Gene loci information

Transcript annotation

  • This transcript has been annotated as Arf-GAP with coiled-coil, ANK repeat and PH domain-containing protein 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_1 g13457 g13457.t1 TTS g13457.t1 30238191 30238191
chr_1 g13457 g13457.t1 isoform g13457.t1 30238784 30241209
chr_1 g13457 g13457.t1 exon g13457.t1.exon1 30238784 30239005
chr_1 g13457 g13457.t1 cds g13457.t1.CDS1 30238784 30239005
chr_1 g13457 g13457.t1 exon g13457.t1.exon2 30239080 30239280
chr_1 g13457 g13457.t1 cds g13457.t1.CDS2 30239080 30239280
chr_1 g13457 g13457.t1 exon g13457.t1.exon3 30239342 30239505
chr_1 g13457 g13457.t1 cds g13457.t1.CDS3 30239342 30239505
chr_1 g13457 g13457.t1 exon g13457.t1.exon4 30239562 30239755
chr_1 g13457 g13457.t1 cds g13457.t1.CDS4 30239562 30239755
chr_1 g13457 g13457.t1 exon g13457.t1.exon5 30239819 30241209
chr_1 g13457 g13457.t1 cds g13457.t1.CDS5 30239819 30241209
chr_1 g13457 g13457.t1 TSS g13457.t1 30241301 30241301

Sequences

>g13457.t1 Gene=g13457 Length=2172
ATGAATAAATTTCACAATATTTTACTCGAACAGTGTTCTAAAACAGTTTTAAAGAATATT
TCTAATTTTCTGAAAAAAGACGTTCGAGAAGTGAAAGACTATAAGCAGATATTTACAAAA
ATATCAGAAAATTATGATGGTGCATTAAATAAAAATTCCCAAGTGAACAAAAATCGACCA
CAAGAGATTATTGAGGCTGAAAATTACGTTTGTTCTACCAAATCACAATTTCAACATTCA
GCTCTCGACTATGTTAATTATATTACATTACTACAACGCAAAAAGCGACCAGAAATTTTA
TCAACTCTCTTGAGCTATGTGTCTGCATGTTCGACATATTTTCATCAAGGGAGTGATTTA
TGTCAAGATTATGACACTTATCTATTCAAAGAATTGGATGAGGAAGTAAATAATATGCGA
GCTGATTACGCTGCACTCGAAAAAGAAATGCAAAAACGGCACAATTATGTATTGGGATAT
TCTGAGAATAATAAAGATATGAATGGCAGTGAAGAATCGAAAGCAAGTGCAGGAAAACAA
ATGGAAGGTTATTTATTTAAACGTACATCTAATGCTTTTAAAACATGGAATCGCAGATGG
TTCTATATGAAAGACAATAAATTATATTATCGTAAAAGGTCGGGTGAAGACATTCCCGTA
ACAATGGAAGATGATTTAAAGTTATGTGCAGTGCGACCATTGATGGATAGTGATAGACGA
TTCTGTTTTGAAGTAATTTCTCCCACAAAAAGTCACATTTTGCAAGCTGATTCAGAAAGC
CAATATCAAGCATGGATTCAAGCACTTCAATCAGCCATTGGAAATGCAATTCAAAATAAT
AGTCGATATTCGAGCCATATGTGTGCAAGCACATCGAGCAATTCGAGTATTTCTTCATCA
ACAGCACCCTCATCAAGTCGTGGTAGTGGTGCAGAAAAGAAAATCAATTGGAGACAAATG
TTGCTTATCCCTGGCAATATGAAATGTGCTGACTGTGGAAATCCTGATCCAAAATGGGCA
TCAATTAATCTTGGCATTACGCTATGTATTGCTTGCTCGGGTGTTCATAGATCGCTCGGT
GTACATTATTCAAAGGTGCGAAGCTTGACATTAGACTGTTGGGAACCAGAAATATTGCGT
GTTATGACCGAATTAGGAAACGAAGTAGTTAATAAAATTTATGAGGCAACATATGATGAA
CTTATGAGTGATGTTGAAAGAGCAACAGAAAATTGTGATGATGAAATTCGTAAAAAGTGG
ATTCATGCAAAATATGTTGATAGAAAATTTGTGCTTCCTTTAGAGAAGAAAATTGAATTA
CTTCCACCAACACTTTTACCGTCACCAAATAAATGGAGTGTAAAGAAAAATCGTCGTCGA
ACTGCACGAAGAAGCGTTAATAACAATAATATTGATATGAAAATTACAACAAAAGAACAT
GACAACAGTGAAGATGAAAAAGAAATTAATGAGGGCATTCTGATGTTAGGTGAAAGTTTG
CTTGAAAGTTCAAGCATTCCAGTTCAATGTAATTTATTCTCAAATTCTGATCAAGAATCA
ACAAGTGGAGAAGAAGATGTGCTTGATGAAGAAGATATTGAAAAATTAAATCCAAATTAT
GTCTTATACAAAGCATCTATTGCCCATAATCTTCCAGTGATGTGTCAAGCACTTGCACTA
GGTGCTGATAAAAATTGGCCAAATCTCGAAAATTTCAATCGAACACCACTTCATCAAGCT
GTTATTGTTGGTTCATTAATGACAAGCGAATTTCTTATACTTAATGGAGCAAATATTAAT
TGTACAGATAGCAGAAACTATACGCCACTTCATTTATCAATTGAATTAGGAAACACAGCT
CTTGCTTATCTATTGCTCAAGCATAAAGCCAAATATGACATTGCCACAGTTGATAATAAA
TTGCCAATTGATTTTGCTGTTCAAACTGCGAATGCTGATGTTGTTACACTTCTCAGATTG
CATCAATTAAATGATGAGATAGGAGCAACAGGAGAAGATAGTGAACCAGGTGGAGATTCA
ACGTACCATGATGTTATGAGAGATTTTTCACATCTAGCAAACAACTTGAGATTGCGAGGT
AATAGTAAACGTGATGGAAGTTCTTCATCATCATCCATCACAAATAATGCAGACAATATT
TCAATGGAGTAA

>g13457.t1 Gene=g13457 Length=723
MNKFHNILLEQCSKTVLKNISNFLKKDVREVKDYKQIFTKISENYDGALNKNSQVNKNRP
QEIIEAENYVCSTKSQFQHSALDYVNYITLLQRKKRPEILSTLLSYVSACSTYFHQGSDL
CQDYDTYLFKELDEEVNNMRADYAALEKEMQKRHNYVLGYSENNKDMNGSEESKASAGKQ
MEGYLFKRTSNAFKTWNRRWFYMKDNKLYYRKRSGEDIPVTMEDDLKLCAVRPLMDSDRR
FCFEVISPTKSHILQADSESQYQAWIQALQSAIGNAIQNNSRYSSHMCASTSSNSSISSS
TAPSSSRGSGAEKKINWRQMLLIPGNMKCADCGNPDPKWASINLGITLCIACSGVHRSLG
VHYSKVRSLTLDCWEPEILRVMTELGNEVVNKIYEATYDELMSDVERATENCDDEIRKKW
IHAKYVDRKFVLPLEKKIELLPPTLLPSPNKWSVKKNRRRTARRSVNNNNIDMKITTKEH
DNSEDEKEINEGILMLGESLLESSSIPVQCNLFSNSDQESTSGEEDVLDEEDIEKLNPNY
VLYKASIAHNLPVMCQALALGADKNWPNLENFNRTPLHQAVIVGSLMTSEFLILNGANIN
CTDSRNYTPLHLSIELGNTALAYLLLKHKAKYDIATVDNKLPIDFAVQTANADVVTLLRL
HQLNDEIGATGEDSEPGGDSTYHDVMRDFSHLANNLRLRGNSKRDGSSSSSSITNNADNI
SME

Protein features from InterProScan

Transcript Database ID Name Start End E.value
20 g13457.t1 CDD cd13250 PH_ACAP 181 276 8.42975E-56
19 g13457.t1 Coils Coil Coil 129 149 -
18 g13457.t1 Coils Coil Coil 391 418 -
17 g13457.t1 Gene3D G3DSA:1.20.1270.60 Arfaptin 1 162 4.5E-40
16 g13457.t1 Gene3D G3DSA:2.30.29.30 - 173 289 5.5E-32
15 g13457.t1 Gene3D G3DSA:3.30.40.160 - 292 438 1.3E-45
14 g13457.t1 Gene3D G3DSA:1.25.40.20 - 536 695 8.7E-40
26 g13457.t1 MobiDBLite mobidb-lite consensus disorder prediction 699 723 -
5 g13457.t1 PANTHER PTHR23180:SF399 CENTAURIN BETA 1A 1 703 8.8E-252
6 g13457.t1 PANTHER PTHR23180 CENTAURIN/ARF 1 703 8.8E-252
9 g13457.t1 PRINTS PR00405 HIV Rev interacting protein signature 326 345 2.0E-20
8 g13457.t1 PRINTS PR00405 HIV Rev interacting protein signature 345 362 2.0E-20
7 g13457.t1 PRINTS PR00405 HIV Rev interacting protein signature 366 387 2.0E-20
3 g13457.t1 Pfam PF16746 BAR domain of APPL family 1 150 1.3E-44
2 g13457.t1 Pfam PF00169 PH domain 180 273 4.7E-17
4 g13457.t1 Pfam PF01412 Putative GTPase activating protein for Arf 318 431 6.8E-38
1 g13457.t1 Pfam PF13637 Ankyrin repeats (many copies) 573 626 5.5E-5
31 g13457.t1 ProSiteProfiles PS50003 PH domain profile. 178 274 18.159
30 g13457.t1 ProSiteProfiles PS50115 ARF GTPase-activating proteins domain profile. 314 438 26.447
27 g13457.t1 ProSiteProfiles PS50297 Ankyrin repeat region circular profile. 537 658 24.108
28 g13457.t1 ProSiteProfiles PS50088 Ankyrin repeat profile. 572 604 11.167
29 g13457.t1 ProSiteProfiles PS50088 Ankyrin repeat profile. 605 637 9.164
21 g13457.t1 SMART SM00233 PH_update 179 276 2.6E-18
22 g13457.t1 SMART SM00105 arf_gap_3 314 438 6.0E-47
24 g13457.t1 SMART SM00248 ANK_2a 572 601 0.16
25 g13457.t1 SMART SM00248 ANK_2a 605 634 0.62
23 g13457.t1 SMART SM00248 ANK_2a 638 667 1400.0
12 g13457.t1 SUPERFAMILY SSF103657 BAR/IMD domain-like 2 201 3.26E-43
11 g13457.t1 SUPERFAMILY SSF50729 PH domain-like 180 282 4.28E-28
13 g13457.t1 SUPERFAMILY SSF57863 ArfGap/RecO-like zinc finger 318 433 2.09E-40
10 g13457.t1 SUPERFAMILY SSF48403 Ankyrin repeat 538 663 4.35E-24

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:0005515 protein binding MF
GO:0005096 GTPase activator 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