Gene loci information

Transcript annotation

  • This transcript has been annotated as ATP-binding cassette sub-family F member 2.

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_3 g2807 g2807.t6 TSS g2807.t6 20371015 20371015
chr_3 g2807 g2807.t6 isoform g2807.t6 20371138 20372785
chr_3 g2807 g2807.t6 exon g2807.t6.exon1 20371138 20371148
chr_3 g2807 g2807.t6 exon g2807.t6.exon2 20371541 20371763
chr_3 g2807 g2807.t6 cds g2807.t6.CDS1 20371567 20371763
chr_3 g2807 g2807.t6 exon g2807.t6.exon3 20371826 20371974
chr_3 g2807 g2807.t6 cds g2807.t6.CDS2 20371826 20371974
chr_3 g2807 g2807.t6 exon g2807.t6.exon4 20372032 20372247
chr_3 g2807 g2807.t6 cds g2807.t6.CDS3 20372032 20372247
chr_3 g2807 g2807.t6 exon g2807.t6.exon5 20372314 20372515
chr_3 g2807 g2807.t6 cds g2807.t6.CDS4 20372314 20372515
chr_3 g2807 g2807.t6 exon g2807.t6.exon6 20372576 20372683
chr_3 g2807 g2807.t6 cds g2807.t6.CDS5 20372576 20372683
chr_3 g2807 g2807.t6 exon g2807.t6.exon7 20372745 20372785
chr_3 g2807 g2807.t6 cds g2807.t6.CDS6 20372745 20372784
chr_3 g2807 g2807.t6 TTS g2807.t6 NA NA

Sequences

>g2807.t6 Gene=g2807 Length=950
TCTCATTAAAGTAACCTAATTTAAAGGAAGAAGAAAAATGCCATCTGATTCAAAGAAAAA
GGAACAGCAACGAAAAAAGGATGCTCGCAATAAGAAGATTAATGAAGCTTCCAAAAAAGA
ACAGCCTCAATCAAATGGTATTGCAAATGGTAAAGAACCCAAAAAAGAATTGACTGAAGA
AGAAATTCTTTGTCAAAAATTAGAGGAGGATGCTAGATTGGCAGCTGATGCACGTTCATC
GACTGGAACACAAGCAAACCATCGTTTATCAAGAGATATTAAAATTGAGAATTTTTCTAT
CACATTTTATGGCAACGAGATTCTATTAGATACAACTTTAGAATTGAATTGTGGAAGACG
TTATGGTTTAGTTGGTAGTAATGGATGTGGAAAATCGACTTTATTGGCTGTTTTAGGAAA
TCGTGAAGTGCCCATACAAGATTTTATTGACATTTTCTTCTTGGCTCGTGAAGTTGCAGC
TTCTTCGAAAACTGCTTTAGAAATGGTCATGGAAGTCGATCAAGAGCGTATCAAACTCGA
AGCACTTGCAGATGAATTAAGCGGATGTGACGATGATGAATCTCAAGAGCAATTGATCGA
TATTTACGATCGACTGGATGAAATGCAATCTGATTTAGCCGAAACTAAAGCATCTCGTAT
TTTACACGGTTTGGGATTTGATAAAGCAATGCAAAGAAAAGCCTGTCAAGATTTTAGTGG
TGGTTGGCGTATGAGAATTGCACTCGCAAGAGCACTCTATGTGAAACCTCATTTGCTGTT
ACTTGATGATCCAACTAATCATCTTGATCTCGAAGCATGTGTGTGGTTGGAAGAAGAGCT
AAAAAATTACAAGAGAATTTTGGTATTGGTATCACACTCACAAGATTTTCTTAATGGAGT
AACGACCAACATTATTCATATGACAAAAAAGAGATTGAAGTACTATACTG

>g2807.t6 Gene=g2807 Length=304
MPSDSKKKEQQRKKDARNKKINEASKKEQPQSNGIANGKEPKKELTEEEILCQKLEEDAR
LAADARSSTGTQANHRLSRDIKIENFSITFYGNEILLDTTLELNCGRRYGLVGSNGCGKS
TLLAVLGNREVPIQDFIDIFFLAREVAASSKTALEMVMEVDQERIKLEALADELSGCDDD
ESQEQLIDIYDRLDEMQSDLAETKASRILHGLGFDKAMQRKACQDFSGGWRMRIALARAL
YVKPHLLLLDDPTNHLDLEACVWLEEELKNYKRILVLVSHSQDFLNGVTTNIIHMTKKRL
KYYT

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g2807.t6 CDD cd03221 ABCF_EF-3 81 299 8.18525E-47
6 g2807.t6 Coils Coil Coil 7 27 -
5 g2807.t6 Gene3D G3DSA:3.40.50.300 - 44 304 4.3E-46
10 g2807.t6 MobiDBLite mobidb-lite consensus disorder prediction 1 44 -
11 g2807.t6 MobiDBLite mobidb-lite consensus disorder prediction 1 26 -
2 g2807.t6 PANTHER PTHR19211 ATP-BINDING TRANSPORT PROTEIN-RELATED 1 304 6.4E-108
3 g2807.t6 PANTHER PTHR19211:SF15 ATP-BINDING CASSETTE SUB-FAMILY F MEMBER 2 1 304 6.4E-108
1 g2807.t6 Pfam PF00005 ABC transporter 98 254 1.5E-21
9 g2807.t6 ProSitePatterns PS00211 ABC transporters family signature. 226 240 -
12 g2807.t6 ProSiteProfiles PS50893 ATP-binding cassette, ABC transporter-type domain profile. 81 304 12.579
8 g2807.t6 SMART SM00382 AAA_5 105 299 1.6E-9
4 g2807.t6 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 76 303 1.87E-38

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

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