Gene loci information

Transcript annotation

  • This transcript has been annotated as Fasciclin-2.

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 g6698 g6698.t4 isoform g6698.t4 18102757 18104056
chr_2 g6698 g6698.t4 exon g6698.t4.exon1 18102757 18102765
chr_2 g6698 g6698.t4 exon g6698.t4.exon2 18102824 18103148
chr_2 g6698 g6698.t4 cds g6698.t4.CDS1 18102901 18103148
chr_2 g6698 g6698.t4 exon g6698.t4.exon3 18103206 18103440
chr_2 g6698 g6698.t4 cds g6698.t4.CDS2 18103206 18103440
chr_2 g6698 g6698.t4 exon g6698.t4.exon4 18103505 18103890
chr_2 g6698 g6698.t4 cds g6698.t4.CDS3 18103505 18103890
chr_2 g6698 g6698.t4 exon g6698.t4.exon5 18103957 18104056
chr_2 g6698 g6698.t4 cds g6698.t4.CDS4 18103957 18104056
chr_2 g6698 g6698.t4 TTS g6698.t4 18104839 18104839
chr_2 g6698 g6698.t4 TSS g6698.t4 NA NA

Sequences

>g6698.t4 Gene=g6698 Length=1055
ACTTGATAGTTAGACCTGTTGAGCGCAGATATTATTCTGCATATAAATGTATAGCTGTAA
ATAAAATTGGAAGAGCTGAACACATTATGGAATTAAGAGAAGCACACTTGCCTTCAGCTG
TAGCACAAGCTAAGCCTATAGAAGTTACAGCAACAACAATAACATTTGATATAATAGGGC
CACCATTTGAAATTGGTATGCCTATAAAAGCTTATACTGCACAATATAAGGAAGAAAGGA
ATCCTGATTGGTTATATGCATTCAATCGAACGTGGTCCACAGACACACCCTATGTCATTG
AAGGATTAAGACCGCAGACAATGTATACCTTTAGATTTGCAGCAAGAAATGATGTGGGTC
TTGGTCAATGGAGCGCTATTAAAGTTCAAGCAACTCCTTCTCGATCAACACCCGAAACGC
CAAAAATTTTAAATCAATTTGCACAAGAAGTTGAAGATGGAGAATTACCTATAATAACTT
CATTGTTTGCAGACAGATTTGAACTTATATGGAACCGACCTCCTGATAATGGAGAACCAA
TCGATTTTTATGCTATAAAATATTGTCCAGGAAACAAAATTAACAATAATTGGAATGAAA
TAGGAAGACTATGCAATGAACAAAGTTATATTGCATACACATTTTCTAATTTTGTGCTTA
AGAGATTAATGCCTGATACATACTATAAGATAGAACTAAGAGCTCATAACGCTATAGGTT
TCTCATCTCCAGCTTATGCATACCTAAAAACAGCTAGAGGAGCAGAATTAAAAGGGGATA
TTGAAAGAATAGAAGAAGAGCATTTTCATTTATCATCCATTTCAATCGTATTGATTGCAA
TTTTAGCAATTATCTTAATATTACTTTTAATTGACCTCACTTTCTGTATTACAAAAGATT
TAGGTATCTTTGCATTAATTTTTTCGCGAAAATCCCATACTACAAATCAAAGAAGACAAA
ATGAAAAAAGAGAGCTAATAACAGTTTTTGGACAACAAAGACAACGTCAGCAACAGCATT
CAAATGATGCAATTGGAAAGAATTCGTCCGTGTAG

>g6698.t4 Gene=g6698 Length=322
MELREAHLPSAVAQAKPIEVTATTITFDIIGPPFEIGMPIKAYTAQYKEERNPDWLYAFN
RTWSTDTPYVIEGLRPQTMYTFRFAARNDVGLGQWSAIKVQATPSRSTPETPKILNQFAQ
EVEDGELPIITSLFADRFELIWNRPPDNGEPIDFYAIKYCPGNKINNNWNEIGRLCNEQS
YIAYTFSNFVLKRLMPDTYYKIELRAHNAIGFSSPAYAYLKTARGAELKGDIERIEEEHF
HLSSISIVLIAILAIILILLLIDLTFCITKDLGIFALIFSRKSHTTNQRRQNEKRELITV
FGQQRQRQQQHSNDAIGKNSSV

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g6698.t4 CDD cd00063 FN3 9 103 4.4691E-13
10 g6698.t4 CDD cd00063 FN3 128 216 3.10796E-10
6 g6698.t4 Gene3D G3DSA:2.60.40.10 Immunoglobulins 5 118 3.5E-16
5 g6698.t4 Gene3D G3DSA:2.60.40.10 Immunoglobulins 119 223 2.3E-11
2 g6698.t4 PANTHER PTHR12231 CTX-RELATED TYPE I TRANSMEMBRANE PROTEIN 1 269 6.4E-49
3 g6698.t4 PANTHER PTHR12231:SF245 AGAP002802-PA 1 269 6.4E-49
1 g6698.t4 Pfam PF00041 Fibronectin type III domain 13 96 7.3E-11
8 g6698.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 239 -
9 g6698.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 240 262 -
7 g6698.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 263 322 -
15 g6698.t4 ProSiteProfiles PS50853 Fibronectin type-III domain profile. 8 106 15.44
16 g6698.t4 ProSiteProfiles PS50853 Fibronectin type-III domain profile. 124 226 11.306
14 g6698.t4 SMART SM00060 FN3_2 9 93 1.1E-5
13 g6698.t4 SMART SM00060 FN3_2 119 213 0.063
4 g6698.t4 SUPERFAMILY SSF49265 Fibronectin type III 8 216 1.73E-25
12 g6698.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 240 262 -

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:0005515 protein binding 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