General information for g6979.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Amphiphysin.
Parent gene
- The parent gene g6979 is located on chr_2: 20327828..20327890 (- strand)
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.t1 | TTS | g6979.t1 | 20313391 | 20313391 |
| chr_2 | g6979 | g6979.t1 | isoform | g6979.t1 | 20314278 | 20327890 |
| chr_2 | g6979 | g6979.t1 | exon | g6979.t1.exon1 | 20314278 | 20314358 |
| chr_2 | g6979 | g6979.t1 | cds | g6979.t1.CDS1 | 20314278 | 20314358 |
| chr_2 | g6979 | g6979.t1 | exon | g6979.t1.exon2 | 20314418 | 20314560 |
| chr_2 | g6979 | g6979.t1 | cds | g6979.t1.CDS2 | 20314418 | 20314560 |
| chr_2 | g6979 | g6979.t1 | exon | g6979.t1.exon3 | 20314941 | 20315384 |
| chr_2 | g6979 | g6979.t1 | cds | g6979.t1.CDS3 | 20314941 | 20315384 |
| chr_2 | g6979 | g6979.t1 | exon | g6979.t1.exon4 | 20316103 | 20316219 |
| chr_2 | g6979 | g6979.t1 | cds | g6979.t1.CDS4 | 20316103 | 20316219 |
| chr_2 | g6979 | g6979.t1 | exon | g6979.t1.exon5 | 20316291 | 20316648 |
| chr_2 | g6979 | g6979.t1 | cds | g6979.t1.CDS5 | 20316291 | 20316648 |
| chr_2 | g6979 | g6979.t1 | exon | g6979.t1.exon6 | 20316711 | 20316901 |
| chr_2 | g6979 | g6979.t1 | cds | g6979.t1.CDS6 | 20316711 | 20316901 |
| chr_2 | g6979 | g6979.t1 | exon | g6979.t1.exon7 | 20316967 | 20317102 |
| chr_2 | g6979 | g6979.t1 | cds | g6979.t1.CDS7 | 20316967 | 20317102 |
| chr_2 | g6979 | g6979.t1 | exon | g6979.t1.exon8 | 20327828 | 20327890 |
| chr_2 | g6979 | g6979.t1 | cds | g6979.t1.CDS8 | 20327828 | 20327890 |
| chr_2 | g6979 | g6979.t1 | TSS | g6979.t1 | 20327937 | 20327937 |
Sequences
>g6979.t1 Gene=g6979 Length=1533
ATGGCTTCTGCAAACAATAAAACTGTATTTTTAAAAAAATATACTCAAAGAACAAAAGAG
AAGATTTTACAAAATTTAGGAAAGGTCGATCGCACAGCTGATGAGATTTTCGATGAACAT
TTAAATAATTTTACACTACAGCAGAACTCTGCAAATAGATTACAAAAAGAATTCAACAAT
TACATACGATGCGTACGAGCGTTACAGGTTGCTTCCAAATCATTAATGGAAGCAATCACA
GAAGTATATGAACCACAATGGTCAGGCTCAGAGGCACTCTATGCTCAAGCCTCTTCAATT
GAAGTTTTATTGCAAGACTTTTCGCACAAATTGGGCGATCAAGTGTTAATTCCGTTAAAC
ACTTACACTGCACAATTTCCAGAGATGAGAAAAAAGATCGACAAGCGTGGTCGAAAGTTA
GTTGATTATGATAGTCAACGTCATTCCTTCCAAAATCTTCAAGCAAATGCAGCTAAACGT
AAGGATGATGTTAAATTAACAAAAGGTCGCGAGAACCTTGAAGAAGCCAAACGAACTTAT
GAACTTTTAAATACTGAGTTGCATGATGAGTTGCCAGCACTATATGATTCACGGATACTG
TTTTTGGTCACAAATCTTCAGACACTATTCGCATCAGAACAAATGTTTCATACTGAAGTT
GCAAAAATTTATTCGGAATTGGAAGCAATTGTTGATAAACTGGCAACTGAATCACAAAGA
GGATCATACACACTTAAGAAATTAAACTCAACGGCAGCAAACAATATACAATCTCCAATT
AAAATCCATGAAAAAACAAGTGTCGCTATCAGTTATCCAGTACCAATCACAAATGGAAAT
TCACCATCGGCTGCTACAAATGGTGCTACATCATCATCATCTCCAGTTTCATCAACTCAT
TCACCAACAACGCCATACGAACATGAACCAAATGAAAAAGCTGTTGCTGCAACTACAACA
ATCGTTACAGAAGCACAGTATCAGAACCAAGAGAGTTTGGGTATAAATGAACCTTCATAT
CAAAACGCATCAGCCGTTATTAATGGTGATGGTGCTGCTGCAAATGTCATCAATAACAAT
ATCGAGTCTGTGCAAACTGATAATGGTATGAACAACTCGATGTCGTCCGCAACTGTGGAA
GCTTCAGAAGAAACGCATCTAAATAACAATAACAGTCAAAATAATAACATTAGTAAGAGC
AACCAAAATATAAATGATAATAATAACCAAATAAGCAATAATCAAAACTTACCGAAAAGT
AATAATATTAACAATAATACGGATGATGATTTGTACGATATTCCGGTTGGTGCCACAACA
ACAAATTTACCACCAGGTGTTTTGTACAGAGTAAAAGCAACATACAAATACGTACGAGAG
GATGCCGATGAACTGAGCTTTGACGTTGGCGATATTGTTAATGTTGTTGAATATGATGAT
CCAGAAGATCAAGAGGATGGATGGTTGATGGGAATAAAAGAAGGCACGAATGAAAAGGGC
ATGTTCCCAGCCAATTTTACAAGACCATTGTAA
>g6979.t1 Gene=g6979 Length=510
MASANNKTVFLKKYTQRTKEKILQNLGKVDRTADEIFDEHLNNFTLQQNSANRLQKEFNN
YIRCVRALQVASKSLMEAITEVYEPQWSGSEALYAQASSIEVLLQDFSHKLGDQVLIPLN
TYTAQFPEMRKKIDKRGRKLVDYDSQRHSFQNLQANAAKRKDDVKLTKGRENLEEAKRTY
ELLNTELHDELPALYDSRILFLVTNLQTLFASEQMFHTEVAKIYSELEAIVDKLATESQR
GSYTLKKLNSTAANNIQSPIKIHEKTSVAISYPVPITNGNSPSAATNGATSSSSPVSSTH
SPTTPYEHEPNEKAVAATTTIVTEAQYQNQESLGINEPSYQNASAVINGDGAAANVINNN
IESVQTDNGMNNSMSSATVEASEETHLNNNNSQNNNISKSNQNINDNNNQISNNQNLPKS
NNINNNTDDDLYDIPVGATTTNLPPGVLYRVKATYKYVREDADELSFDVGDIVNVVEYDD
PEDQEDGWLMGIKEGTNEKGMFPANFTRPL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 19 | g6979.t1 | CDD | cd11790 | SH3_Amphiphysin | 447 | 510 | 3.71038E-35 |
| 18 | g6979.t1 | Coils | Coil | Coil | 166 | 190 | - |
| 17 | g6979.t1 | Gene3D | G3DSA:1.20.1270.60 | Arfaptin | 17 | 241 | 1.0E-72 |
| 16 | g6979.t1 | Gene3D | G3DSA:2.30.30.40 | SH3 Domains | 438 | 510 | 4.1E-29 |
| 22 | g6979.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 282 | 312 | - |
| 23 | g6979.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 282 | 305 | - |
| 24 | g6979.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 364 | 386 | - |
| 3 | g6979.t1 | PANTHER | PTHR46514 | AMPHIPHYSIN | 11 | 509 | 1.7E-157 |
| 4 | g6979.t1 | PANTHER | PTHR46514:SF3 | AMPHIPHYSIN | 11 | 509 | 1.7E-157 |
| 12 | g6979.t1 | PRINTS | PR01251 | Amphiphysin signature | 21 | 38 | 1.6E-27 |
| 11 | g6979.t1 | PRINTS | PR01251 | Amphiphysin signature | 49 | 59 | 1.6E-27 |
| 13 | g6979.t1 | PRINTS | PR01251 | Amphiphysin signature | 81 | 93 | 1.6E-27 |
| 6 | g6979.t1 | PRINTS | PR01251 | Amphiphysin signature | 116 | 130 | 1.6E-27 |
| 8 | g6979.t1 | PRINTS | PR01251 | Amphiphysin signature | 138 | 149 | 1.6E-27 |
| 5 | g6979.t1 | PRINTS | PR01251 | Amphiphysin signature | 175 | 184 | 1.6E-27 |
| 7 | g6979.t1 | PRINTS | PR01251 | Amphiphysin signature | 186 | 196 | 1.6E-27 |
| 9 | g6979.t1 | PRINTS | PR01251 | Amphiphysin signature | 442 | 451 | 1.6E-27 |
| 10 | g6979.t1 | PRINTS | PR01251 | Amphiphysin signature | 463 | 477 | 1.6E-27 |
| 1 | g6979.t1 | Pfam | PF03114 | BAR domain | 11 | 228 | 1.7E-34 |
| 2 | g6979.t1 | Pfam | PF14604 | Variant SH3 domain | 453 | 507 | 2.2E-9 |
| 26 | g6979.t1 | ProSiteProfiles | PS51021 | BAR domain profile. | 22 | 240 | 35.451 |
| 25 | g6979.t1 | ProSiteProfiles | PS50002 | Src homology 3 (SH3) domain profile. | 446 | 510 | 21.859 |
| 20 | g6979.t1 | SMART | SM00721 | 5bar | 10 | 233 | 6.1E-65 |
| 21 | g6979.t1 | SMART | SM00326 | SH3_2 | 449 | 510 | 1.5E-11 |
| 14 | g6979.t1 | SUPERFAMILY | SSF103657 | BAR/IMD domain-like | 24 | 234 | 1.99E-58 |
| 15 | g6979.t1 | SUPERFAMILY | SSF50044 | SH3-domain | 441 | 509 | 1.84E-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
- This transcript has been annotated with K12562 (amphiphysin)
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.
