General information for g1854.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Filamin-A.
Parent gene
- The parent gene g1854 is located on chr_3: 13366472..13372997 (+ 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 | g1854 | g1854.t1 | isoform | g1854.t1 | 13366472 | 13372997 |
| chr_3 | g1854 | g1854.t1 | exon | g1854.t1.exon1 | 13366472 | 13366531 |
| chr_3 | g1854 | g1854.t1 | cds | g1854.t1.CDS1 | 13366472 | 13366531 |
| chr_3 | g1854 | g1854.t1 | exon | g1854.t1.exon2 | 13369495 | 13369849 |
| chr_3 | g1854 | g1854.t1 | cds | g1854.t1.CDS2 | 13369495 | 13369849 |
| chr_3 | g1854 | g1854.t1 | exon | g1854.t1.exon3 | 13369917 | 13370069 |
| chr_3 | g1854 | g1854.t1 | cds | g1854.t1.CDS3 | 13369917 | 13370069 |
| chr_3 | g1854 | g1854.t1 | exon | g1854.t1.exon4 | 13370131 | 13370407 |
| chr_3 | g1854 | g1854.t1 | cds | g1854.t1.CDS4 | 13370131 | 13370407 |
| chr_3 | g1854 | g1854.t1 | exon | g1854.t1.exon5 | 13370538 | 13370552 |
| chr_3 | g1854 | g1854.t1 | cds | g1854.t1.CDS5 | 13370538 | 13370552 |
| chr_3 | g1854 | g1854.t1 | exon | g1854.t1.exon6 | 13371031 | 13371285 |
| chr_3 | g1854 | g1854.t1 | cds | g1854.t1.CDS6 | 13371031 | 13371285 |
| chr_3 | g1854 | g1854.t1 | exon | g1854.t1.exon7 | 13371339 | 13371933 |
| chr_3 | g1854 | g1854.t1 | cds | g1854.t1.CDS7 | 13371339 | 13371933 |
| chr_3 | g1854 | g1854.t1 | exon | g1854.t1.exon8 | 13371995 | 13372683 |
| chr_3 | g1854 | g1854.t1 | cds | g1854.t1.CDS8 | 13371995 | 13372683 |
| chr_3 | g1854 | g1854.t1 | exon | g1854.t1.exon9 | 13372742 | 13372997 |
| chr_3 | g1854 | g1854.t1 | cds | g1854.t1.CDS9 | 13372742 | 13372997 |
| chr_3 | g1854 | g1854.t1 | TSS | g1854.t1 | NA | NA |
| chr_3 | g1854 | g1854.t1 | TTS | g1854.t1 | NA | NA |
Sequences
>g1854.t1 Gene=g1854 Length=2655
ATGGCACAACCACAAGCGTTAGGCGAGTTTCTTCAACAGAATCAAACTATTGCGCCAAGA
GATTATTGCGATCAAGAAGAAGAAATGATTGAAGCTGAACGTGATTTGGCAGAAGATGCA
GAGTGGAAGCGCATCCAACAAAATACTTTTACGCGATGGGCCAATGAACATTTGAAGATC
ATCGACAAGACTATAATGAGCTTGGAAACTGATTTATCAGATGGCCTCGCTTTAATTGCT
CTCATCGAAGTACTTTCACAAAAGAAAATGAGCAAACACAATAAACGTCCAACATTTCGA
TCCCAAAAATTGGAAAATGTCTCTGTCGCACTTAAATTTCTTGAACGTGAAGGAATCAAG
ATTATCAATATCGACTCAACTGACATTGTTGATTGCAAACTGAAATTGATTCTCGGTCTC
ATTTGGCTCCTAATTTTGCACTACTCAATCTCTATGCCAATTTGGGATACTGAGGTCGAT
CCAAATGATAAGCAAACTCCAAAGCAACGTTTGCTTAATTGGGTCAAAAATCGTGTACCC
GATTTACCAATTCATAATTTTACTACAGATTGGAATGATGGTAAAGCCATTGGTGCTCTT
GTTGATAACGTTGCTCCAGGTTTATGTCCAGATTGGGCATCATGGGATCCTAAAGATGCA
CTTCAAAATGCTACTGAAGCCATGGGATTGGCTGATGACTGGCTTGGTGTTCGTCAATTG
ATCAAGCCTGATGAAATGACTAATCCAAATATTGATGAGCAATCAATGATGACATATTTG
TCACAATATCCAAGTGCAAAACTCAAACCAGGTGCTCCACTTCGTCAACCAACAAATCCA
AACAGTACTCCACCACCTCGAGTTCGCTGCTACGGTCCAGGCATTGAACCCTCAGGTCCT
ATCGTTAATGCACCAGCCAATTTTACAGTTGAAACATTTTCAGCTGGAAAAGGAAATGTT
GAAGTTACTGTATTGAATCCCAACGGACTCCCTGAACAGGTTGATTGTCGTTTCAATAAT
GATAAAGCATTGACTTATTCTGTCTCATATATTCCAAAAATGGAAGGAGTTCATAAAGTC
ATTGTTAAATTTAATGGACGTGATGTTCCTAAAAGTCCATTTGATGTTAAAGTTGAAGGC
GTTGCTGGTGATGCAGAAAAGGTCACAGCAAGTGGTCCAGGATTACAACCAGATGGTGTT
ATGGTTAAGAAGCCAACTTATTTCGATATTCATACAAAAGATGCAGGCAAGGGAGTACCC
GAAGTTATTATTTTGGATCCGTCAGGTCACAAAACTTCTGTCGCTGCCAAAGTTCGTCAA
ATTGAAAACAATTTGTGGCGTTGTGATTATACACCTGCAGCTGTTGGTTTGCATTCTATT
AATGTTTTCTATGCTGGAAAAGCTATCAAGAATAGTCCATTTGGTGTTCGTGTTTCTCCA
ACATCTGATTCAAAGAAAGTTCGTGCATTTGGTCGTGGATTACAGCCTACCGGTGTCAGA
GTTGGTGATGTTGCTGATTTTAGAATTTCAACCGAAGGTGCAGGAGAAGGTGTTCCTCAT
GTTCAAATTATTGGACCTGGCGGTCAACCTACTCCATTTGAATTGAAAGCAATCAACAAT
TCAACATTTGATGGCAATTATAAACCAACAAAAGAAGGAAGATATCGTGTCATGATTACT
TTTGCTGGACAAGAAATTCCTAAATCACCATTTGATGTCGCAGTTGGACCAAAGAAGGAA
TCATCTATTAAAGCATTCGGGCCTGGTCTTCATAGTGGTATTGTTAATAAACCTGCTAAA
TTTGTTGTTGAAACTAATGGAGAGACTGGTGCTCTCGGCTTTTCTGTTGCTGGTCCAAGT
CAAGCTAAAATTGAGTGCCATGATAACGGCGATGGAAGTGCCCTTGTTACATATTATCCA
ACTGCACCTGGAGAATATGCTGTTCATATTTTGTGCGATGAAGAAGATATCAATAAATCA
CCATACATGTCTCAAATAATTTTACCACCACCAGAAGTTACTCCGGAAAATGTAAAAGTC
TATGGTCAAGGAATTGAGCCAAATGGTGTAGAAGTTGGAAAGAAAACTCAATTTACTATT
GATCATAAGCAAGCTGGTATTGCTCCTCTTGAAGTTAAAGTAACAGATAGCATTGGTCGA
GCAGTTCCTGTTCAAGTAATGGAAACATCAGAAAATGTGAAGCAAGTCTATTACACAGCA
ACAACTACAAAACCACTTACAGTTGAAGTCAATTATGGCGGCGTTGCTGCTCCAAATTCA
CCTTTCCGTGTCTATGCTAGTGCACCATTGGATCCATCAAAAGTTCAAGTTTTTGGTCCA
TGGATTGATAATCCAGATGTTAAACCTAATCAAACTACTCATTTCATTGTTGATGCAACT
GAAGCTGGTAATGGAGATTTGGAAGTTAGTGTAATTAATGATGTTACAAAACAAGCAGTT
CCCGTTAATTTAATTGACAATGAAGATAATACATATACGGTTGAGTTAAAACCAGAAGCT
CCTGGTACATATACCACAAACTTAAATTATGGTGGTCTCAAAGTGCCATTCAATAAGAAA
ACAGTTATTAGTACTCAAACAACACAAGTTGATGTCTCAAAAGTACAAGTGGAAGGATTA
GAACAGAGTAAGTAA
>g1854.t1 Gene=g1854 Length=884
MAQPQALGEFLQQNQTIAPRDYCDQEEEMIEAERDLAEDAEWKRIQQNTFTRWANEHLKI
IDKTIMSLETDLSDGLALIALIEVLSQKKMSKHNKRPTFRSQKLENVSVALKFLEREGIK
IINIDSTDIVDCKLKLILGLIWLLILHYSISMPIWDTEVDPNDKQTPKQRLLNWVKNRVP
DLPIHNFTTDWNDGKAIGALVDNVAPGLCPDWASWDPKDALQNATEAMGLADDWLGVRQL
IKPDEMTNPNIDEQSMMTYLSQYPSAKLKPGAPLRQPTNPNSTPPPRVRCYGPGIEPSGP
IVNAPANFTVETFSAGKGNVEVTVLNPNGLPEQVDCRFNNDKALTYSVSYIPKMEGVHKV
IVKFNGRDVPKSPFDVKVEGVAGDAEKVTASGPGLQPDGVMVKKPTYFDIHTKDAGKGVP
EVIILDPSGHKTSVAAKVRQIENNLWRCDYTPAAVGLHSINVFYAGKAIKNSPFGVRVSP
TSDSKKVRAFGRGLQPTGVRVGDVADFRISTEGAGEGVPHVQIIGPGGQPTPFELKAINN
STFDGNYKPTKEGRYRVMITFAGQEIPKSPFDVAVGPKKESSIKAFGPGLHSGIVNKPAK
FVVETNGETGALGFSVAGPSQAKIECHDNGDGSALVTYYPTAPGEYAVHILCDEEDINKS
PYMSQIILPPPEVTPENVKVYGQGIEPNGVEVGKKTQFTIDHKQAGIAPLEVKVTDSIGR
AVPVQVMETSENVKQVYYTATTTKPLTVEVNYGGVAAPNSPFRVYASAPLDPSKVQVFGP
WIDNPDVKPNQTTHFIVDATEAGNGDLEVSVINDVTKQAVPVNLIDNEDNTYTVELKPEA
PGTYTTNLNYGGLKVPFNKKTVISTQTTQVDVSKVQVEGLEQSK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 30 | g1854.t1 | CDD | cd00014 | CH | 45 | 131 | 5.06355E-21 |
| 31 | g1854.t1 | CDD | cd00014 | CH | 167 | 263 | 2.87936E-14 |
| 26 | g1854.t1 | Coils | Coil | Coil | 23 | 43 | - |
| 25 | g1854.t1 | Gene3D | G3DSA:1.10.418.10 | - | 28 | 153 | 4.6E-46 |
| 24 | g1854.t1 | Gene3D | G3DSA:1.10.418.10 | - | 155 | 268 | 1.2E-39 |
| 23 | g1854.t1 | Gene3D | G3DSA:2.60.40.10 | Immunoglobulins | 280 | 378 | 9.4E-30 |
| 22 | g1854.t1 | Gene3D | G3DSA:2.60.40.10 | Immunoglobulins | 379 | 480 | 4.1E-28 |
| 20 | g1854.t1 | Gene3D | G3DSA:2.60.40.10 | Immunoglobulins | 481 | 581 | 1.2E-26 |
| 19 | g1854.t1 | Gene3D | G3DSA:2.60.40.10 | Immunoglobulins | 582 | 667 | 3.3E-27 |
| 21 | g1854.t1 | Gene3D | G3DSA:2.60.40.10 | Immunoglobulins | 671 | 767 | 4.3E-22 |
| 18 | g1854.t1 | Gene3D | G3DSA:2.60.40.10 | Immunoglobulins | 768 | 883 | 5.0E-21 |
| 9 | g1854.t1 | PANTHER | PTHR38537 | JITTERBUG, ISOFORM N | 24 | 882 | 0.0 |
| 10 | g1854.t1 | PANTHER | PTHR38537:SF10 | FILAMIN-C | 24 | 882 | 0.0 |
| 7 | g1854.t1 | Pfam | PF00307 | Calponin homology (CH) domain | 46 | 149 | 1.6E-22 |
| 8 | g1854.t1 | Pfam | PF00307 | Calponin homology (CH) domain | 166 | 263 | 1.5E-12 |
| 3 | g1854.t1 | Pfam | PF00630 | Filamin/ABP280 repeat | 285 | 375 | 3.0E-15 |
| 4 | g1854.t1 | Pfam | PF00630 | Filamin/ABP280 repeat | 383 | 474 | 9.2E-16 |
| 1 | g1854.t1 | Pfam | PF00630 | Filamin/ABP280 repeat | 482 | 572 | 2.7E-15 |
| 6 | g1854.t1 | Pfam | PF00630 | Filamin/ABP280 repeat | 581 | 662 | 1.1E-14 |
| 2 | g1854.t1 | Pfam | PF00630 | Filamin/ABP280 repeat | 673 | 763 | 1.7E-10 |
| 5 | g1854.t1 | Pfam | PF00630 | Filamin/ABP280 repeat | 770 | 856 | 6.5E-12 |
| 27 | g1854.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 135 | - |
| 29 | g1854.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 136 | 155 | - |
| 28 | g1854.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 156 | 884 | - |
| 40 | g1854.t1 | ProSitePatterns | PS00019 | Actinin-type actin-binding domain signature 1. | 46 | 55 | - |
| 41 | g1854.t1 | ProSitePatterns | PS00020 | Actinin-type actin-binding domain signature 2. | 121 | 145 | - |
| 42 | g1854.t1 | ProSiteProfiles | PS50021 | Calponin homology (CH) domain profile. | 44 | 149 | 24.359 |
| 43 | g1854.t1 | ProSiteProfiles | PS50021 | Calponin homology (CH) domain profile. | 165 | 268 | 18.631 |
| 49 | g1854.t1 | ProSiteProfiles | PS50194 | Filamin/ABP280 repeat profile. | 280 | 378 | 30.938 |
| 44 | g1854.t1 | ProSiteProfiles | PS50194 | Filamin/ABP280 repeat profile. | 380 | 478 | 27.404 |
| 47 | g1854.t1 | ProSiteProfiles | PS50194 | Filamin/ABP280 repeat profile. | 479 | 575 | 29.151 |
| 45 | g1854.t1 | ProSiteProfiles | PS50194 | Filamin/ABP280 repeat profile. | 575 | 666 | 24.877 |
| 46 | g1854.t1 | ProSiteProfiles | PS50194 | Filamin/ABP280 repeat profile. | 670 | 766 | 23.911 |
| 48 | g1854.t1 | ProSiteProfiles | PS50194 | Filamin/ABP280 repeat profile. | 767 | 864 | 23.068 |
| 32 | g1854.t1 | SMART | SM00033 | ch_5 | 46 | 147 | 2.7E-24 |
| 33 | g1854.t1 | SMART | SM00033 | ch_5 | 167 | 263 | 6.3E-17 |
| 39 | g1854.t1 | SMART | SM00557 | flmn_3 | 284 | 381 | 2.3E-32 |
| 36 | g1854.t1 | SMART | SM00557 | flmn_3 | 384 | 481 | 6.1E-37 |
| 37 | g1854.t1 | SMART | SM00557 | flmn_3 | 483 | 578 | 3.7E-30 |
| 35 | g1854.t1 | SMART | SM00557 | flmn_3 | 579 | 669 | 2.6E-24 |
| 34 | g1854.t1 | SMART | SM00557 | flmn_3 | 674 | 769 | 1.2E-20 |
| 38 | g1854.t1 | SMART | SM00557 | flmn_3 | 771 | 880 | 5.9E-14 |
| 11 | g1854.t1 | SUPERFAMILY | SSF47576 | Calponin-homology domain, CH-domain | 27 | 263 | 2.65E-75 |
| 17 | g1854.t1 | SUPERFAMILY | SSF81296 | E set domains | 285 | 380 | 3.87E-25 |
| 12 | g1854.t1 | SUPERFAMILY | SSF81296 | E set domains | 383 | 495 | 5.87E-27 |
| 16 | g1854.t1 | SUPERFAMILY | SSF81296 | E set domains | 461 | 578 | 1.27E-26 |
| 15 | g1854.t1 | SUPERFAMILY | SSF81296 | E set domains | 581 | 666 | 3.6E-21 |
| 14 | g1854.t1 | SUPERFAMILY | SSF81296 | E set domains | 674 | 768 | 6.07E-20 |
| 13 | g1854.t1 | SUPERFAMILY | SSF81296 | E set domains | 749 | 856 | 5.14E-22 |
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 transcript has been annotated with K04437 (filamin)
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. There were no conditions that were differentially expressed