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.t2 TTS g6979.t2 20313391 20313391
chr_2 g6979 g6979.t2 isoform g6979.t2 20314278 20327890
chr_2 g6979 g6979.t2 exon g6979.t2.exon1 20314278 20314358
chr_2 g6979 g6979.t2 cds g6979.t2.CDS1 20314278 20314358
chr_2 g6979 g6979.t2 exon g6979.t2.exon2 20314418 20314560
chr_2 g6979 g6979.t2 cds g6979.t2.CDS2 20314418 20314560
chr_2 g6979 g6979.t2 exon g6979.t2.exon3 20315058 20315384
chr_2 g6979 g6979.t2 cds g6979.t2.CDS3 20315058 20315384
chr_2 g6979 g6979.t2 exon g6979.t2.exon4 20316103 20316219
chr_2 g6979 g6979.t2 cds g6979.t2.CDS4 20316103 20316219
chr_2 g6979 g6979.t2 exon g6979.t2.exon5 20316291 20316648
chr_2 g6979 g6979.t2 cds g6979.t2.CDS5 20316291 20316648
chr_2 g6979 g6979.t2 exon g6979.t2.exon6 20316711 20316901
chr_2 g6979 g6979.t2 cds g6979.t2.CDS6 20316711 20316901
chr_2 g6979 g6979.t2 exon g6979.t2.exon7 20316967 20317102
chr_2 g6979 g6979.t2 cds g6979.t2.CDS7 20316967 20317102
chr_2 g6979 g6979.t2 exon g6979.t2.exon8 20327828 20327890
chr_2 g6979 g6979.t2 cds g6979.t2.CDS8 20327828 20327890
chr_2 g6979 g6979.t2 TSS g6979.t2 20327937 20327937

Sequences

>g6979.t2 Gene=g6979 Length=1416
ATGGCTTCTGCAAACAATAAAACTGTATTTTTAAAAAAATATACTCAAAGAACAAAAGAG
AAGATTTTACAAAATTTAGGAAAGGTCGATCGCACAGCTGATGAGATTTTCGATGAACAT
TTAAATAATTTTACACTACAGCAGAACTCTGCAAATAGATTACAAAAAGAATTCAACAAT
TACATACGATGCGTACGAGCGTTACAGGTTGCTTCCAAATCATTAATGGAAGCAATCACA
GAAGTATATGAACCACAATGGTCAGGCTCAGAGGCACTCTATGCTCAAGCCTCTTCAATT
GAAGTTTTATTGCAAGACTTTTCGCACAAATTGGGCGATCAAGTGTTAATTCCGTTAAAC
ACTTACACTGCACAATTTCCAGAGATGAGAAAAAAGATCGACAAGCGTGGTCGAAAGTTA
GTTGATTATGATAGTCAACGTCATTCCTTCCAAAATCTTCAAGCAAATGCAGCTAAACGT
AAGGATGATGTTAAATTAACAAAAGGTCGCGAGAACCTTGAAGAAGCCAAACGAACTTAT
GAACTTTTAAATACTGAGTTGCATGATGAGTTGCCAGCACTATATGATTCACGGATACTG
TTTTTGGTCACAAATCTTCAGACACTATTCGCATCAGAACAAATGTTTCATACTGAAGTT
GCAAAAATTTATTCGGAATTGGAAGCAATTGTTGATAAACTGGCAACTGAATCACAAAGA
GGATCATACACACTTAAGAAATTAAACTCAACGGCAGCAAACAATATACAATCTCCAATT
AAAATCCATGAAAAAACAAGTGTCGCTATCAGTTATCCAGTACCAATCACAAATGGAAAT
TCACCATCGGCTGCTACAAATGGTGCTACATCATCATCATCTCCAGTTTCATCAACTCAT
TCACCAACAACGCCATACGAACATGAACCAAATGAAAAAGCTGTTGCTGCAACTACAACA
ATCGTTACAGAAGCACAGTATCAGAACCAAGAGAGTTTGGGTATAAATGAACCTTCATAT
CAAAACGCATCAGCCGTTATTAATGGTGATGGTGCTGCTGCAAATGTCATCAATAACAAT
ATCGAGTCTGTGCAAACTGATAATGGTATGAACAACTCGATGTCGTCCGCAACTGTGGAA
GCTTCAGAAGAAACGCATCTAAATAACAATAACAGTCAAAATAATAACATTAGTGCCACA
ACAACAAATTTACCACCAGGTGTTTTGTACAGAGTAAAAGCAACATACAAATACGTACGA
GAGGATGCCGATGAACTGAGCTTTGACGTTGGCGATATTGTTAATGTTGTTGAATATGAT
GATCCAGAAGATCAAGAGGATGGATGGTTGATGGGAATAAAAGAAGGCACGAATGAAAAG
GGCATGTTCCCAGCCAATTTTACAAGACCATTGTAA

>g6979.t2 Gene=g6979 Length=471
MASANNKTVFLKKYTQRTKEKILQNLGKVDRTADEIFDEHLNNFTLQQNSANRLQKEFNN
YIRCVRALQVASKSLMEAITEVYEPQWSGSEALYAQASSIEVLLQDFSHKLGDQVLIPLN
TYTAQFPEMRKKIDKRGRKLVDYDSQRHSFQNLQANAAKRKDDVKLTKGRENLEEAKRTY
ELLNTELHDELPALYDSRILFLVTNLQTLFASEQMFHTEVAKIYSELEAIVDKLATESQR
GSYTLKKLNSTAANNIQSPIKIHEKTSVAISYPVPITNGNSPSAATNGATSSSSPVSSTH
SPTTPYEHEPNEKAVAATTTIVTEAQYQNQESLGINEPSYQNASAVINGDGAAANVINNN
IESVQTDNGMNNSMSSATVEASEETHLNNNNSQNNNISATTTNLPPGVLYRVKATYKYVR
EDADELSFDVGDIVNVVEYDDPEDQEDGWLMGIKEGTNEKGMFPANFTRPL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
19 g6979.t2 CDD cd11790 SH3_Amphiphysin 408 471 2.0049E-35
18 g6979.t2 Coils Coil Coil 166 190 -
17 g6979.t2 Gene3D G3DSA:1.20.1270.60 Arfaptin 17 241 8.4E-73
16 g6979.t2 Gene3D G3DSA:2.30.30.40 SH3 Domains 398 471 3.2E-29
22 g6979.t2 MobiDBLite mobidb-lite consensus disorder prediction 282 312 -
23 g6979.t2 MobiDBLite mobidb-lite consensus disorder prediction 282 305 -
24 g6979.t2 MobiDBLite mobidb-lite consensus disorder prediction 366 399 -
3 g6979.t2 PANTHER PTHR46514 AMPHIPHYSIN 11 470 4.0E-156
4 g6979.t2 PANTHER PTHR46514:SF3 AMPHIPHYSIN 11 470 4.0E-156
11 g6979.t2 PRINTS PR01251 Amphiphysin signature 21 38 8.4E-28
10 g6979.t2 PRINTS PR01251 Amphiphysin signature 49 59 8.4E-28
13 g6979.t2 PRINTS PR01251 Amphiphysin signature 81 93 8.4E-28
6 g6979.t2 PRINTS PR01251 Amphiphysin signature 116 130 8.4E-28
9 g6979.t2 PRINTS PR01251 Amphiphysin signature 138 149 8.4E-28
5 g6979.t2 PRINTS PR01251 Amphiphysin signature 175 184 8.4E-28
7 g6979.t2 PRINTS PR01251 Amphiphysin signature 186 196 8.4E-28
8 g6979.t2 PRINTS PR01251 Amphiphysin signature 403 412 8.4E-28
12 g6979.t2 PRINTS PR01251 Amphiphysin signature 424 438 8.4E-28
1 g6979.t2 Pfam PF03114 BAR domain 11 228 1.4E-34
2 g6979.t2 Pfam PF14604 Variant SH3 domain 414 468 2.0E-9
26 g6979.t2 ProSiteProfiles PS51021 BAR domain profile. 22 240 35.451
25 g6979.t2 ProSiteProfiles PS50002 Src homology 3 (SH3) domain profile. 407 471 21.859
20 g6979.t2 SMART SM00721 5bar 10 233 6.1E-65
21 g6979.t2 SMART SM00326 SH3_2 410 471 1.5E-11
14 g6979.t2 SUPERFAMILY SSF103657 BAR/IMD domain-like 24 234 1.03E-58
15 g6979.t2 SUPERFAMILY SSF50044 SH3-domain 401 470 1.44E-17

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