Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative ATP-binding cassette sub-family A member 3.

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 g8800 g8800.t2 TSS g8800.t2 33189902 33189902
chr_2 g8800 g8800.t2 isoform g8800.t2 33189929 33191678
chr_2 g8800 g8800.t2 exon g8800.t2.exon1 33189929 33190318
chr_2 g8800 g8800.t2 cds g8800.t2.CDS1 33189929 33190318
chr_2 g8800 g8800.t2 exon g8800.t2.exon2 33190584 33190850
chr_2 g8800 g8800.t2 cds g8800.t2.CDS2 33190584 33190850
chr_2 g8800 g8800.t2 exon g8800.t2.exon3 33190908 33191678
chr_2 g8800 g8800.t2 cds g8800.t2.CDS3 33190908 33191678
chr_2 g8800 g8800.t2 TTS g8800.t2 33191967 33191967

Sequences

>g8800.t2 Gene=g8800 Length=1428
ATGTCGTTTGATAAATTAAAAATTTTGCTGTGGAAAAATTGGATTTTACAAACGCGAAGA
CCAATTTCTGCCATTTTTCAATTATTATTTCCGATTGTAGTTGTAATTCTTACAACATGG
GCACGAAATTCTTTTGGTGGTGAATATGGAGTTTTCACAAAAGTTAAAGCTAATGAATAT
AATTTCACAAGTCTATCAGAGTGTACTTTTGAAAATAAACCAATAACAAAAGTGTTTTTT
GCTCCAAATTTTGAAGCATATAGAAATTTGGTTGAAATTTCATTTGAAAATTTGGAAATT
GTTGGTTTTAACAATAGTCGTGAAATTTGGGAGGAAATCGACAAATTGGATGATCAAATT
GGAATAATTTTATTGTCAAGTGACTCAGAGGTGACAAACACACTACCGAAAAATATAACA
CATTCAATTTCTATTCGATTTCGATATGCTGATCGAGTTTGTGAATTATACCTTCAACAT
GCTTTGGAAAGAGGATTCATTAAATCATTAGCTGCTAATTCTAATTTAGAAGATGTTATT
GTCAAGAATTTTCCTTATGAAGAGCAATTTAAACAAATATTTACTGAAGTAATAATTCAT
ATACTTCCATTATTTTTGGTCTTCAGTATGTTTGCAACAGTTCAAAGTGTGATCAAAAGT
GTAGCATCAGAACGTGAAAGTAAAATGAAAGAACTAATGAAAATTATGGGACTTTCATCA
GTTCTTCATTGGTCAGCGTGGTTTATAAAATGTATCATAATGTCAACAATATCTTATACA
GTTGTGACACTTTTCCTATGCGTAGCAATCATTGGAAATGAAGCAATTTTCCAACTTAGC
AATTTCTTTCTTATTTGGCTTTTCTTTTTCCTCTATTGTATTGGTGTAATTACATTCTGT
TTTATGGTCAGCACAATCTTTACAAAAGCAACAGTTGCTACAAATGTTGGTTTGATGCTT
TTCTTCTCAACTTATGTTCCCTATTATGTTTATGGAACAAACTTTGAGACGCTAAATCAT
ATTGTAAAATGGTTTTTTTGCATTCCAATCAACACATCACTTGGTCAAGGAATTTCAATG
GTATTAAATTTGGAATTGAACAAACAAGGCATCACTTTTTCAAATCTATTTACGCAAGTT
AATGGATTTAATTTTACATTCTTTGAAATTTTAATGATTATGATAATTGCAAGTATGATT
CATATTTTGATAATGACTTATCTTGAACTCGTCTTCCCTGGTGACGTTGGAGTTGCAAAG
CCATGGCATTTTCCTTTTACATTTTGTTTTGATTCGATGAGAAACAATCATAAAAATGCA
CACAATTATACAAACACTGATAATGGCAATATTTTTATTTCAAATGATGATATAGAAGAA
GAACCAAAGCATTTAAATGTGAAAGTTCGTATTAAAAACTTAACAAAA

>g8800.t2 Gene=g8800 Length=476
MSFDKLKILLWKNWILQTRRPISAIFQLLFPIVVVILTTWARNSFGGEYGVFTKVKANEY
NFTSLSECTFENKPITKVFFAPNFEAYRNLVEISFENLEIVGFNNSREIWEEIDKLDDQI
GIILLSSDSEVTNTLPKNITHSISIRFRYADRVCELYLQHALERGFIKSLAANSNLEDVI
VKNFPYEEQFKQIFTEVIIHILPLFLVFSMFATVQSVIKSVASERESKMKELMKIMGLSS
VLHWSAWFIKCIIMSTISYTVVTLFLCVAIIGNEAIFQLSNFFLIWLFFFLYCIGVITFC
FMVSTIFTKATVATNVGLMLFFSTYVPYYVYGTNFETLNHIVKWFFCIPINTSLGQGISM
VLNLELNKQGITFSNLFTQVNGFNFTFFEILMIMIIASMIHILIMTYLELVFPGDVGVAK
PWHFPFTFCFDSMRNNHKNAHNYTNTDNGNIFISNDDIEEEPKHLNVKVRIKNLTK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g8800.t2 PANTHER PTHR19229:SF36 ATP-BINDING CASSETTE, SUB-FAMILY A (ABC1), MEMBER 3B 4 476 5.7E-55
3 g8800.t2 PANTHER PTHR19229 ATP-BINDING CASSETTE TRANSPORTER SUBFAMILY A ABCA 4 476 5.7E-55
1 g8800.t2 Pfam PF12698 ABC-2 family transporter protein 25 402 2.0E-24
14 g8800.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 20 -
22 g8800.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 21 41 -
18 g8800.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 42 196 -
25 g8800.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 197 221 -
13 g8800.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 222 240 -
21 g8800.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 241 271 -
17 g8800.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 272 282 -
20 g8800.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 283 303 -
12 g8800.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 304 309 -
24 g8800.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 310 330 -
16 g8800.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 331 341 -
23 g8800.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 342 364 -
11 g8800.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 365 384 -
19 g8800.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 385 408 -
15 g8800.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 409 476 -
10 g8800.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 21 40 -
6 g8800.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 199 221 -
4 g8800.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 241 272 -
5 g8800.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 282 304 -
8 g8800.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 311 330 -
7 g8800.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 340 362 -
9 g8800.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 383 405 -

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:0055085 transmembrane transport BP
GO:0042626 ATPase-coupled transmembrane transporter activity MF
GO:0016021 integral component of 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. There were no conditions that were differentially expressed