Gene loci information

Transcript annotation

  • This transcript has been annotated as 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_1 g13175 g13175.t2 isoform g13175.t2 28327552 28330266
chr_1 g13175 g13175.t2 exon g13175.t2.exon1 28327552 28327624
chr_1 g13175 g13175.t2 TSS g13175.t2 28327560 28327560
chr_1 g13175 g13175.t2 exon g13175.t2.exon2 28328101 28328704
chr_1 g13175 g13175.t2 cds g13175.t2.CDS1 28328102 28328704
chr_1 g13175 g13175.t2 exon g13175.t2.exon3 28329294 28330266
chr_1 g13175 g13175.t2 cds g13175.t2.CDS2 28329294 28330265
chr_1 g13175 g13175.t2 TTS g13175.t2 NA NA

Sequences

>g13175.t2 Gene=g13175 Length=1650
AGAAAACGAAAAAAAAAATACGGTTGTGAAAAAAGTTTGTGATAAGATTAAGTTCAGATA
AAGAAAATTTCTGAATGACGACGTCAGCGTGGGATAAATTTCTTTTGCTATCATGGAAGA
ATTGGCTGATACAAATTCGACATCCAATTCAAACTGTGTTAGAAGTAATGATACCAATTT
TAGTTTGTGCATTTCTGATTCTCATCAGAGGACTTGTTGATGTGTCAGAAGAAACAGAAG
CTTTAAAATTTCCTCCTATTGTAACAAATGAGTTTGTGGAACGAAATTTCACATATCAAC
GTGTTATTGCCTATTCGCCAAATAATCCTGTTTTAAACCAAATTGTGAAGAATGCTGCTG
ATCAAATATTTAATTTCAGTCACATATCATTTTCAAATCAAACTGAATTAGAAGGGAATG
CACTAACTGCCTCTCCTTTTGTTAGCATTGAATTTGATCAAAGCTTAGCAAACCTTCAAT
CAATTAAAGATTTTCCAAATAATATTCATTATGCATTAAGATTTCCAGCAGAATTGCGTA
CAGAAAATGAAATTTTGAATGAAATGGGAGGATTTACAAGCAATTGGGCAACAAATATTC
GTTTTGGCCTAGACTTTCTTCCGGGACCAAGAAACGGAAACGAATTCGACGGAGGTGAAC
CGCCAGGATACATCAGACAAGGATTTATTTTCATTCAAAATTTAATTGATCGTGAAATAA
TAAGAGCTAAAATTGGTAATCGATCATTTCAATTCCCTGACTTGTACATACAAAGAATGC
CGTTTCCTGAGTATGTTACTGATGTTCTTGGACTAGTGATGGAATTTGCTATTCCTTTAA
TTTTCTTGGTTGCTTTTATGGTCAGTGCGATCAACAATATTAAATATATAGCTATCGAAA
GAGAATTACAATTGAAAGAAGCAATGAAAATTATGGGACTACCAGGTTATATGCATTGGA
TCGCATGGTTTACAAAATGTATGATATTTCAAATAGTTATAATTTCTGTAATTACTGGGC
TAGTCAAAATACCATTCGAGTCAAAGGGTGGTCTTTCAGTTTTTACTCATACCGAATGGT
CAGTGCTGTGGGTTTTCTTTTTTCTTTACGCTATGGCAGGAGTCACATTTTCATTTATGT
TCTCAACATTCTTCGCAAAAGCTAATACGTGCAGCATTGTAGGCGCAATTGTTTGGTTAA
TGATGCTTCAACCTTACAGTATAATGAACATGAATTATTCAAACATAGGTCTCGGACCAA
AACTTGGTGCCTCTTTGCTAGTTAATACTGGCATGGGATTTGGTTTTAAAGTTCTTGGAA
GATATGAGAGCGCATTAATTGGTGTCAATTGGAATAATCTTTTTCAACCTGTCACACCTG
ATGATGATCTTACACTTGGATATATAATGTTAGTTCTTCTTGCAGCATCTGTGCTTCAAA
TGCTCATCGCTTTATATGTAGAAAAAATAAAACCAGGTGAATATGGTGTACCAGAAAAAT
GGTATTTCCCATTATCTCCAAGCTTTTGGTGTGGCGGCAAAGCAACTTCAAACTCAGAAA
TTCCCGATATGCCCAAACACAATCCTAATTATGAAAGCGAACCTGTTGGTAAAAATGCTG
GAATCAAAATTCGTGGGTTAAGAAAAACAT

>g13175.t2 Gene=g13175 Length=525
MTTSAWDKFLLLSWKNWLIQIRHPIQTVLEVMIPILVCAFLILIRGLVDVSEETEALKFP
PIVTNEFVERNFTYQRVIAYSPNNPVLNQIVKNAADQIFNFSHISFSNQTELEGNALTAS
PFVSIEFDQSLANLQSIKDFPNNIHYALRFPAELRTENEILNEMGGFTSNWATNIRFGLD
FLPGPRNGNEFDGGEPPGYIRQGFIFIQNLIDREIIRAKIGNRSFQFPDLYIQRMPFPEY
VTDVLGLVMEFAIPLIFLVAFMVSAINNIKYIAIERELQLKEAMKIMGLPGYMHWIAWFT
KCMIFQIVIISVITGLVKIPFESKGGLSVFTHTEWSVLWVFFFLYAMAGVTFSFMFSTFF
AKANTCSIVGAIVWLMMLQPYSIMNMNYSNIGLGPKLGASLLVNTGMGFGFKVLGRYESA
LIGVNWNNLFQPVTPDDDLTLGYIMLVLLAASVLQMLIALYVEKIKPGEYGVPEKWYFPL
SPSFWCGGKATSNSEIPDMPKHNPNYESEPVGKNAGIKIRGLRKT

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g13175.t2 PANTHER PTHR19229:SF139 ATP-BINDING CASSETTE, SUB-FAMILY A (ABC1), MEMBER 14 7 524 5.5E-83
3 g13175.t2 PANTHER PTHR19229 ATP-BINDING CASSETTE TRANSPORTER SUBFAMILY A ABCA 7 524 5.5E-83
1 g13175.t2 Pfam PF12698 ABC-2 family transporter protein 28 460 8.1E-15
11 g13175.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 27 -
17 g13175.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 28 48 -
14 g13175.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 49 250 -
21 g13175.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 251 274 -
12 g13175.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 275 294 -
18 g13175.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 295 317 -
13 g13175.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 318 336 -
16 g13175.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 337 356 -
10 g13175.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 357 362 -
19 g13175.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 363 383 -
15 g13175.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 384 440 -
20 g13175.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 441 462 -
9 g13175.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 463 525 -
4 g13175.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 244 266 -
7 g13175.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 295 317 -
6 g13175.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 337 359 -
8 g13175.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 366 383 -
5 g13175.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 439 461 -

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