General information for g1856.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Filamin-A.
Parent gene
- The parent gene g1856 is located on chr_3: 13403608..13404108 (+ 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 | g1856 | g1856.t2 | isoform | g1856.t2 | 13377486 | 13378926 |
| chr_3 | g1856 | g1856.t2 | exon | g1856.t2.exon1 | 13377486 | 13378046 |
| chr_3 | g1856 | g1856.t2 | cds | g1856.t2.CDS1 | 13377646 | 13378046 |
| chr_3 | g1856 | g1856.t2 | exon | g1856.t2.exon2 | 13378110 | 13378316 |
| chr_3 | g1856 | g1856.t2 | cds | g1856.t2.CDS2 | 13378110 | 13378316 |
| chr_3 | g1856 | g1856.t2 | exon | g1856.t2.exon3 | 13378381 | 13378926 |
| chr_3 | g1856 | g1856.t2 | cds | g1856.t2.CDS3 | 13378381 | 13378522 |
| chr_3 | g1856 | g1856.t2 | TTS | g1856.t2 | 13379163 | 13379163 |
| chr_3 | g1856 | g1856.t2 | TSS | g1856.t2 | NA | NA |
Sequences
>g1856.t2 Gene=g1856 Length=1314
GAAAATCGATGGACCACATGCACAACAAGTATCAACCGGTGACTATCGCAGTGTAAAATT
GTACGGACCTGCTGTTGAGACACTTCAAGTTTATGAAGGAATTCCAGCAAGTTTTTATAT
CAATGTTGCTGATGCTGGTGCAGGATTAATTGGCGTTGAAATGACATCAAGTGAAGGAGG
TGCAGTTGAAAATTATGAAGTTGAAGAGCGTGGTGATGGAAACTATTTAGTGACATTTAT
TCCACCAAAACAAAACACCACAATTACCGCAAAGGTTTCATTCGCTAAGCATAATGTTCC
TAATTCCCCGTTCGTTATGCGTGTCTTGCCACCAGTTGCAATTAAATCTGGCAATTTGGT
ACTTTCTGGTGACATTTCAAAGAAAACGCTTTCTGCTTCAGTTCCAGCAAACTTCCAAAT
TGACACAGGAAAAGCTGGTATGGGTGAGATCAAAGTTGTTATCAATGGTCCACAAGGAAA
ACCAATGGTTCCAAGAATTGAACGTGGCAAAGATGGAAAATACTCTGTTAGTTTTGTTCC
TGATGAATTGGGTCCATACAACGTTTCAGTTATGTATGCTGGAAAGGAAATCGAAAATTC
GCCATTTGTGATGCAATCTACACCATCTGGTGATGCAAATAAATGCAAATTTGTTAATAA
TGCAGCAGAAAAGGTTATTTTTGGCAAGAAAAATCGTTTAACAGTCGATGCACGTGAAGC
TGGAACTGGTAATGTTACATGCAAAATTGTAAAATCATCTAATGGACAAATCATAGATAC
AGAAATTGTTGAAAAAGATGGATTTTTTGATATCTTTTATTTACTTGCTGAGCCTGGAAC
ATACGATGTTGATGTGAAATTTGGTGGAAAACAAGTGCCTAATGGATTAATGAGAATGAC
GGTAAAATAATTTTAATCAATTACTCTCTTCGTTAAAATTGTTATTAACTTTTATTTGGT
GTCTGTCAATCAATGAATATCATCTAATTATTTAGAGAAAGTTCTCTATATATACAAATA
TTTATTTGACCCTCGAAAGTCTTTTTAACGTGCGTTTGTTTTCATATCTAATCTATTGTG
AGGATTATTTATAAAAAACATGAACTTTGTAACACAAAAATATTGAAAATTCTTTCTCAT
TTTCTATAATTCATTGGTGATGGTTGTTATTTTTTTTTAAAAATAAATATCTTCTGGGTA
AAATACACACAATACAAGGATTAAAAACAATTGTTAGCCGAATAATGGTATATATTTGCA
TACAGATAAAGAAAAAAAATATAAATATTTATTTTATTGCAGAAAAAACACAAA
>g1856.t2 Gene=g1856 Length=249
MTSSEGGAVENYEVEERGDGNYLVTFIPPKQNTTITAKVSFAKHNVPNSPFVMRVLPPVA
IKSGNLVLSGDISKKTLSASVPANFQIDTGKAGMGEIKVVINGPQGKPMVPRIERGKDGK
YSVSFVPDELGPYNVSVMYAGKEIENSPFVMQSTPSGDANKCKFVNNAAEKVIFGKKNRL
TVDAREAGTGNVTCKIVKSSNGQIIDTEIVEKDGFFDIFYLLAEPGTYDVDVKFGGKQVP
NGLMRMTVK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g1856.t2 | Gene3D | G3DSA:2.60.40.10 | Immunoglobulins | 1 | 63 | 0.0000000 |
| 10 | g1856.t2 | Gene3D | G3DSA:2.60.40.10 | Immunoglobulins | 64 | 154 | 0.0000000 |
| 12 | g1856.t2 | Gene3D | G3DSA:2.60.40.10 | Immunoglobulins | 155 | 249 | 0.0000000 |
| 3 | g1856.t2 | PANTHER | PTHR38537 | JITTERBUG, ISOFORM N | 4 | 243 | 0.0000000 |
| 4 | g1856.t2 | PANTHER | PTHR38537:SF10 | FILAMIN-C | 4 | 243 | 0.0000000 |
| 1 | g1856.t2 | Pfam | PF00630 | Filamin/ABP280 repeat | 78 | 149 | 0.0000000 |
| 2 | g1856.t2 | Pfam | PF00630 | Filamin/ABP280 repeat | 157 | 241 | 0.0000000 |
| 14 | g1856.t2 | ProSiteProfiles | PS50194 | Filamin/ABP280 repeat profile. | 1 | 55 | 10.3690000 |
| 15 | g1856.t2 | ProSiteProfiles | PS50194 | Filamin/ABP280 repeat profile. | 58 | 153 | 24.6510000 |
| 13 | g1856.t2 | ProSiteProfiles | PS50194 | Filamin/ABP280 repeat profile. | 154 | 248 | 17.7870000 |
| 8 | g1856.t2 | SMART | SM00557 | flmn_3 | 62 | 156 | 0.0000000 |
| 9 | g1856.t2 | SMART | SM00557 | flmn_3 | 158 | 249 | 0.0000054 |
| 6 | g1856.t2 | SUPERFAMILY | SSF81296 | E set domains | 4 | 56 | 0.0000028 |
| 5 | g1856.t2 | SUPERFAMILY | SSF81296 | E set domains | 39 | 156 | 0.0000000 |
| 7 | g1856.t2 | SUPERFAMILY | SSF81296 | E set domains | 136 | 248 | 0.0000000 |
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 |
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. There were no conditions that were differentially expressed