Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Amphiphysin.

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_2 g6979 g6979.t4 isoform g6979.t4 20313201 20317102
chr_2 g6979 g6979.t4 exon g6979.t4.exon1 20313201 20314358
chr_2 g6979 g6979.t4 TTS g6979.t4 20313391 20313391
chr_2 g6979 g6979.t4 cds g6979.t4.CDS1 20314278 20314358
chr_2 g6979 g6979.t4 exon g6979.t4.exon2 20314418 20314560
chr_2 g6979 g6979.t4 cds g6979.t4.CDS2 20314418 20314560
chr_2 g6979 g6979.t4 exon g6979.t4.exon3 20316103 20316219
chr_2 g6979 g6979.t4 cds g6979.t4.CDS3 20316103 20316219
chr_2 g6979 g6979.t4 exon g6979.t4.exon4 20316291 20316648
chr_2 g6979 g6979.t4 cds g6979.t4.CDS4 20316291 20316648
chr_2 g6979 g6979.t4 exon g6979.t4.exon5 20316711 20316901
chr_2 g6979 g6979.t4 cds g6979.t4.CDS5 20316711 20316875
chr_2 g6979 g6979.t4 exon g6979.t4.exon6 20316967 20317102
chr_2 g6979 g6979.t4 TSS g6979.t4 20327937 20327937

Sequences

>g6979.t4 Gene=g6979 Length=2103
ATTTTACAAAATTTAGGAAAGGTCGATCGCACAGCTGATGAGATTTTCGATGAACATTTA
AATAATTTTACACTACAGCAGAACTCTGCAAATAGATTACAAAAAGAATTCAACAATTAC
ATACGATGCGTACGAGCGTTACAGGTTGCTTCCAAATCATTAATGGAAGCAATCACAGAA
GTATATGAACCACAATGGTCAGGCTCAGAGGCACTCTATGCTCAAGCCTCTTCAATTGAA
GTTTTATTGCAAGACTTTTCGCACAAATTGGGCGATCAAGTGTTAATTCCGTTAAACACT
TACACTGCACAATTTCCAGAGATGAGAAAAAAGATCGACAAGCGTGGTCGAAAGTTAGTT
GATTATGATAGTCAACGTCATTCCTTCCAAAATCTTCAAGCAAATGCAGCTAAACGTAAG
GATGATGTTAAATTAACAAAAGGTCGCGAGAACCTTGAAGAAGCCAAACGAACTTATGAA
CTTTTAAATACTGAGTTGCATGATGAGTTGCCAGCACTATATGATTCACGGATACTGTTT
TTGGTCACAAATCTTCAGACACTATTCGCATCAGAACAAATGTTTCATACTGAAGTTGCA
AAAATTTATTCGGAATTGGAAGCAATTGTTGATAAACTGGCAACTGAATCACAAAGAGGA
TCATACACACTTAAGAAATTAAACTCAACGGCAGCAAACAATATACAATCTCCAATTAAA
ATCCATGAAAAAACAAGTGTCGCTATCAGTTATCCAGTACCAATCACAAATGGAAATTCA
CCATCGGCTGCTACAAATGGTGGTGCCACAACAACAAATTTACCACCAGGTGTTTTGTAC
AGAGTAAAAGCAACATACAAATACGTACGAGAGGATGCCGATGAACTGAGCTTTGACGTT
GGCGATATTGTTAATGTTGTTGAATATGATGATCCAGAAGATCAAGAGGATGGATGGTTG
ATGGGAATAAAAGAAGGCACGAATGAAAAGGGCATGTTCCCAGCCAATTTTACAAGACCA
TTGTAAAGTGAAGAGCTTTTTTTGTTGTATTTTATTTGTTCGTTCGTCTATTATATCTAC
CTATATTTTATTTTAACCTATTGATCATCGAAATTATATTTCTAATCAAAAAAAAAAACT
TTTACAATTTTTTAGTCCTTATTTTAATGGAAAATAACACCAAAAACTACCCGATAAAAA
CAATAAAAAAAGGTTTGAGGGTTTTGCTTCCAATTTTTAAGAGTAGCTATAAGATTTTTA
ACACACTCTTCATAGCGAACCGAAACGATGAAAATAATAATATTTAACTTTTCTGAAACT
TACATTTATATATACACATATTATACAAAATGTGAAAATTTTATAAATTTGTAATATATA
TTTAAAATGTTTTAAAAATCTCTGTCCTATGTCTGACGAAAACCAATTGCCAAAACATTT
TAAAAAAAACAATTTTTATCTTTCAACATTTATTGTCCGCTCATTTCTGATGTGCCTTTT
TAGATGAAAGAGAGAGATAGTTAAAATAGTAAAAAATTATTCATTTTGAGGGTGAAATTT
TGTACACTGTTAAGTACTGGAAAATAAAAAACCCGTGCTCATATTTGTTAATTATTATTA
AAGATCTATTAAAATACAGTTAATTTTTTCTGCTATTAAATATCAGTCTCTAATATTCTC
AAACATAAAAAAATGCATTAAATTGTTTTCTGTGAAGTAAATAAAAATTACTTCTGTCTA
TCATTTCTCGTTTCTCTTTATACTCTTTTTTGTTGTTTAATTCACAATTATTTAATAATT
ATTAAAAATGAAGAAAGTTTTATTTGTAATTTAATTTAAACAAAAAATGAAATAAATTGA
TTGTAGAAGATGCGATAAAATATGAGATAAAAGAAATAAAATGTGTAGAAATTAAAACAT
GATCTTATTTCAGTATGCAAGTAATTTTTTTATTTCAGCATAATATATTTGATTATATCA
TTTAAGCATTTTTTGATCGATAAGATTAAGATGCATAATAGATATTTATTGAAATGAGCT
TAAAATAAAATCACATTATTTTGAAGAGCTTTCACTTTTAATAAATTTACAGTATATGTA
AGT

>g6979.t4 Gene=g6979 Length=287
MEAITEVYEPQWSGSEALYAQASSIEVLLQDFSHKLGDQVLIPLNTYTAQFPEMRKKIDK
RGRKLVDYDSQRHSFQNLQANAAKRKDDVKLTKGRENLEEAKRTYELLNTELHDELPALY
DSRILFLVTNLQTLFASEQMFHTEVAKIYSELEAIVDKLATESQRGSYTLKKLNSTAANN
IQSPIKIHEKTSVAISYPVPITNGNSPSAATNGGATTTNLPPGVLYRVKATYKYVREDAD
ELSFDVGDIVNVVEYDDPEDQEDGWLMGIKEGTNEKGMFPANFTRPL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
17 g6979.t4 CDD cd11790 SH3_Amphiphysin 224 287 8.70135E-36
16 g6979.t4 Coils Coil Coil 91 115 -
15 g6979.t4 Gene3D G3DSA:1.20.1270.60 Arfaptin 1 166 3.4E-52
14 g6979.t4 Gene3D G3DSA:2.30.30.40 SH3 Domains 215 287 1.6E-29
4 g6979.t4 PANTHER PTHR46514 AMPHIPHYSIN 1 180 9.2E-119
6 g6979.t4 PANTHER PTHR46514:SF3 AMPHIPHYSIN 1 180 9.2E-119
3 g6979.t4 PANTHER PTHR46514 AMPHIPHYSIN 211 286 9.2E-119
5 g6979.t4 PANTHER PTHR46514:SF3 AMPHIPHYSIN 211 286 9.2E-119
7 g6979.t4 PRINTS PR01251 Amphiphysin signature 6 18 3.3E-17
11 g6979.t4 PRINTS PR01251 Amphiphysin signature 41 55 3.3E-17
10 g6979.t4 PRINTS PR01251 Amphiphysin signature 63 74 3.3E-17
9 g6979.t4 PRINTS PR01251 Amphiphysin signature 219 228 3.3E-17
8 g6979.t4 PRINTS PR01251 Amphiphysin signature 240 254 3.3E-17
1 g6979.t4 Pfam PF03114 BAR domain 2 153 2.5E-23
2 g6979.t4 Pfam PF14604 Variant SH3 domain 230 284 9.5E-10
21 g6979.t4 ProSiteProfiles PS51021 BAR domain profile. 1 165 28.366
20 g6979.t4 ProSiteProfiles PS50002 Src homology 3 (SH3) domain profile. 223 287 21.859
18 g6979.t4 SMART SM00721 5bar 1 158 3.5E-15
19 g6979.t4 SMART SM00326 SH3_2 226 287 1.5E-11
12 g6979.t4 SUPERFAMILY SSF103657 BAR/IMD domain-like 2 159 3.66E-43
13 g6979.t4 SUPERFAMILY SSF50044 SH3-domain 218 286 7.35E-18

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:0005737 cytoplasm CC

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