g3146.t4 MobiDBLite mobidb-lite consensus disorder prediction 164 186 -
11 g3146.t4 MobiDBLite mobidb-lite consensus disorder prediction 221 248 -
8 g3146.t4 MobiDBLite mobidb-lite consensus disorder prediction 281 300 -
5 g3146.t4 MobiDBLite mobidb-lite consensus disorder prediction 301 317 -
2 g3146.t4 PANTHER PTHR13434 PROTEIN CASC3 11 315 9.2E-40
1 g3146.t4 Pfam PF09405 CASC3/Barentsz eIF4AIII binding 73 205 5.2E-25
3 g3146.t4 SMART SM01044 Btz_2 74 206 7.6E-37

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:0006397 mRNA processing BP
GO:0003723 RNA binding MF
GO:0035145 exon-exon junction complex CC

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