Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative 4F2 cell-surface antigen heavy chain.

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 g2332 g2332.t7 TTS g2332.t7 16878904 16878904
chr_3 g2332 g2332.t7 isoform g2332.t7 16879713 16882318
chr_3 g2332 g2332.t7 exon g2332.t7.exon1 16879713 16880753
chr_3 g2332 g2332.t7 cds g2332.t7.CDS1 16879713 16880753
chr_3 g2332 g2332.t7 exon g2332.t7.exon2 16881094 16881293
chr_3 g2332 g2332.t7 cds g2332.t7.CDS2 16881094 16881293
chr_3 g2332 g2332.t7 exon g2332.t7.exon3 16882195 16882318
chr_3 g2332 g2332.t7 cds g2332.t7.CDS3 16882195 16882318
chr_3 g2332 g2332.t7 TSS g2332.t7 16882297 16882297

Sequences

>g2332.t7 Gene=g2332 Length=1365
ATGAGTGAGGAAAAGTTAAATAGTAATAAACTAGATTTCGAGACGAAAAGACAGAGTCTC
AATAATCAAGAAGATAATCGTGAGTCTTATAAGCCAATTTCTGAAGACAGCGCATTTGAG
CACGTCACTGGTGAAACAGTCAAAAACTCTAATATGGTACGCGAAAAGAGTAACGAGCAT
CTTCAAGATGGAGCTGATGAAAAAATGTTGGGATCTGATGATAAAGAGACCCTTGCTTTA
AAAAGCATCGAAGTAAAATTTATTCCCAGTGATCAAAATCAGAATGGCGATGCTAAAATT
GAAATTGAGAATGGCGGTGAAAAGACATTCACTGGCATGACCAAAGAAGAGTTGATGAAA
TACGCAAATGATCCGTTTTGGATCAAATTGAGATGGTTTTTGTTTGTGCTTTTCTGGCTA
GCATGGATCGGAATGTTAGTAGGAGCAATTGCAATCATTGTTCTTGCACCGAAGTGTGCA
GCACCTACACCTTTAGTGTGGTATAAGAAAGGTCCTCTCGCTAAAATTGAAAGTACTAAT
GTCGATGATTCAATAATTGAAAAGATGAAAGAATTTGAAATTCAAGGTGTTATTTATGAA
TTGCCTTCAGACGCAACATACAAAGTCGAGTCTGGCCAAATGCATGATGATATCAAAGAA
ATGGTGAAAAAATTTAAAGCTAAGGACATTCATGTTGTTATTGATTTAACTCCAAACGTT
GTCACAGAAGATGATCAATTGTTTAAGGATGCCCTAAAAGGTTCTCGAGAAAGCTTTGAT
GCTTTTGTAACAAATGACAAGCAATTGAATTGGATACAAGTTGATGGAACAAAATCAGCT
TGGAAGAAATTTAATAATACTTACTTCTTGAATCAATTTGGTGATTATTACGACATTCGT
CTCAACAAACCTATCGTTCAAAATAGATTAACAAATGTCATTAAAAAATTAACAGAAATT
GGAGTTAAAGGATTTCGATTTGTTAACGCTAAATATATTGTTACTGAATCGGAATTTATA
GATGAAATTCCTAATTCAAAAGCACATGGTTTAAACAAAGAAGATTTTGGTTTCTATATG
CACAGTCAACGAGAATTTTCACAAGAACTCAAAGATATTATTCTTTATTATAATAGTTTT
GTATTAAATGTTACAAATGATGAAGGATTTTTAGCTATTCGAGATGATATTTCTAATCAT
ATTGAAAGTTTTGTTGACAATAAAAGAATCAATGCATTTGAACTGCCACGATTTGGATTT
ATAACCAAATTTTTCCATGATGCAAAAACCAAAAATGTTGCCAAAAGTCTCTTTGACGTT
TTTGAAAATTTAAGCGGTAACGTTGATTTGTCATTAGTATGGACT

>g2332.t7 Gene=g2332 Length=455
MSEEKLNSNKLDFETKRQSLNNQEDNRESYKPISEDSAFEHVTGETVKNSNMVREKSNEH
LQDGADEKMLGSDDKETLALKSIEVKFIPSDQNQNGDAKIEIENGGEKTFTGMTKEELMK
YANDPFWIKLRWFLFVLFWLAWIGMLVGAIAIIVLAPKCAAPTPLVWYKKGPLAKIESTN
VDDSIIEKMKEFEIQGVIYELPSDATYKVESGQMHDDIKEMVKKFKAKDIHVVIDLTPNV
VTEDDQLFKDALKGSRESFDAFVTNDKQLNWIQVDGTKSAWKKFNNTYFLNQFGDYYDIR
LNKPIVQNRLTNVIKKLTEIGVKGFRFVNAKYIVTESEFIDEIPNSKAHGLNKEDFGFYM
HSQREFSQELKDIILYYNSFVLNVTNDEGFLAIRDDISNHIESFVDNKRINAFELPRFGF
ITKFFHDAKTKNVAKSLFDVFENLSGNVDLSLVWT

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g2332.t7 Coils Coil Coil 3 23 -
6 g2332.t7 Gene3D G3DSA:3.20.20.80 Glycosidases 216 373 5.9E-17
7 g2332.t7 Gene3D G3DSA:3.90.400.10 - 240 300 5.9E-17
13 g2332.t7 MobiDBLite mobidb-lite consensus disorder prediction 1 53 -
14 g2332.t7 MobiDBLite mobidb-lite consensus disorder prediction 1 35 -
3 g2332.t7 PANTHER PTHR46673:SF1 4F2 CELL-SURFACE ANTIGEN HEAVY CHAIN 92 210 3.4E-31
4 g2332.t7 PANTHER PTHR46673 4F2 CELL-SURFACE ANTIGEN HEAVY CHAIN 92 210 3.4E-31
1 g2332.t7 Pfam PF16028 Solute carrier family 3 member 2 N-terminus 97 173 3.0E-37
2 g2332.t7 Pfam PF00128 Alpha amylase, catalytic domain 215 397 2.3E-12
9 g2332.t7 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 131 -
11 g2332.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 132 156 -
10 g2332.t7 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 157 455 -
5 g2332.t7 SUPERFAMILY SSF51445 (Trans)glycosidases 106 342 2.8E-24
12 g2332.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 133 155 -

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:0006865 amino acid transport BP
GO:0005975 carbohydrate metabolic process BP
GO:0003824 catalytic activity MF

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. There were no conditions that were differentially expressed