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.t3 isoform g2332.t3 16878900 16880745
chr_3 g2332 g2332.t3 exon g2332.t3.exon1 16878900 16879262
chr_3 g2332 g2332.t3 TTS g2332.t3 16878904 16878904
chr_3 g2332 g2332.t3 cds g2332.t3.CDS1 16879049 16879262
chr_3 g2332 g2332.t3 exon g2332.t3.exon2 16879474 16879972
chr_3 g2332 g2332.t3 cds g2332.t3.CDS2 16879474 16879972
chr_3 g2332 g2332.t3 exon g2332.t3.exon3 16880198 16880745
chr_3 g2332 g2332.t3 cds g2332.t3.CDS3 16880198 16880741
chr_3 g2332 g2332.t3 TSS g2332.t3 16881309 16881309

Sequences

>g2332.t3 Gene=g2332 Length=1410
TGGCATGACCAAAGAAGAGTTGATGAAATACGCAAATGATCCGTTTTGGATCAAATTGAG
ATGGTTTTTGTTTGTGCTTTTCTGGCTAGCATGGATCGGAATGTTAGTAGGAGCAATTGC
AATCATTGTTCTTGCACCGAAGTGTGCAGCACCTACACCTTTAGTGTGGTATAAGAAAGG
TCCTCTCGCTAAAATTGAAAGTACTAATGTCGATGATTCAATAATTGAAAAGATGAAAGA
ATTTGAAATTCAAGGTGTTATTTATGAATTGCCTTCAGACGCAACATACAAAGTCGAGTC
TGGCCAAATGCATGATGATATCAAAGAAATGGTGAAAAAATTTAAAGCTAAGGACATTCA
TGTTGTTATTGATTTAACTCCAAACGTTGTCACAGAAGATGATCAATTGTTTAAGGATGC
CCTAAAAGGTTCTCGAGAAAGCTTTGATGCTTTTGTAACAAATGACAAGCAATTGAATTG
GATACAAGTTGATGGAACAAAATCAGCTTGGAAGAAATTTAATAATACTTACTTCTTGAA
TCAATTTGAACTCAAAGATATTATTCTTTATTATAATAGTTTTGTATTAAATGTTACAAA
TGATGAAGGATTTTTAGCTATTCGAGATGATATTTCTAATCATATTGAAAGTTTTGTTGA
CAATAAAAGAATCAATGCATTTGAACTGCCACGATTTGGATTTATAACCAAATTTTTCCA
TGATGCAAAAACCAAAAATGTTGCCAAAAGTCTCTTTGACGTTTTTGAAAATTTAAGCGG
TAACGTTGATTTGTCATTAGTATGGACTCAAATTCAATATACAAAGAATACTTATAATAA
TTTCGAAGAATCTGCATACAAGCTATTCATCAGTTTCTTGCGTGGCGTTCAAATTGCACC
TTTTGATGATCTCGTTTACATAGATGATGATAACGGTGAAACATATAATAAGCTAAAAAC
TGAACGTGCTTCACGTGCTACTGTTTTTGAACATGGAAATTTTAATTTCTATTTAAGCAA
CAATACTGATGCATTCGCATATTCTAGAGTCAAACCTGGAAATCCAGGAATTTTTGTGGT
CGTCAACCCAACAAATGAAAAAATTCGTGCTAATTTTTCTAGTAACTTTGGCGGTTCAGA
TTTGTCAATGTTAATTGGAAGTAAGAATTTTGGGAACAATTTAATAAAATCTAAGATCAA
TCCAGATAACATTGAGTTGCCTCAACAATCCACTGCCATCTTCACATTCGTTCCAGAATA
AATATTTTAATGTGTTTGTCTAATGTCTTTTGAATCATTAACTAATAATTGATGACAATA
TCCCTATAATTGTATTCCTAGAGAATCGTTTTAAAAATATTGTATTAATGTTTAATCGTA
TCAATAAAGTTAGAATCAGCATATAGAAAA

>g2332.t3 Gene=g2332 Length=418
MTKEELMKYANDPFWIKLRWFLFVLFWLAWIGMLVGAIAIIVLAPKCAAPTPLVWYKKGP
LAKIESTNVDDSIIEKMKEFEIQGVIYELPSDATYKVESGQMHDDIKEMVKKFKAKDIHV
VIDLTPNVVTEDDQLFKDALKGSRESFDAFVTNDKQLNWIQVDGTKSAWKKFNNTYFLNQ
FELKDIILYYNSFVLNVTNDEGFLAIRDDISNHIESFVDNKRINAFELPRFGFITKFFHD
AKTKNVAKSLFDVFENLSGNVDLSLVWTQIQYTKNTYNNFEESAYKLFISFLRGVQIAPF
DDLVYIDDDNGETYNKLKTERASRATVFEHGNFNFYLSNNTDAFAYSRVKPGNPGIFVVV
NPTNEKIRANFSSNFGGSDLSMLIGSKNFGNNLIKSKINPDNIELPQQSTAIFTFVPE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g2332.t3 Gene3D G3DSA:3.20.20.80 Glycosidases 104 231 2.2E-8
7 g2332.t3 Gene3D G3DSA:3.90.400.10 - 128 196 2.2E-8
3 g2332.t3 PANTHER PTHR46673 4F2 CELL-SURFACE ANTIGEN HEAVY CHAIN 2 137 1.8E-29
1 g2332.t3 Pfam PF16028 Solute carrier family 3 member 2 N-terminus 1 61 7.8E-31
2 g2332.t3 Pfam PF00128 Alpha amylase, catalytic domain 103 266 4.8E-6
8 g2332.t3 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 19 -
10 g2332.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 20 44 -
9 g2332.t3 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 45 418 -
5 g2332.t3 SUPERFAMILY SSF51445 (Trans)glycosidases 3 215 4.52E-11
4 g2332.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 21 43 -

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

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.

Raw TPM values