Gene loci information

Transcript annotation

  • This transcript has been annotated as ABC transporter G family member 23.

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 g10140 g10140.t6 TTS g10140.t6 7729074 7729074
chr_1 g10140 g10140.t6 isoform g10140.t6 7729467 7732048
chr_1 g10140 g10140.t6 exon g10140.t6.exon1 7729467 7729674
chr_1 g10140 g10140.t6 cds g10140.t6.CDS1 7729467 7729674
chr_1 g10140 g10140.t6 exon g10140.t6.exon2 7729742 7730104
chr_1 g10140 g10140.t6 cds g10140.t6.CDS2 7729742 7730104
chr_1 g10140 g10140.t6 exon g10140.t6.exon3 7730378 7730968
chr_1 g10140 g10140.t6 cds g10140.t6.CDS3 7730378 7730968
chr_1 g10140 g10140.t6 exon g10140.t6.exon4 7731026 7731844
chr_1 g10140 g10140.t6 cds g10140.t6.CDS4 7731026 7731844
chr_1 g10140 g10140.t6 exon g10140.t6.exon5 7731912 7732048
chr_1 g10140 g10140.t6 cds g10140.t6.CDS5 7731912 7732018
chr_1 g10140 g10140.t6 TSS g10140.t6 7732067 7732067

Sequences

>g10140.t6 Gene=g10140 Length=2118
TTCTTGTTTGTCAGCACACTTGATCACATCATGAATAGTGTTGAAGTCAGAGATGCTTTC
ATTAGTTATCACAATGAAAGTACAAAACAAAAGTTTATTTTAAATGGATTAAATATGACA
GTTGCACCAAGTTCAATATATGCTTTAATTGGTGCTTCGGGATGTGGTAAAACAACTTTA
CTTTCTTGTATTTTGGGAATGAAAGAACTTGATTCTGGGACAATAAAAGTTTTGGGACAT
AAAGTTACATCAAAAAAACAAAATAAAGTTGCACGGTCAATTGGTTTTATGCCACAGGAT
ATTGCACTTTCACCACAATTAACAATCGGTGAAACATTAAAATATTTCGGAAATATTTTC
CTTATGAGTGAACAAAAATTAGAAGAAAGATCACATATGATCAAAGAATTGCTTGAACTA
CCGCCTGATGATAGATTAATTGAAAATTTATCAGGTGGTCAAAGAAGAAGAGTGTCATTA
GCAGCAGCAATCATTCATAATCCTCAAATTTTAATTCTTGATGAACCTACAGTCGGTGTT
GATTCAATACTTCGCGACAAAATTTGGAAATTTTTAATTAAATCAACACGCGAAAGCAAT
TTATCAATTATCATCACAACTCACTATATTTCTGAAGCACAACAGTCAGATAGATGTGGA
ATGATGAGAGATGGTGTTCTACTGGCTGAGGATTCACCAAGAAACATTTTGCTAAAATAT
GAAGCAGATAGCTTAGATGAAGCATTTTTAAATTTATGCAAATTGAATAAACAAGTTTTG
CCAAATTCGCAAAATCCAATAGAAGTTGTATGTGATGGATACGTAAAGAATGACATTGGT
GCAGGTCAAGAGAAAATTGATGAATTGTCTCATTTCAAAGGAAAGCTTTTATATTACATT
CAAATTATTTCTGCTTTATTTTCTAAAGAATGGGCATGCTTTAAGCGTGGTAAAATGGAT
CTTTTATCAAATCTACTATATCTAACATTTTTAAGTATTATGCTTATGTTTGGTCCAGGC
TCTGATCCAAGAGGTTTAAAAATAGGAATTGTAAATAAGGAAGTGCTTGATCCATCATAC
TGTAAAGATTATTTAAGACAGAATATTTCATATCGTAATGAGTTCAATGACTGCATTTAT
GAACATTTGTCGTGTCATTTTCTAAATGAAATTCAAGATGAAGATTTTATCAAGGTTCAT
TACAACAATTTCAATGATTCTTACAAAGATGCAAAACAAGGAAAATTAATTGCTGTCCTT
GAAATTCAAAGAAATTTCTCTGAAGCTCTTCAGTATTTGCACGAGAATTTCAATGCAAAT
GGTATTGAATTTAGTCAAGTTGGAGTGCATTTGGATCAAACTGATATGCAAATTTCAACA
TTCGTTCATAATCGACTTATGAAAGCTTATTTCAAATTTGCTGAGAAAGTCATGGTTGGT
TGTAAATATAACAAAGATTTTGTCAAGCCACCTTTGAATATATCACCAATGTTTGGTTCA
CTTTACAAAAGTTTTAAGAAATCAATCCTACCTTTGTTTATTTTACAAGGAGCATATTTT
CAATCATTTGGTTCATCATGCTACAGAATATCACAGAGTAAAGTAGATGGAATTTGGAAT
CGAACACTTTTAGCTGGAGTCAATCCAATTGAAATCTTGATAGTTCAATTTATTTTTTCA
ATCGTCATAATGTTTGTGTCATTTTTAAGTGGAATATTGGTGTTGTTTTTGTCAATCGGA
ATCACAGATTTCACAACAATTTTCGTTTCATTCATATTGGGAATCTCGTTTTGCACAGCT
GGCATTTTTATGAGTGTGTTGTTGTCATCGGTAACAAAAAATGCAAGTTTTATAACAGCG
TTTATATTTGGTGGATCAATTCTAGCGGTAACAACATCGGGTTTGTTTTGGCCTGTTGAC
GGTCAACCAGAATGGCTTCAGCAAATTTCTTATTTTTTGCCATTTGCTTACACATCAGAT
TCTTTACGTGATATTGTTATGAAAGGATCAACATTTCTTGATTTTAATGTCATTAAAGGA
TTTGTAAATATTTTCTTTTGGATTATTGCGACATTTTTGTTATCATTTTTGGTGATGAAG
AAGAAAAAATTTTCATAG

>g10140.t6 Gene=g10140 Length=695
MNSVEVRDAFISYHNESTKQKFILNGLNMTVAPSSIYALIGASGCGKTTLLSCILGMKEL
DSGTIKVLGHKVTSKKQNKVARSIGFMPQDIALSPQLTIGETLKYFGNIFLMSEQKLEER
SHMIKELLELPPDDRLIENLSGGQRRRVSLAAAIIHNPQILILDEPTVGVDSILRDKIWK
FLIKSTRESNLSIIITTHYISEAQQSDRCGMMRDGVLLAEDSPRNILLKYEADSLDEAFL
NLCKLNKQVLPNSQNPIEVVCDGYVKNDIGAGQEKIDELSHFKGKLLYYIQIISALFSKE
WACFKRGKMDLLSNLLYLTFLSIMLMFGPGSDPRGLKIGIVNKEVLDPSYCKDYLRQNIS
YRNEFNDCIYEHLSCHFLNEIQDEDFIKVHYNNFNDSYKDAKQGKLIAVLEIQRNFSEAL
QYLHENFNANGIEFSQVGVHLDQTDMQISTFVHNRLMKAYFKFAEKVMVGCKYNKDFVKP
PLNISPMFGSLYKSFKKSILPLFILQGAYFQSFGSSCYRISQSKVDGIWNRTLLAGVNPI
EILIVQFIFSIVIMFVSFLSGILVLFLSIGITDFTTIFVSFILGISFCTAGIFMSVLLSS
VTKNASFITAFIFGGSILAVTTSGLFWPVDGQPEWLQQISYFLPFAYTSDSLRDIVMKGS
TFLDFNVIKGFVNIFFWIIATFLLSFLVMKKKKFS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g10140.t6 Gene3D G3DSA:3.40.50.300 - 1 257 6.3E-59
3 g10140.t6 PANTHER PTHR43038 ATP-BINDING CASSETTE, SUB-FAMILY H, MEMBER 1 1 693 3.4E-164
4 g10140.t6 PANTHER PTHR43038:SF2 RH61964P 1 693 3.4E-164
2 g10140.t6 Pfam PF00005 ABC transporter 24 167 5.7E-32
1 g10140.t6 Pfam PF12698 ABC-2 family transporter protein 321 683 3.6E-22
12 g10140.t6 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 310 -
13 g10140.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 311 328 -
9 g10140.t6 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 329 546 -
17 g10140.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 547 571 -
11 g10140.t6 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 572 576 -
15 g10140.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 577 598 -
8 g10140.t6 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 599 604 -
16 g10140.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 605 627 -
10 g10140.t6 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 628 666 -
14 g10140.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 667 689 -
7 g10140.t6 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 690 695 -
23 g10140.t6 ProSitePatterns PS00211 ABC transporters family signature. 140 154 -
25 g10140.t6 ProSiteProfiles PS50893 ATP-binding cassette, ABC transporter-type domain profile. 4 239 19.688
24 g10140.t6 SMART SM00382 AAA_5 33 223 9.8E-9
5 g10140.t6 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 4 227 3.22E-52
20 g10140.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 499 521 -
21 g10140.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 542 571 -
22 g10140.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 576 598 -
19 g10140.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 605 627 -
18 g10140.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 667 689 -

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:0005524 ATP binding MF
GO:0016887 ATP hydrolysis activity MF

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