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.t1 TTS g1918.t1 13858854 13858854
chr_3 g1918 g1918.t1 isoform g1918.t1 13858998 13861272
chr_3 g1918 g1918.t1 exon g1918.t1.exon1 13858998 13860566
chr_3 g1918 g1918.t1 cds g1918.t1.CDS1 13858998 13860566
chr_3 g1918 g1918.t1 exon g1918.t1.exon2 13860649 13860708
chr_3 g1918 g1918.t1 cds g1918.t1.CDS2 13860649 13860708
chr_3 g1918 g1918.t1 exon g1918.t1.exon3 13860830 13860897
chr_3 g1918 g1918.t1 cds g1918.t1.CDS3 13860830 13860897
chr_3 g1918 g1918.t1 exon g1918.t1.exon4 13860963 13861133
chr_3 g1918 g1918.t1 cds g1918.t1.CDS4 13860963 13861133
chr_3 g1918 g1918.t1 exon g1918.t1.exon5 13861230 13861272
chr_3 g1918 g1918.t1 cds g1918.t1.CDS5 13861230 13861272
chr_3 g1918 g1918.t1 TSS g1918.t1 13861357 13861357

Sequences

>g1918.t1 Gene=g1918 Length=1911
ATGAGTCGAGAAGATTTGATTACAAATTTAGAGATCTATTTAGATCAAGCTGTTGATCCA
TCAAAAGAAGAATTTGATATATCCTGCGTTGATGCGTTTTGTCATTTACTTAAGAATGAA
CCAGATCTTTGCTCCAATGCCACAAGACTACTTGCCGCAAAGATTCAATCTCAAAACACT
AAGGAAAGTTTGTTCGCTTTGGATTGTCTGGAAGAATGCATGGACACGCTTGGATCCAGT
TTTCAAATAGAAGTGAATAAATTTAAATTCCTCAATGAATTGATTCGTTTAGTGAGTAAA
AAATTTCAAGGCGATAAGACACCCCGTGAAATTCAAGATCGAATTTTAGATATTTTATTT
ACTTGGACTGATAAATTCCCAGAATTGGGAAAAATTAAAGAAGCTTACACGATGCTAAGA
ACGCAAGGAGTTGTTCATGAACCACAGAAAAATGTTATTGCTCCAAGTAGCAAAAAATCG
ACTGATAGTACTTTAAAGCTTATGGAATCCGAAAAATTCAAAAGACTACTGCAAAGCAAG
AATCAAAAAGACATTGAAGCTGCTAATTTAATGATTCAAAATATGGTGAGAGACAATGAT
CGCCGTATTCAAATTCAGAATCGCCGTTTAATGGATCTTCAAAGTGCAAATGAAAATTCA
ATCCTATTAAAAGAAATGTTAGATGAGTTTGATCCAAATGAGGTGTCTGAAGATACACTC
AGTACTCTGCAGGAAATTTACAACAATTGTGTCAAATTAAAGCCAACTGTGTGTCGACTT
GCCGAAGAAAGTCATGATTCTGAAGCATTTATGAGTAAAATACTCGAAACAAACGAAGTT
CTTAATAAAACAATTGAACTTTATACAGCGATTATAATAAATAAAACTCCAACAGTAAAG
AAAACTTTACCCAAGAAAACTAATGCAGTAACAAATTTACTAGATGTTGCCGAAGTCACA
AACGAAACATCAACTTCATCGAACGCTTCAAATGGTACACTTAACGAACTCAATGAGATT
TTTTCAACATCTACGACAACACCAAATATTACTAACAATACGCATATTGACAATATTTTA
TTAACGCCACAAATTGTTCCGACTCTACAACAGACGACAACTTCCAACACTTCCGCTTCA
AGTTCAAGTATTGATATTATGGCATTAATTAATAGTCATAAGCAAATAAAATCATCTAAT
GATGATTTACTTGGAAATTTTAATGCATCACAGGAGAGCCCAATAAAAATTACTCAATCT
AAAACAAATGAAAAACCACAAAAAGCTCAACTAAGCGAGCTTGACTCAATTATTAGTGGT
ATGAAATCAAAACTTCTAACAGGAGATTCAGAAGATCAAGAAATTTCAAAAGAAATTGAT
GATGTTATGCTTATTAGTGAGACTCCTCAAGAAGAGAAAATTGTAAAGTTGATTGAGGAT
ACAGTGATTGCTCCAGTAAATGAATATACTGAAAAAAAAGTTGCATTAAAAGATATTAGC
ATAGATATAAGTGAAATTCAACCTAGTGAAGTTGAAGCTCCGAGAACAATTTTAGACGAG
AAGAAAGGTTTGAAAGTTATCGTTAATTTTACAAAAGATCGACCGGCAAAAGATGTCGTT
GTTTTAGTTATTTCGGTAAATAATCAAGGGCCTGTTGCAATTAACAATTTTCAATTTGAT
GCTAGTGTATCCAAACCATGTAAATTGAGAATCCTTGAGGCTTCGGGACGTGACTTGCCT
GGTTTGAAGCCATTTAAACCGCCAACAGAGACCATTAATCAAGTTTTATTGCTTCTCAAC
CCCACGCAACAGCCTGTTAACATGGTTGCAATTTTAACTTATAACGTTCAAGGCGATGAA
GATGAAGAAAAAGTATCGATAGAAGTCAAAGACATTCCTTTCCAAAGTTAA

>g1918.t1 Gene=g1918 Length=636
MSREDLITNLEIYLDQAVDPSKEEFDISCVDAFCHLLKNEPDLCSNATRLLAAKIQSQNT
KESLFALDCLEECMDTLGSSFQIEVNKFKFLNELIRLVSKKFQGDKTPREIQDRILDILF
TWTDKFPELGKIKEAYTMLRTQGVVHEPQKNVIAPSSKKSTDSTLKLMESEKFKRLLQSK
NQKDIEAANLMIQNMVRDNDRRIQIQNRRLMDLQSANENSILLKEMLDEFDPNEVSEDTL
STLQEIYNNCVKLKPTVCRLAEESHDSEAFMSKILETNEVLNKTIELYTAIIINKTPTVK
KTLPKKTNAVTNLLDVAEVTNETSTSSNASNGTLNELNEIFSTSTTTPNITNNTHIDNIL
LTPQIVPTLQQTTTSNTSASSSSIDIMALINSHKQIKSSNDDLLGNFNASQESPIKITQS
KTNEKPQKAQLSELDSIISGMKSKLLTGDSEDQEISKEIDDVMLISETPQEEKIVKLIED
TVIAPVNEYTEKKVALKDISIDISEIQPSEVEAPRTILDEKKGLKVIVNFTKDRPAKDVV
VLVISVNNQGPVAINNFQFDASVSKPCKLRILEASGRDLPGLKPFKPPTETINQVLLLLN
PTQQPVNMVAILTYNVQGDEDEEKVSIEVKDIPFQS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g1918.t1 Gene3D G3DSA:1.25.40.90 - 3 159 0.0000000
14 g1918.t1 Gene3D G3DSA:1.20.5.170 - 160 201 0.0000000
15 g1918.t1 Gene3D G3DSA:1.20.58.160 - 202 296 0.0000000
12 g1918.t1 Gene3D G3DSA:2.60.40.1230 - 487 635 0.0000000
5 g1918.t1 PANTHER PTHR45905:SF1 GOLGI-LOCALIZED, GAMMA-ADAPTIN EAR CONTAINING, ARF BINDING PROTEIN 9 622 0.0000000
6 g1918.t1 PANTHER PTHR45905 GOLGI-LOCALIZED, GAMMA-ADAPTIN EAR CONTAINING, ARF BINDING PROTEIN 9 622 0.0000000
3 g1918.t1 Pfam PF00790 VHS domain 8 143 0.0000000
4 g1918.t1 Pfam PF18308 GGA N-GAT domain 170 202 0.0000002
1 g1918.t1 Pfam PF03127 GAT domain 218 291 0.0000000
2 g1918.t1 Pfam PF02883 Adaptin C-terminal domain 515 622 0.0000000
16 g1918.t1 ProSiteProfiles PS50179 VHS domain profile. 17 147 25.8330000
17 g1918.t1 ProSiteProfiles PS50909 GAT domain profile. 166 293 19.8600000
18 g1918.t1 ProSiteProfiles PS50180 Gamma-adaptin ear (GAE) domain profile. 511 631 30.5890000
11 g1918.t1 SMART SM00288 VHS_2 10 143 0.0000000
10 g1918.t1 SMART SM00809 alpha_adaptinc2 508 633 0.0000000
9 g1918.t1 SUPERFAMILY SSF48464 ENTH/VHS domain 8 145 0.0000000
8 g1918.t1 SUPERFAMILY SSF89009 GAT-like domain 169 292 0.0000000
7 g1918.t1 SUPERFAMILY SSF49348 Clathrin adaptor appendage domain 495 626 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