General information for g1856.t6
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.t6 | isoform | g1856.t6 | 13402283 | 13404108 |
| chr_3 | g1856 | g1856.t6 | exon | g1856.t6.exon1 | 13402283 | 13403365 |
| chr_3 | g1856 | g1856.t6 | cds | g1856.t6.CDS1 | 13402540 | 13403365 |
| chr_3 | g1856 | g1856.t6 | exon | g1856.t6.exon2 | 13403424 | 13404108 |
| chr_3 | g1856 | g1856.t6 | cds | g1856.t6.CDS2 | 13403424 | 13403608 |
| chr_3 | g1856 | g1856.t6 | TTS | g1856.t6 | 13404143 | 13404143 |
| chr_3 | g1856 | g1856.t6 | TSS | g1856.t6 | NA | NA |
Sequences
>g1856.t6 Gene=g1856 Length=1768
GAAGTCCTTTCCAATTTACTGTTGGACCATTGCGCGATACTGGTGCACATTTGGTTAAAG
CGGGCGGTCCTGGCTTAGATCATGGCGAAGTTGGTCAACCAAATGAATTCAATGTTTGGA
CTCGTGAAGCTGGTGGTGGTACGTTGGCGATTTCTGTTGAAGGTCCAAGCAAGGCCGAGA
TTGATTTTAGAGATCGTAAAGATGGATCTTGTGACGTCTCTTATATTGTATCAGAACCAG
GAGATTATCGTGTTGGCATGAAATTTAATGATCGCCATATACCTGATTCTCCATTCAAAG
TTTTCATTCAACCATCAATGATTGAAGCTCACAAGCTTGAAGTCGCACAATTTCCTGATG
GTCCCGTTCAGCCAGATAAACCAGCTCAATTTATTGTTCGTAAAAATGGTGCTGTAGGAA
ATTTAGATGCAAAAGTAGTTGCACCATCAAATACAGAAGATGATTGCTTCATTCAATTGA
TGGATCCTGACAATTACTCTGTTCGTTTCTATCCTCGCGAAAATGGCATTCATGCTATTC
ATACAAAATTCAATGGTGTTCACATCAACGGAAGTCCTTTCCGTATTAAGGTAGGCAAAG
ATGATGCTGATCCAGCTGCTGTTCATGCAAGTGGTGATGGTCTTCATGAAGGTAAAACTG
GTCAAAAGATGGACTTTATCATCGACACATGCAATGCTGGTTGCGGTTTACTATCTGTAA
CAATGGATGGACCTTCAAAAGTTTCAATGGATTGTACAGAAGTTGAAGAGGGTTACAAAG
TCCGTTATACTCCTCTCCTTCCTGGTGACTACTATTGCACTGTTAAATACAATCACATGC
ACATCGTAGGATCACCTTTCAAAATTGTTGTCGATGGCGAAAAACTTGCAGATGGTGGTG
GTCAAGAAACTACAACTGTCAACGTCGACACAGTTGTAAAAATTGCAAAGGGTGGCAAAA
ACATTGGCCCAGTCATGCCTCACTTCAATTCAGATGCATCTAAAGTCATTGCTAAGGGAT
TGGCACTTAAGAAGGCATATCTTGGTAAACAAAACTCATTCACAATTAATTGTGGTAATG
CAGGTAACAATATCCTTTATGTTGGAATGTATGGTCCAAAAGGTCCCTGCGAAGAATGCT
TCATTAAACATACTGGACGTAATAACTACAATGTCAATTATTTAGTGCGTGAAAGAGGCG
ATTATATTTTAATCATCAAATGGGGCGATGATCACATCCCTGGAAGCCCTTATCGCGTAG
AATGCTAGAATCACTGCATGATAATGAAATTATCTTACTTAAGACAATATGCAATTTTAA
TGAACAATCGAGATCTGAAATATTTTGACAACTACAGCTTTTGAAAAATTTATTATTATC
GTCCAAAACTTTTCTCATTTCAAGATTTCCCTCAGAATTTTATCAAAATGAACTTTCGTT
TATTGAAATAATTCATTCTTATCAGTTGCAATTGTATTTTTATTATCCTTTTTACGATTA
TCTATTATGATTATCATATTATTTTTAAACTATTGATAAGTTTTAATTGATTGTTTTATA
CCCTTCGATCCTCAATCATCCATTCATTTTTCCATGAAAACAACAAAAAACATGTATCAA
TGATTTTTAATTAAAAATATTATATTTGAGAATATTGTCCTTTAATTATCATATACCAAT
CACACACACAAATATATTTTATTGTGTTTTACTTTTATGACTTTCTTGAGAAAGAATTAT
GTAAGTTTTTTGAAAAATATCAATGAAA
>g1856.t6 Gene=g1856 Length=336
MKFNDRHIPDSPFKVFIQPSMIEAHKLEVAQFPDGPVQPDKPAQFIVRKNGAVGNLDAKV
VAPSNTEDDCFIQLMDPDNYSVRFYPRENGIHAIHTKFNGVHINGSPFRIKVGKDDADPA
AVHASGDGLHEGKTGQKMDFIIDTCNAGCGLLSVTMDGPSKVSMDCTEVEEGYKVRYTPL
LPGDYYCTVKYNHMHIVGSPFKIVVDGEKLADGGGQETTTVNVDTVVKIAKGGKNIGPVM
PHFNSDASKVIAKGLALKKAYLGKQNSFTINCGNAGNNILYVGMYGPKGPCEECFIKHTG
RNNYNVNYLVRERGDYILIIKWGDDHIPGSPYRVEC
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g1856.t6 | Gene3D | G3DSA:2.60.40.10 | Immunoglobulins | 20 | 115 | 0.000 |
| 12 | g1856.t6 | Gene3D | G3DSA:2.60.40.10 | Immunoglobulins | 116 | 213 | 0.000 |
| 13 | g1856.t6 | Gene3D | G3DSA:2.60.40.10 | Immunoglobulins | 239 | 336 | 0.000 |
| 3 | g1856.t6 | PANTHER | PTHR38537 | JITTERBUG, ISOFORM N | 1 | 335 | 0.000 |
| 4 | g1856.t6 | PANTHER | PTHR38537:SF10 | FILAMIN-C | 1 | 335 | 0.000 |
| 1 | g1856.t6 | Pfam | PF00630 | Filamin/ABP280 repeat | 117 | 202 | 0.000 |
| 2 | g1856.t6 | Pfam | PF00630 | Filamin/ABP280 repeat | 245 | 333 | 0.000 |
| 17 | g1856.t6 | ProSiteProfiles | PS50194 | Filamin/ABP280 repeat profile. | 1 | 17 | 8.931 |
| 16 | g1856.t6 | ProSiteProfiles | PS50194 | Filamin/ABP280 repeat profile. | 40 | 112 | 20.253 |
| 15 | g1856.t6 | ProSiteProfiles | PS50194 | Filamin/ABP280 repeat profile. | 114 | 205 | 26.438 |
| 14 | g1856.t6 | ProSiteProfiles | PS50194 | Filamin/ABP280 repeat profile. | 242 | 336 | 26.171 |
| 10 | g1856.t6 | SMART | SM00557 | flmn_3 | 23 | 115 | 0.000 |
| 9 | g1856.t6 | SMART | SM00557 | flmn_3 | 118 | 208 | 0.000 |
| 8 | g1856.t6 | SMART | SM00557 | flmn_3 | 246 | 336 | 0.000 |
| 7 | g1856.t6 | SUPERFAMILY | SSF81296 | E set domains | 2 | 114 | 0.000 |
| 6 | g1856.t6 | SUPERFAMILY | SSF81296 | E set domains | 118 | 207 | 0.000 |
| 5 | g1856.t6 | SUPERFAMILY | SSF81296 | E set domains | 246 | 335 | 0.000 |
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