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.t2 isoform g13457.t2 30240083 30249146
chr_1 g13457 g13457.t2 exon g13457.t2.exon1 30240083 30241297
chr_1 g13457 g13457.t2 cds g13457.t2.CDS1 30240085 30241297
chr_1 g13457 g13457.t2 exon g13457.t2.exon2 30248733 30248849
chr_1 g13457 g13457.t2 cds g13457.t2.CDS2 30248733 30248849
chr_1 g13457 g13457.t2 exon g13457.t2.exon3 30249007 30249146
chr_1 g13457 g13457.t2 cds g13457.t2.CDS3 30249007 30249056
chr_1 g13457 g13457.t2 TSS g13457.t2 30249146 30249146
chr_1 g13457 g13457.t2 TTS g13457.t2 NA NA

Sequences

>g13457.t2 Gene=g13457 Length=1472
AGTGAAACAAAAATAATAAAAGTTATTAAATTAGTGCTGTTATTTCTCGGTTTTTGTTAA
TGTGTTGATTGTTTTATTGAAAAAATAGTTATGGCGTGTATTGCTTTCAATGAAGTTCTA
TCAGATTCTCCAAGTTTTAGATATCAGCTGGAAGAGATCGAAAAAGATATCGATAATTTG
GAGCAAAAGTTAGAAAAAGTTCTTAAATTAGCTACATTAAGCTGCGATTCGGGTCGTCAG
TTTGTAGTGAATCAGAGTGCATTTGCTACATCATTATGGGAATTACAAAAACATTTTCCC
GAGGACAAAGATGCTTTAACAAAAATAATTCATTGCTTACAGGAAATGAATAAATTTCAC
AATATTTTACTCGAACAGTGTTCTAAAACAGTTTTAAAGAATATTTCTAATTTTCTGAAA
AAAGACGTTCGAGAAGTGAAAGACTATAAGCAGATATTTACAAAAATATCAGAAAATTAT
GATGGTGCATTAAATAAAAATTCCCAAGTGAACAAAAATCGACCACAAGAGATTATTGAG
GCTGAAAATTACGTTTGTTCTACCAAATCACAATTTCAACATTCAGCTCTCGACTATGTT
AATTATATTACATTACTACAACGCAAAAAGCGACCAGAAATTTTATCAACTCTCTTGAGC
TATGTGTCTGCATGTTCGACATATTTTCATCAAGGGAGTGATTTATGTCAAGATTATGAC
ACTTATCTATTCAAAGAATTGGATGAGGAAGTAAATAATATGCGAGCTGATTACGCTGCA
CTCGAAAAAGAAATGCAAAAACGGCACAATTATGTATTGGGATATTCTGAGAATAATAAA
GATATGAATGGCAGTGAAGAATCGAAAGCAAGTGCAGGAAAACAAATGGAAGGTTATTTA
TTTAAACGTACATCTAATGCTTTTAAAACATGGAATCGCAGATGGTTCTATATGAAAGAC
AATAAATTATATTATCGTAAAAGGTCGGGTGAAGACATTCCCGTAACAATGGAAGATGAT
TTAAAGTTATGTGCAGTGCGACCATTGATGGATAGTGATAGACGATTCTGTTTTGAAGTA
ATTTCTCCCACAAAAAGTCACATTTTGCAAGCTGATTCAGAAAGCCAATATCAAGCATGG
ATTCAAGCACTTCAATCAGCCATTGGAAATGCAATTCAAAATAATAGTCGATATTCGAGC
CATATGTGTGCAAGCACATCGAGCAATTCGAGTATTTCTTCATCAACAGCACCCTCATCA
AGTCGTGGTAGTGGTGCAGAAAAGAAAATCAATTGGAGACAAATGTTGCTTATCCCTGGC
AATATGAAATGTGCTGACTGTGGAAATCCTGATCCAAAATGGGCATCAATTAATCTTGGC
ATTACGCTATGTATTGCTTGCTCGGGTGTTCATAGATCGCTCGGTGTACATTATTCAAAG
GTGCGAAGCTTGACATTAGACTGTTGGGAACC

>g13457.t2 Gene=g13457 Length=460
MACIAFNEVLSDSPSFRYQLEEIEKDIDNLEQKLEKVLKLATLSCDSGRQFVVNQSAFAT
SLWELQKHFPEDKDALTKIIHCLQEMNKFHNILLEQCSKTVLKNISNFLKKDVREVKDYK
QIFTKISENYDGALNKNSQVNKNRPQEIIEAENYVCSTKSQFQHSALDYVNYITLLQRKK
RPEILSTLLSYVSACSTYFHQGSDLCQDYDTYLFKELDEEVNNMRADYAALEKEMQKRHN
YVLGYSENNKDMNGSEESKASAGKQMEGYLFKRTSNAFKTWNRRWFYMKDNKLYYRKRSG
EDIPVTMEDDLKLCAVRPLMDSDRRFCFEVISPTKSHILQADSESQYQAWIQALQSAIGN
AIQNNSRYSSHMCASTSSNSSISSSTAPSSSRGSGAEKKINWRQMLLIPGNMKCADCGNP
DPKWASINLGITLCIACSGVHRSLGVHYSKVRSLTLDCWE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
18 g13457.t2 CDD cd07603 BAR_ACAPs 17 213 4.16237E-88
17 g13457.t2 CDD cd13250 PH_ACAP 266 361 3.50295E-56
16 g13457.t2 Coils Coil Coil 13 40 -
15 g13457.t2 Coils Coil Coil 214 234 -
14 g13457.t2 Gene3D G3DSA:1.20.1270.60 Arfaptin 2 247 2.4E-64
13 g13457.t2 Gene3D G3DSA:2.30.29.30 - 258 374 2.7E-32
12 g13457.t2 Gene3D G3DSA:3.30.40.160 - 384 460 1.8E-28
4 g13457.t2 PANTHER PTHR23180:SF399 CENTAURIN BETA 1A 3 460 1.5E-179
5 g13457.t2 PANTHER PTHR23180 CENTAURIN/ARF 3 460 1.5E-179
7 g13457.t2 PRINTS PR00405 HIV Rev interacting protein signature 411 430 1.1E-17
8 g13457.t2 PRINTS PR00405 HIV Rev interacting protein signature 430 447 1.1E-17
6 g13457.t2 PRINTS PR00405 HIV Rev interacting protein signature 451 460 1.1E-17
2 g13457.t2 Pfam PF16746 BAR domain of APPL family 4 235 3.6E-70
1 g13457.t2 Pfam PF00169 PH domain 265 358 2.4E-17
3 g13457.t2 Pfam PF01412 Putative GTPase activating protein for Arf 403 460 1.2E-24
22 g13457.t2 ProSiteProfiles PS50003 PH domain profile. 263 359 18.159
21 g13457.t2 ProSiteProfiles PS50115 ARF GTPase-activating proteins domain profile. 399 460 21.445
19 g13457.t2 SMART SM00233 PH_update 264 361 2.6E-18
20 g13457.t2 SMART SM00105 arf_gap_3 399 460 5.5E-5
10 g13457.t2 SUPERFAMILY SSF103657 BAR/IMD domain-like 5 286 2.44E-63
9 g13457.t2 SUPERFAMILY SSF50729 PH domain-like 265 367 1.99E-28
11 g13457.t2 SUPERFAMILY SSF57863 ArfGap/RecO-like zinc finger 402 460 3.66E-26

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:0005096 GTPase activator 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