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.t4 TTS g12695.t4 25318873 25318873
chr_1 g12695 g12695.t4 isoform g12695.t4 25319417 25321396
chr_1 g12695 g12695.t4 exon g12695.t4.exon1 25319417 25319975
chr_1 g12695 g12695.t4 cds g12695.t4.CDS1 25319417 25319975
chr_1 g12695 g12695.t4 exon g12695.t4.exon2 25320041 25320165
chr_1 g12695 g12695.t4 cds g12695.t4.CDS2 25320041 25320165
chr_1 g12695 g12695.t4 exon g12695.t4.exon3 25320224 25320401
chr_1 g12695 g12695.t4 cds g12695.t4.CDS3 25320224 25320401
chr_1 g12695 g12695.t4 exon g12695.t4.exon4 25321347 25321396
chr_1 g12695 g12695.t4 cds g12695.t4.CDS4 25321347 25321396
chr_1 g12695 g12695.t4 TSS g12695.t4 25321604 25321604

Sequences

>g12695.t4 Gene=g12695 Length=912
ATGACAAAAAAAAGTTTCAATATTTTTCATATATCGAACGATGATTCAAGTGGAAACAAT
GTACATCGAACAAGTGATGTTGAGAAAATTGACAAAACACGAGTGGAACCGAGAAACAAT
TGGCGTGATCTTATAGCTTATTGGATATTCGGTTTATGCAATAATTTTGGATATGTAGTT
ATGCTTACAGCTGCAAAAGATATTTTACAAGAATTAGGATCATCTTCTGAAGTTCACCAT
GGCTCAAGCAATCGACCATGCAATCTTGTTTCAACTGGTGCTGTCTTACTTGCGGATGTT
ATTCCTGGTCTATGCATTAAATTTCTATCTCCTTTTCTTCCATTTTGGCATGCAACGCGA
ATTTCAATATCATGTTTAATAGCAATTGGAGGATTTATTGTAGTAGGGTTTGCAACTGAG
CAATGGATCGCATTGACGGGAGTAGCAATGACTTCTTTTGCATCAGGACTAGGCGAACCA
ACTTTCTTAGCTTATTCAGCATTCTTTAATAAAAATGTCATATCTACTTGGTCTTCTGGT
ACTGGTGGTGCTGGAATTTTCGGTGCCTTAGCATATTCAGTATTGCGTGAAATTGGTTTG
AATAATCAACAAACTATGCTCGTTATGGTGAGTGTGCCTGCTGCCGAATTCTTGACATTC
TTCTTCTTACTGTCAAAGCCTGCTAGTAAACGCATTGAAGACCAGCACAAGGGTGATAAA
GTTGTTGATGACATTCCACCGATGACATCATTCAAAGAAAAGATTATTTACATCAAACAG
CTGCTACATTTCATGATACCGCTCTGCTTAGTCTATCTCTTTGAGTATTATATCAATCAA
GGCTTATTTGAAATGGCTTATTTCCCAGAAAATATTCTTGATCTTGATAGCAAGCAACAA
TATCGATGGTAT

>g12695.t4 Gene=g12695 Length=304
MTKKSFNIFHISNDDSSGNNVHRTSDVEKIDKTRVEPRNNWRDLIAYWIFGLCNNFGYVV
MLTAAKDILQELGSSSEVHHGSSNRPCNLVSTGAVLLADVIPGLCIKFLSPFLPFWHATR
ISISCLIAIGGFIVVGFATEQWIALTGVAMTSFASGLGEPTFLAYSAFFNKNVISTWSSG
TGGAGIFGALAYSVLREIGLNNQQTMLVMVSVPAAEFLTFFFLLSKPASKRIEDQHKGDK
VVDDIPPMTSFKEKIIYIKQLLHFMIPLCLVYLFEYYINQGLFEMAYFPENILDLDSKQQ
YRWY

Protein features from InterProScan

Transcript Database ID Name Start End E.value
16 g12695.t4 Gene3D G3DSA:1.20.1250.20 MFS general substrate transporter like domains 16 242 3.3E-10
3 g12695.t4 PANTHER PTHR10981 BATTENIN 32 304 5.4E-83
4 g12695.t4 PANTHER PTHR10981:SF0 BATTENIN 32 304 5.4E-83
8 g12695.t4 PRINTS PR01315 CLN3 Batten’s disease protein (battenin) signature 47 69 2.6E-37
5 g12695.t4 PRINTS PR01315 CLN3 Batten’s disease protein (battenin) signature 95 111 2.6E-37
7 g12695.t4 PRINTS PR01315 CLN3 Batten’s disease protein (battenin) signature 147 169 2.6E-37
6 g12695.t4 PRINTS PR01315 CLN3 Batten’s disease protein (battenin) signature 177 197 2.6E-37
1 g12695.t4 Pfam PF02487 CLN3 protein 45 236 2.3E-59
2 g12695.t4 Pfam PF02487 CLN3 protein 249 304 1.3E-13
21 g12695.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 44 -
30 g12695.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 45 65 -
17 g12695.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 66 85 -
29 g12695.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 86 109 -
22 g12695.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 110 114 -
26 g12695.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 115 135 -
20 g12695.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 136 141 -
27 g12695.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 142 168 -
23 g12695.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 169 173 -
31 g12695.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 174 195 -
18 g12695.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 196 206 -
25 g12695.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 207 224 -
24 g12695.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 225 255 -
28 g12695.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 256 278 -
19 g12695.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 279 304 -
15 g12695.t4 SUPERFAMILY SSF103473 MFS general substrate transporter 22 274 1.29E-13
13 g12695.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 44 65 -
12 g12695.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 94 116 -
11 g12695.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 123 145 -
10 g12695.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 173 195 -
9 g12695.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 207 224 -
14 g12695.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 256 278 -

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

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