Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative ADP-ribosylation factor-binding protein GGA2.

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 g1918 g1918.t12 TTS g1918.t12 13858854 13858854
chr_3 g1918 g1918.t12 isoform g1918.t12 13858998 13861272
chr_3 g1918 g1918.t12 exon g1918.t12.exon1 13858998 13859281
chr_3 g1918 g1918.t12 cds g1918.t12.CDS1 13858998 13859281
chr_3 g1918 g1918.t12 exon g1918.t12.exon2 13859342 13860566
chr_3 g1918 g1918.t12 cds g1918.t12.CDS2 13859342 13860566
chr_3 g1918 g1918.t12 exon g1918.t12.exon3 13860649 13860708
chr_3 g1918 g1918.t12 cds g1918.t12.CDS3 13860649 13860708
chr_3 g1918 g1918.t12 exon g1918.t12.exon4 13860830 13860897
chr_3 g1918 g1918.t12 cds g1918.t12.CDS4 13860830 13860897
chr_3 g1918 g1918.t12 exon g1918.t12.exon5 13860963 13861272
chr_3 g1918 g1918.t12 cds g1918.t12.CDS5 13860963 13861146
chr_3 g1918 g1918.t12 TSS g1918.t12 13861357 13861357

Sequences

>g1918.t12 Gene=g1918 Length=1947
ATGAGTCGAGAAGATTTGATTACAAATTTAGAGATCTATTTAGGTAAAAATAATTTTTTA
TTTATTGAAATTTACATTTTGATTTGTGAGAAAAATTTTTTAATGCGTAAAATTTTATGA
CATATTATGATTATTCAAGATCAAGCTGTTGATCCATCAAAAGAAGAATTTGATATATCC
TGCGTTGATGCGTTTTGTCATTTACTTAAGAATGAACCAGATCTTTGCTCCAATGCCACA
AGACTACTTGCCGCAAAGATTCAATCTCAAAACACTAAGGAAAGTTTGTTCGCTTTGGAT
TGTCTGGAAGAATGCATGGACACGCTTGGATCCAGTTTTCAAATAGAAGTGAATAAATTT
AAATTCCTCAATGAATTGATTCGTTTAGTGAGTAAAAAATTTCAAGGCGATAAGACACCC
CGTGAAATTCAAGATCGAATTTTAGATATTTTATTTACTTGGACTGATAAATTCCCAGAA
TTGGGAAAAATTAAAGAAGCTTACACGATGCTAAGAACGCAAGGAGTTGTTCATGAACCA
CAGAAAAATGTTATTGCTCCAAGTAGCAAAAAATCGACTGATAGTACTTTAAAGCTTATG
GAATCCGAAAAATTCAAAAGACTACTGCAAAGCAAGAATCAAAAAGACATTGAAGCTGCT
AATTTAATGATTCAAAATATGGTGAGAGACAATGATCGCCGTATTCAAATTCAGAATCGC
CGTTTAATGGATCTTCAAAGTGCAAATGAAAATTCAATCCTATTAAAAGAAATGTTAGAT
GAGTTTGATCCAAATGAGGTGTCTGAAGATACACTCAGTACTCTGCAGGAAATTTACAAC
AATTGTGTCAAATTAAAGCCAACTGTGTGTCGACTTGCCGAAGAAAGTCATGATTCTGAA
GCATTTATGAGTAAAATACTCGAAACAAACGAAGTTCTTAATAAAACAATTGAACTTTAT
ACAGCGATTATAATAAATAAAACTCCAACAGTAAAGAAAACTTTACCCAAGAAAACTAAT
GCAGTAACAAATTTACTAGATGTTGCCGAAGTCACAAACGAAACATCAACTTCATCGAAC
GCTTCAAATGGTACACTTAACGAACTCAATGAGATTTTTTCAACATCTACGACAACACCA
AATATTACTAACAATACGCATATTGACAATATTTTATTAACGCCACAAATTGTTCCGACT
CTACAACAGACGACAACTTCCAACACTTCCGCTTCAAGTTCAAGTATTGATATTATGGCA
TTAATTAATAGTCATAAGCAAATAAAATCATCTAATGATGATTTACTTGGAAATTTTAAT
GCATCACAGGAGAGCCCAATAAAAATTACTCAATCTAAAACAAATGAAAAACCACAAAAA
GCTCAACTAAGCGAGCTTGACTCAATTATTAGTGGTATGAAATCAAAACTTCTAACAGGA
GATTCAGAAGATCAAGAAATTTCAAAAGAAATTGATGATGTTATGCTTATTAGTGAGACT
CCTCAAGAAGAGAAAATTGTAAAGTTGATTGAGGATACAGTGATTGCTCCAGTAAATGAA
TATACTGAAAAAAAAGTTGCATTAAAAGATATTAGCATAGATATAAGTGAAATTCAACCT
AGTGAAGTTGAAGCTCCGAGAACAATTTTAGACGAGAAGAAAGTTATTTCGGTAAATAAT
CAAGGGCCTGTTGCAATTAACAATTTTCAATTTGATGCTAGTGTATCCAAACCATGTAAA
TTGAGAATCCTTGAGGCTTCGGGACGTGACTTGCCTGGTTTGAAGCCATTTAAACCGCCA
ACAGAGACCATTAATCAAGTTTTATTGCTTCTCAACCCCACGCAACAGCCTGTTAACATG
GTTGCAATTTTAACTTATAACGTTCAAGGCGATGAAGATGAAGAAAAAGTATCGATAGAA
GTCAAAGACATTCCTTTCCAAAGTTAA

>g1918.t12 Gene=g1918 Length=606
MIIQDQAVDPSKEEFDISCVDAFCHLLKNEPDLCSNATRLLAAKIQSQNTKESLFALDCL
EECMDTLGSSFQIEVNKFKFLNELIRLVSKKFQGDKTPREIQDRILDILFTWTDKFPELG
KIKEAYTMLRTQGVVHEPQKNVIAPSSKKSTDSTLKLMESEKFKRLLQSKNQKDIEAANL
MIQNMVRDNDRRIQIQNRRLMDLQSANENSILLKEMLDEFDPNEVSEDTLSTLQEIYNNC
VKLKPTVCRLAEESHDSEAFMSKILETNEVLNKTIELYTAIIINKTPTVKKTLPKKTNAV
TNLLDVAEVTNETSTSSNASNGTLNELNEIFSTSTTTPNITNNTHIDNILLTPQIVPTLQ
QTTTSNTSASSSSIDIMALINSHKQIKSSNDDLLGNFNASQESPIKITQSKTNEKPQKAQ
LSELDSIISGMKSKLLTGDSEDQEISKEIDDVMLISETPQEEKIVKLIEDTVIAPVNEYT
EKKVALKDISIDISEIQPSEVEAPRTILDEKKVISVNNQGPVAINNFQFDASVSKPCKLR
ILEASGRDLPGLKPFKPPTETINQVLLLLNPTQQPVNMVAILTYNVQGDEDEEKVSIEVK
DIPFQS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g1918.t12 Gene3D G3DSA:1.25.40.90 - 2 149 0.0000000
14 g1918.t12 Gene3D G3DSA:1.20.5.170 - 150 191 0.0000000
15 g1918.t12 Gene3D G3DSA:1.20.58.160 - 192 286 0.0000000
12 g1918.t12 Gene3D G3DSA:2.60.40.1230 - 511 605 0.0000000
5 g1918.t12 PANTHER PTHR45905:SF1 GOLGI-LOCALIZED, GAMMA-ADAPTIN EAR CONTAINING, ARF BINDING PROTEIN 5 592 0.0000000
6 g1918.t12 PANTHER PTHR45905 GOLGI-LOCALIZED, GAMMA-ADAPTIN EAR CONTAINING, ARF BINDING PROTEIN 5 592 0.0000000
3 g1918.t12 Pfam PF00790 VHS domain 5 133 0.0000000
4 g1918.t12 Pfam PF18308 GGA N-GAT domain 160 192 0.0000002
1 g1918.t12 Pfam PF03127 GAT domain 208 281 0.0000000
2 g1918.t12 Pfam PF02883 Adaptin C-terminal domain 514 592 0.0000000
16 g1918.t12 ProSiteProfiles PS50179 VHS domain profile. 7 137 25.8330000
17 g1918.t12 ProSiteProfiles PS50909 GAT domain profile. 156 283 19.8600000
18 g1918.t12 ProSiteProfiles PS50180 Gamma-adaptin ear (GAE) domain profile. 478 601 20.5180000
11 g1918.t12 SMART SM00288 VHS_2 5 133 0.0000000
10 g1918.t12 SMART SM00809 alpha_adaptinc2 475 603 0.0000470
9 g1918.t12 SUPERFAMILY SSF48464 ENTH/VHS domain 5 135 0.0000000
8 g1918.t12 SUPERFAMILY SSF89009 GAT-like domain 159 282 0.0000000
7 g1918.t12 SUPERFAMILY SSF49348 Clathrin adaptor appendage domain 513 596 0.0000000

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:0006886 intracellular protein transport BP
GO:0016192 vesicle-mediated transport BP

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