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.t2 isoform g2807.t2 20370884 20373452
chr_3 g2807 g2807.t2 exon g2807.t2.exon1 20370884 20371148
chr_3 g2807 g2807.t2 exon g2807.t2.exon2 20371541 20371763
chr_3 g2807 g2807.t2 cds g2807.t2.CDS1 20371567 20371763
chr_3 g2807 g2807.t2 exon g2807.t2.exon3 20371826 20371974
chr_3 g2807 g2807.t2 cds g2807.t2.CDS2 20371826 20371974
chr_3 g2807 g2807.t2 exon g2807.t2.exon4 20372032 20372247
chr_3 g2807 g2807.t2 cds g2807.t2.CDS3 20372032 20372247
chr_3 g2807 g2807.t2 exon g2807.t2.exon5 20372314 20372515
chr_3 g2807 g2807.t2 cds g2807.t2.CDS4 20372314 20372515
chr_3 g2807 g2807.t2 exon g2807.t2.exon6 20372576 20372683
chr_3 g2807 g2807.t2 cds g2807.t2.CDS5 20372576 20372683
chr_3 g2807 g2807.t2 exon g2807.t2.exon7 20372745 20373129
chr_3 g2807 g2807.t2 cds g2807.t2.CDS6 20372745 20373129
chr_3 g2807 g2807.t2 exon g2807.t2.exon8 20373186 20373216
chr_3 g2807 g2807.t2 cds g2807.t2.CDS7 20373186 20373216
chr_3 g2807 g2807.t2 exon g2807.t2.exon9 20373278 20373452
chr_3 g2807 g2807.t2 cds g2807.t2.CDS8 20373278 20373450
chr_3 g2807 g2807.t2 TTS g2807.t2 20374045 20374045
chr_3 g2807 g2807.t2 TSS g2807.t2 NA NA

Sequences

>g2807.t2 Gene=g2807 Length=1754
TTTTTATTGGATTTTCTTTAATTTTTCACTTTTTACAAATTCAAACTTTTATAATCGCTT
CTCACGATTTTTTTGTTGTTATTATTTTCACTTCACTTGTTATTCCCATCATTTCTTTTT
TTGTTTTTCAAAGTTAGTCGCCCCCTAACTTTTTTCGCTAGTTGAAAAATTAAAATTTCA
TTAATTCTCTGTAAAACGCTATCGAAAAAAAATACGGTATTGATTAATATATAATTGGGC
GTGTATTAAAAGTATCTCATTAAAGTAACCTAATTTAAAGGAAGAAGAAAAATGCCATCT
GATTCAAAGAAAAAGGAACAGCAACGAAAAAAGGATGCTCGCAATAAGAAGATTAATGAA
GCTTCCAAAAAAGAACAGCCTCAATCAAATGGTATTGCAAATGGTAAAGAACCCAAAAAA
GAATTGACTGAAGAAGAAATTCTTTGTCAAAAATTAGAGGAGGATGCTAGATTGGCAGCT
GATGCACGTTCATCGACTGGAACACAAGCAAACCATCGTTTATCAAGAGATATTAAAATT
GAGAATTTTTCTATCACATTTTATGGCAACGAGATTCTATTAGATACAACTTTAGAATTG
AATTGTGGAAGACGTTATGGTTTAGTTGGTAGTAATGGATGTGGAAAATCGACTTTATTG
GCTGTTTTAGGAAATCGTGAAGTGCCCATACAAGATTTTATTGACATTTTCTTCTTGGCT
CGTGAAGTTGCAGCTTCTTCGAAAACTGCTTTAGAAATGGTCATGGAAGTCGATCAAGAG
CGTATCAAACTCGAAGCACTTGCAGATGAATTAAGCGGATGTGACGATGATGAATCTCAA
GAGCAATTGATCGATATTTACGATCGACTGGATGAAATGCAATCTGATTTAGCCGAAACT
AAAGCATCTCGTATTTTACACGGTTTGGGATTTGATAAAGCAATGCAAAGAAAAGCCTGT
CAAGATTTTAGTGGTGGTTGGCGTATGAGAATTGCACTCGCAAGAGCACTCTATGTGAAA
CCTCATTTGCTGTTACTTGATGATCCAACTAATCATCTTGATCTCGAAGCATGTGTGTGG
TTGGAAGAAGAGCTAAAAAATTACAAGAGAATTTTGGTATTGGTATCACACTCACAAGAT
TTTCTTAATGGAGTAACGACCAACATTATTCATATGACAAAAAAGAGATTGAAGTACTAT
ACTGGTAATTATGACACTTTCGTTAAAACACGTTTAGAACTGCTCACTAATCAAATGAAG
CAGTACAATTGGGAGCAAGATCAAATTGCTCACATGAAGCAATACATTGCACGATTCGGA
AAAGGATCTAATGCGAGACAAGCACAATCGAAAGAGAAAGTCCTAGCCAAAATGGTGGCA
GGTGGTCTAACTGAAAAAAATATCGATGAAAAAACATTGAGTTTCTATTTTCCCTCATGT
CAAAAGCTTCCACCACCGATAATTATGGTTCAAGACGTGTCTTTTCGTTATAATGATAAA
ACACCATATATATACAAGAATTTAGAATTTGGTATTGATTTAGAAACTCGATTAGCATTG
GTGGGTCCTAACGGTGCCGGAAAATCAACTTTATTGAAGCTTTTGTGTCAAGAAATTGTT
CCAACATCAGGAATGATTAGATGCAATCCACATTTGAAAATTGCAAAATATAATCAGCAT
TTGCATGAACTTCTTGATATGGAAATTAGTCCTTTAGACTATATGCTCAAATCGTTCCCC
GAGGTTAAAGAAAA

>g2807.t2 Gene=g2807 Length=487
MPSDSKKKEQQRKKDARNKKINEASKKEQPQSNGIANGKEPKKELTEEEILCQKLEEDAR
LAADARSSTGTQANHRLSRDIKIENFSITFYGNEILLDTTLELNCGRRYGLVGSNGCGKS
TLLAVLGNREVPIQDFIDIFFLAREVAASSKTALEMVMEVDQERIKLEALADELSGCDDD
ESQEQLIDIYDRLDEMQSDLAETKASRILHGLGFDKAMQRKACQDFSGGWRMRIALARAL
YVKPHLLLLDDPTNHLDLEACVWLEEELKNYKRILVLVSHSQDFLNGVTTNIIHMTKKRL
KYYTGNYDTFVKTRLELLTNQMKQYNWEQDQIAHMKQYIARFGKGSNARQAQSKEKVLAK
MVAGGLTEKNIDEKTLSFYFPSCQKLPPPIIMVQDVSFRYNDKTPYIYKNLEFGIDLETR
LALVGPNGAGKSTLLKLLCQEIVPTSGMIRCNPHLKIAKYNQHLHELLDMEISPLDYMLK
SFPEVKE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g2807.t2 CDD cd03221 ABCF_EF-3 81 299 2.12243E-45
10 g2807.t2 Coils Coil Coil 7 27 -
8 g2807.t2 Gene3D G3DSA:3.40.50.300 - 46 335 2.6E-50
9 g2807.t2 Gene3D G3DSA:3.40.50.300 - 380 483 2.5E-18
14 g2807.t2 MobiDBLite mobidb-lite consensus disorder prediction 1 44 -
15 g2807.t2 MobiDBLite mobidb-lite consensus disorder prediction 1 26 -
4 g2807.t2 PANTHER PTHR19211 ATP-BINDING TRANSPORT PROTEIN-RELATED 1 486 7.3E-194
5 g2807.t2 PANTHER PTHR19211:SF15 ATP-BINDING CASSETTE SUB-FAMILY F MEMBER 2 1 486 7.3E-194
3 g2807.t2 Pfam PF00005 ABC transporter 98 254 4.5E-21
1 g2807.t2 Pfam PF12848 ABC transporter 293 363 2.0E-22
2 g2807.t2 Pfam PF00005 ABC transporter 408 453 2.9E-11
13 g2807.t2 ProSitePatterns PS00211 ABC transporters family signature. 226 240 -
16 g2807.t2 ProSiteProfiles PS50893 ATP-binding cassette, ABC transporter-type domain profile. 81 322 15.466
12 g2807.t2 SMART SM00382 AAA_5 105 299 1.6E-9
6 g2807.t2 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 76 335 3.01E-40
7 g2807.t2 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 371 470 1.31E-17

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