Gene loci information

Transcript annotation

  • This transcript has been annotated as Battenin.

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_1 g12695 g12695.t2 TTS g12695.t2 25318873 25318873
chr_1 g12695 g12695.t2 isoform g12695.t2 25318994 25319972
chr_1 g12695 g12695.t2 exon g12695.t2.exon1 25318994 25319356
chr_1 g12695 g12695.t2 cds g12695.t2.CDS1 25318994 25319356
chr_1 g12695 g12695.t2 exon g12695.t2.exon2 25319414 25319972
chr_1 g12695 g12695.t2 cds g12695.t2.CDS2 25319414 25319881
chr_1 g12695 g12695.t2 TSS g12695.t2 NA NA

Sequences

>g12695.t2 Gene=g12695 Length=922
GCGAATTTCAATATCATGTTTAATAGCAATTGGAGGATTTATTGTAGTAGGGTTTGCAAC
TGAGCAATGGATCGCATTGACGGGAGTAGCAATGACTTCTTTTGCATCAGGACTAGGCGA
ACCAACTTTCTTAGCTTATTCAGCATTCTTTAATAAAAATGTCATATCTACTTGGTCTTC
TGGTACTGGTGGTGCTGGAATTTTCGGTGCCTTAGCATATTCAGTATTGCGTGAAATTGG
TTTGAATAATCAACAAACTATGCTCGTTATGGTGAGTGTGCCTGCTGCCGAATTCTTGAC
ATTCTTCTTCTTACTGTCAAAGCCTGCTAGTAAACGCATTGAAGACCAGCACAAGGGTGA
TAAAGTTGTTGATGACATTCCACCGATGACATCATTCAAAGAAAAGATTATTTACATCAA
ACAGCTGCTACATTTCATGATACCGCTCTGCTTAGTCTATCTCTTTGAGTATTATATCAA
TCAAGGCTTATTTGAAATGGCTTATTTCCCAGAAAATATTCTTGATCTTGATAGCAAGCA
ACAATATCGATGGTATCAGGTCACATATCAAATTGGTGTTTTCATATCGAGATCATCAGT
TAATGTTGTTCATATTAAGCAAATTTGGATTATGGCTGTATTGCAAGGATTGAATGTTAT
TTTCTTCATGTTTGAAGCTATTTATATGTTCACTCCAAGCATTTGGATTATTTTTGGACT
GATTTTGTTTGAAGGACTTTTAGGCGGTGGTGCTTATGTTAATACATTTTATAGAATGAG
TCGTGAAATTCCAGCAACTCGAAGAGAATATGCAATGTCTGTAGTTACATTATCTGATTC
TCTTGGAATAACACTTGCTGGGTTCCTTGCTATGCCAACACACAATTGGATCTGTAGCAC
ACCAGGACCAAGAATACCATAA

>g12695.t2 Gene=g12695 Length=276
MTSFASGLGEPTFLAYSAFFNKNVISTWSSGTGGAGIFGALAYSVLREIGLNNQQTMLVM
VSVPAAEFLTFFFLLSKPASKRIEDQHKGDKVVDDIPPMTSFKEKIIYIKQLLHFMIPLC
LVYLFEYYINQGLFEMAYFPENILDLDSKQQYRWYQVTYQIGVFISRSSVNVVHIKQIWI
MAVLQGLNVIFFMFEAIYMFTPSIWIIFGLILFEGLLGGGAYVNTFYRMSREIPATRREY
AMSVVTLSDSLGITLAGFLAMPTHNWICSTPGPRIP

Protein features from InterProScan

Transcript Database ID Name Start End E.value
17 g12695.t2 Gene3D G3DSA:1.20.1250.20 MFS general substrate transporter like domains 13 272 2.0E-9
3 g12695.t2 PANTHER PTHR10981 BATTENIN 2 273 4.0E-101
4 g12695.t2 PANTHER PTHR10981:SF0 BATTENIN 2 273 4.0E-101
6 g12695.t2 PRINTS PR01315 CLN3 Batten’s disease protein (battenin) signature 28 48 2.3E-51
7 g12695.t2 PRINTS PR01315 CLN3 Batten’s disease protein (battenin) signature 154 169 2.3E-51
5 g12695.t2 PRINTS PR01315 CLN3 Batten’s disease protein (battenin) signature 179 191 2.3E-51
8 g12695.t2 PRINTS PR01315 CLN3 Batten’s disease protein (battenin) signature 202 226 2.3E-51
9 g12695.t2 PRINTS PR01315 CLN3 Batten’s disease protein (battenin) signature 239 268 2.3E-51
1 g12695.t2 Pfam PF02487 CLN3 protein 1 87 1.0E-25
2 g12695.t2 Pfam PF02487 CLN3 protein 99 269 1.6E-69
23 g12695.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 24 -
26 g12695.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 25 46 -
19 g12695.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 47 57 -
25 g12695.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 58 75 -
21 g12695.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 76 106 -
28 g12695.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 107 129 -
18 g12695.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 130 177 -
30 g12695.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 178 198 -
22 g12695.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 199 203 -
29 g12695.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 204 227 -
20 g12695.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 228 238 -
27 g12695.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 239 261 -
24 g12695.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 262 276 -
16 g12695.t2 SUPERFAMILY SSF103473 MFS general substrate transporter 24 262 5.1E-13
14 g12695.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 24 46 -
10 g12695.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 58 75 -
13 g12695.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 107 129 -
15 g12695.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 178 200 -
12 g12695.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 205 227 -
11 g12695.t2 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:0016020 membrane 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