Gene loci information

Transcript annotation

  • This transcript has been annotated as Gelsolin.

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 g1280 g1280.t20 TTS g1280.t20 9418880 9418880
chr_3 g1280 g1280.t20 isoform g1280.t20 9418995 9421224
chr_3 g1280 g1280.t20 exon g1280.t20.exon1 9418995 9419156
chr_3 g1280 g1280.t20 cds g1280.t20.CDS1 9419092 9419156
chr_3 g1280 g1280.t20 exon g1280.t20.exon2 9419201 9419939
chr_3 g1280 g1280.t20 cds g1280.t20.CDS2 9419201 9419939
chr_3 g1280 g1280.t20 exon g1280.t20.exon3 9420003 9420077
chr_3 g1280 g1280.t20 cds g1280.t20.CDS3 9420003 9420077
chr_3 g1280 g1280.t20 exon g1280.t20.exon4 9420134 9420248
chr_3 g1280 g1280.t20 cds g1280.t20.CDS4 9420134 9420248
chr_3 g1280 g1280.t20 exon g1280.t20.exon5 9420321 9420377
chr_3 g1280 g1280.t20 cds g1280.t20.CDS5 9420321 9420358
chr_3 g1280 g1280.t20 exon g1280.t20.exon6 9421190 9421224
chr_3 g1280 g1280.t20 TSS g1280.t20 9421282 9421282

Sequences

>g1280.t20 Gene=g1280 Length=1183
GCTACTTTACTTGTTTTAGATTTCCAAAGTCAAAGTATCTTGAATACGCAAAACATGTGG
AAACTGTGCTGTGTTTTAATAATCGCTATAAGCGCGTTAAATTCAATAGAATGTGCAACA
ACTCAAAGTAGACCAAGTCAAGTAGTCATCCCGCAAGCATTCATAAATGCAGGAAAAACA
AAAGGTTTAGAGATTTGGAGGATTGAGAATTTTAAAGTTGTTGCTGTGCAAAAAAATACC
TATGGCCAATTTCACACCGGCGATTCTTACATTGTATTGAATACAATGGAGAATAAAAAT
AAGCAACTTTCATGGGATGTTCATTTTTGGCTTGGACTTGAAACAACGCAAGATGAGGCA
GGTGCTGCTGCAATTTACACTGTACAACTTGATGATGCTCTTGGAGGAGCACCAGTTCAA
CATCGTGAAGTTCAAGAGCAAGAATCACAACTTTTCTTAGGATATTTCAAGAGCAGTGGT
GGAATTAAATATTTGCCTGGTGGTGTTGCGAGCGGATTTAGAAAAACAGAAATAAATGCA
ATTGGTGAGAAACGCCTATTTCAAGTAAAAGGAAAGAAAAATGTTCGCGTTCGTCAAGTT
GATTTGACAATTGGGTCAATGAATAAAGGCGATTGCTTTGTTCTTGATGCTGGCAATAAA
GTCTATATTTATGTTGGACCAAAAGCTAAACGAGTTGAGAAAATGAAGGCAACAAGTTTT
GCAAATCAAGTGCGTGATGAAGACCATCATGGACGATCATCTGTTGAAATTGTTGATGAA
TTTTCAAATGATGTTGATAAGGCTCATTTCTTTGAAGTGCTTGGTTCAGGTTCAATTGAA
CAAGTGCCAGATGAAAGCGTTGCTGAAGATGATGAGGCATTTGAAAGAAAAGAAGAAGCT
GCAACAACTTTGAGTAAAGTTAGTGATGCATCAGGAAGCTTGAAAGTTGAACAAATTAAT
CAAAAACCATTGAAACAAGAAATGCTGAATACTAACGATTGCTTTATTCTTGATACTGGA
AAAAAAACAAGCAATGTCACGTGCTCAGGGATTTATTCAAACGAAGAAATATCCTGCATG
GACTAAAGTAACAAAAATCAATGAATTCACCGAAACAACTCCATTCAAGCAATATTTCTT
TACATGGCGTGATCATGGTGCATCACATTCTCGCCTTATTTGA

>g1280.t20 Gene=g1280 Length=343
MWKLCCVLIIAISALNSIECATTQSRPSQVVIPQAFINAGKTKGLEIWRIENFKVVAVQK
NTYGQFHTGDSYIVLNTMENKNKQLSWDVHFWLGLETTQDEAGAAAIYTVQLDDALGGAP
VQHREVQEQESQLFLGYFKSSGGIKYLPGGVASGFRKTEINAIGEKRLFQVKGKKNVRVR
QVDLTIGSMNKGDCFVLDAGNKVYIYVGPKAKRVEKMKATSFANQVRDEDHHGRSSVEIV
DEFSNDVDKAHFFEVLGSGSIEQVPDESVAEDDEAFERKEEAATTLSKVSDASGSLKVEQ
INQKPLKQEMLNTNDCFILDTGKKTSNVTCSGIYSNEEISCMD

Protein features from InterProScan

Transcript Database ID Name Start End E.value
23 g1280.t20 CDD cd11290 gelsolin_S1_like 36 150 2.83701E-62
22 g1280.t20 CDD cd11289 gelsolin_S2_like 165 257 4.23752E-36
16 g1280.t20 Gene3D G3DSA:3.40.20.10 Severin 32 163 2.7E-47
14 g1280.t20 Gene3D G3DSA:3.40.20.10 Severin 164 268 1.0E-27
15 g1280.t20 Gene3D G3DSA:3.40.20.10 Severin 277 328 7.1E-10
3 g1280.t20 PANTHER PTHR11977 VILLIN 26 324 1.4E-116
4 g1280.t20 PANTHER PTHR11977:SF55 GELSOLIN 26 324 1.4E-116
8 g1280.t20 PRINTS PR00597 Gelsolin family signature 62 78 1.4E-12
6 g1280.t20 PRINTS PR00597 Gelsolin family signature 88 106 1.4E-12
7 g1280.t20 PRINTS PR00597 Gelsolin family signature 121 141 1.4E-12
5 g1280.t20 PRINTS PR00597 Gelsolin family signature 177 197 1.4E-12
2 g1280.t20 Pfam PF00626 Gelsolin repeat 52 135 2.3E-14
1 g1280.t20 Pfam PF00626 Gelsolin repeat 176 241 1.4E-10
18 g1280.t20 Phobius SIGNAL_PEPTIDE Signal peptide region 1 20 -
19 g1280.t20 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 3 -
20 g1280.t20 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 4 15 -
21 g1280.t20 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 16 20 -
17 g1280.t20 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 21 343 -
26 g1280.t20 SMART SM00262 VILL_6 43 141 3.1E-24
25 g1280.t20 SMART SM00262 VILL_6 164 259 2.1E-24
10 g1280.t20 SUPERFAMILY SSF55753 Actin depolymerizing proteins 34 176 1.08E-37
11 g1280.t20 SUPERFAMILY SSF55753 Actin depolymerizing proteins 165 259 1.78E-19
9 g1280.t20 SUPERFAMILY SSF55753 Actin depolymerizing proteins 279 323 2.83E-6
13 g1280.t20 SignalP_EUK SignalP-noTM SignalP-noTM 1 20 -
24 g1280.t20 SignalP_GRAM_NEGATIVE SignalP-noTM SignalP-noTM 1 21 -
12 g1280.t20 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.

Raw TPM values