General information for g1280.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Gelsolin.
Parent gene
- The parent gene g1280 is located on chr_3: 9419667..9421548 (- 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_3 | g1280 | g1280.t2 | isoform | g1280.t2 | 9414926 | 9421548 |
| chr_3 | g1280 | g1280.t2 | exon | g1280.t2.exon1 | 9414926 | 9415159 |
| chr_3 | g1280 | g1280.t2 | exon | g1280.t2.exon2 | 9418898 | 9419939 |
| chr_3 | g1280 | g1280.t2 | cds | g1280.t2.CDS1 | 9418995 | 9419939 |
| chr_3 | g1280 | g1280.t2 | exon | g1280.t2.exon3 | 9420003 | 9420077 |
| chr_3 | g1280 | g1280.t2 | cds | g1280.t2.CDS2 | 9420003 | 9420077 |
| chr_3 | g1280 | g1280.t2 | exon | g1280.t2.exon4 | 9420134 | 9420248 |
| chr_3 | g1280 | g1280.t2 | cds | g1280.t2.CDS3 | 9420134 | 9420248 |
| chr_3 | g1280 | g1280.t2 | exon | g1280.t2.exon5 | 9420321 | 9420377 |
| chr_3 | g1280 | g1280.t2 | cds | g1280.t2.CDS4 | 9420321 | 9420358 |
| chr_3 | g1280 | g1280.t2 | exon | g1280.t2.exon6 | 9421190 | 9421548 |
| chr_3 | g1280 | g1280.t2 | TSS | g1280.t2 | NA | NA |
| chr_3 | g1280 | g1280.t2 | TTS | g1280.t2 | NA | NA |
Sequences
>g1280.t2 Gene=g1280 Length=1882
TTTCCATCGTGGAAGAATTTTTTTTGGAAAATTTGTTTACAATTTGAATTTTTGAAAAAT
AACCGTCATATTCTCAAGAAATTTCTTTTATTTTGCAAACATGTCTTGATTGATCAATCA
ATAGCATGATTCATGTTAATTTTGATAATAAATTTACACTTAAAAGAGAATTACTCTCCT
AATGTTATTTATTTCTCTCATACAATTTTTGTATAAAAACTCTCAAGTTTACTCAAAAAT
CAACTGTACATCACTCATCACTGTTCAGTCGGTTGTAAACTTCTGTAGTGTAAAAGTGAA
AATTAATAAAAACGCCGGTATCAAGCTACTTTACTTGTTTTAGATTTCCAAAGTCAAAGT
ATCTTGAATACGCAAAACATGTGGAAACTGTGCTGTGTTTTAATAATCGCTATAAGCGCG
TTAAATTCAATAGAATGTGCAACAACTCAAAGTAGACCAAGTCAAGTAGTCATCCCGCAA
GCATTCATAAATGCAGGAAAAACAAAAGGTTTAGAGATTTGGAGGATTGAGAATTTTAAA
GTTGTTGCTGTGCAAAAAAATACCTATGGCCAATTTCACACCGGCGATTCTTACATTGTA
TTGAATACAATGGAGAATAAAAATAAGCAACTTTCATGGGATGTTCATTTTTGGCTTGGA
CTTGAAACAACGCAAGATGAGGCAGGTGCTGCTGCAATTTACACTGTACAACTTGATGAT
GCTCTTGGAGGAGCACCAGTTCAACATCGTGAAGTTCAAGAGCAAGAATCACAACTTTTC
TTAGGATATTTCAAGAGCAGTGGTGGAATTAAATATTTGCCTGGTGGTGTTGCGAGCGGA
TTTAGAAAAACAGAAATAAATGCAATTGGTGAGAAACGCCTATTTCAAGTAAAAGGAAAG
AAAAATGTTCGCGTTCGTCAAGTTGATTTGACAATTGGGTCAATGAATAAAGGCGATTGC
TTTGTTCTTGATGCTGGCAATAAAGTCTATATTTATGTTGGACCAAAAGCTAAACGAGTT
GAGAAAATGAAGGCAACAAGTTTTGCAAATCAAGTGCGTGATGAAGACCATCATGGACGA
TCATCTGTTGAAATTGTTGATGAATTTTCAAATGATGTTGATAAGGCTCATTTCTTTGAA
GTGCTTGGTTCAGGTTCAATTGAACAAGTGCCAGATGAAAGCGTTGCTGAAGATGATGAG
GCATTTGAAAGAAAAGAAGAAGCTGCAACAACTTTGAGTAAAGTTAGTGATGCATCAGGA
AGCTTGAAAGTTGAACAAATTAATCAAAAACCATTGAAACAAGAAATGCTGAATACTAAC
GATTGCTTTATTCTTGATACTGGAAGTGGTATTTATGTTTGGATTGGTAAGAAATCAACT
GAACAAGAGAAAAAACAAGCAATGTCACGTGCTCAGGGATTTATTCAAACGAAGAAATAT
CCTGCATGGACTAAAGTAACAAAAATCAATGAATTCACCGAAACAACTCCATTCAAGCAA
TATTTCTTTACATGGCGTGATCATGGTGCATCACATTCTCGCCTTATTTGAATGAAACAA
TGAGACATTCAAACATATTATAATCAAATATACTCTACAATGAATATTAATGTAATCTGT
AATAGATTTTTACTAACAGATTTAAAATAAAATAAACAGAAATTTTTCATCTTCATAATT
TTCATTTTTTTTTCCACTTGTCAGTGACCAGATGATTTCTCATTTATAACATCTTCTCGT
TTTTCACTTTTTCTCTCTATATCTTTTCATGAAGTGAGATATTTTGGGTAGTGTTCAAGA
TGCTAATTATTAGATTATTACTGCAAATTAACTATGGAATTTAACATATATTTAAAACAT
TTTAAATTTTCTTTCATTTACA
>g1280.t2 Gene=g1280 Length=390
MWKLCCVLIIAISALNSIECATTQSRPSQVVIPQAFINAGKTKGLEIWRIENFKVVAVQK
NTYGQFHTGDSYIVLNTMENKNKQLSWDVHFWLGLETTQDEAGAAAIYTVQLDDALGGAP
VQHREVQEQESQLFLGYFKSSGGIKYLPGGVASGFRKTEINAIGEKRLFQVKGKKNVRVR
QVDLTIGSMNKGDCFVLDAGNKVYIYVGPKAKRVEKMKATSFANQVRDEDHHGRSSVEIV
DEFSNDVDKAHFFEVLGSGSIEQVPDESVAEDDEAFERKEEAATTLSKVSDASGSLKVEQ
INQKPLKQEMLNTNDCFILDTGSGIYVWIGKKSTEQEKKQAMSRAQGFIQTKKYPAWTKV
TKINEFTETTPFKQYFFTWRDHGASHSRLI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 26 | g1280.t2 | CDD | cd11290 | gelsolin_S1_like | 36 | 150 | 6.19028E-61 |
| 24 | g1280.t2 | CDD | cd11289 | gelsolin_S2_like | 165 | 257 | 1.46958E-35 |
| 25 | g1280.t2 | CDD | cd11292 | gelsolin_S3_like | 281 | 376 | 6.86218E-43 |
| 18 | g1280.t2 | Gene3D | G3DSA:3.40.20.10 | Severin | 32 | 163 | 3.6E-47 |
| 16 | g1280.t2 | Gene3D | G3DSA:3.40.20.10 | Severin | 164 | 268 | 1.3E-27 |
| 17 | g1280.t2 | Gene3D | G3DSA:3.40.20.10 | Severin | 277 | 388 | 3.2E-35 |
| 4 | g1280.t2 | PANTHER | PTHR11977 | VILLIN | 26 | 388 | 9.5E-143 |
| 5 | g1280.t2 | PANTHER | PTHR11977:SF55 | GELSOLIN | 26 | 388 | 9.5E-143 |
| 10 | g1280.t2 | PRINTS | PR00597 | Gelsolin family signature | 62 | 78 | 6.6E-17 |
| 8 | g1280.t2 | PRINTS | PR00597 | Gelsolin family signature | 88 | 106 | 6.6E-17 |
| 9 | g1280.t2 | PRINTS | PR00597 | Gelsolin family signature | 121 | 141 | 6.6E-17 |
| 7 | g1280.t2 | PRINTS | PR00597 | Gelsolin family signature | 308 | 330 | 6.6E-17 |
| 6 | g1280.t2 | PRINTS | PR00597 | Gelsolin family signature | 337 | 356 | 6.6E-17 |
| 3 | g1280.t2 | Pfam | PF00626 | Gelsolin repeat | 52 | 135 | 2.9E-14 |
| 1 | g1280.t2 | Pfam | PF00626 | Gelsolin repeat | 176 | 241 | 1.7E-10 |
| 2 | g1280.t2 | Pfam | PF00626 | Gelsolin repeat | 304 | 360 | 2.3E-14 |
| 20 | g1280.t2 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 20 | - |
| 21 | g1280.t2 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 3 | - |
| 22 | g1280.t2 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 4 | 15 | - |
| 23 | g1280.t2 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 16 | 20 | - |
| 19 | g1280.t2 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 21 | 390 | - |
| 30 | g1280.t2 | SMART | SM00262 | VILL_6 | 43 | 141 | 3.1E-24 |
| 29 | g1280.t2 | SMART | SM00262 | VILL_6 | 164 | 259 | 2.1E-24 |
| 28 | g1280.t2 | SMART | SM00262 | VILL_6 | 285 | 379 | 1.4E-30 |
| 11 | g1280.t2 | SUPERFAMILY | SSF55753 | Actin depolymerizing proteins | 34 | 176 | 1.43E-37 |
| 13 | g1280.t2 | SUPERFAMILY | SSF55753 | Actin depolymerizing proteins | 165 | 259 | 2.29E-19 |
| 12 | g1280.t2 | SUPERFAMILY | SSF55753 | Actin depolymerizing proteins | 280 | 381 | 1.44E-24 |
| 15 | g1280.t2 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 20 | - |
| 27 | g1280.t2 | SignalP_GRAM_NEGATIVE | SignalP-noTM | SignalP-noTM | 1 | 21 | - |
| 14 | g1280.t2 | SignalP_GRAM_POSITIVE | SignalP-TM | SignalP-TM | 1 | 23 | - |
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:0051015 | actin filament binding | MF |
KEGG
Orthology
This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).
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.
