General information for g5641.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Protein cappuccino.
Parent gene
- The parent gene g5641 is located on chr_2: 10813609..10820834 (+ 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_2 | g5641 | g5641.t1 | TSS | g5641.t1 | 10812977 | 10812977 |
| chr_2 | g5641 | g5641.t1 | isoform | g5641.t1 | 10813609 | 10820834 |
| chr_2 | g5641 | g5641.t1 | exon | g5641.t1.exon1 | 10813609 | 10813807 |
| chr_2 | g5641 | g5641.t1 | cds | g5641.t1.CDS1 | 10813609 | 10813807 |
| chr_2 | g5641 | g5641.t1 | exon | g5641.t1.exon2 | 10814045 | 10814332 |
| chr_2 | g5641 | g5641.t1 | cds | g5641.t1.CDS2 | 10814045 | 10814332 |
| chr_2 | g5641 | g5641.t1 | exon | g5641.t1.exon3 | 10814996 | 10815427 |
| chr_2 | g5641 | g5641.t1 | cds | g5641.t1.CDS3 | 10814996 | 10815427 |
| chr_2 | g5641 | g5641.t1 | exon | g5641.t1.exon4 | 10815650 | 10815826 |
| chr_2 | g5641 | g5641.t1 | cds | g5641.t1.CDS4 | 10815650 | 10815826 |
| chr_2 | g5641 | g5641.t1 | exon | g5641.t1.exon5 | 10816959 | 10817137 |
| chr_2 | g5641 | g5641.t1 | cds | g5641.t1.CDS5 | 10816959 | 10817137 |
| chr_2 | g5641 | g5641.t1 | exon | g5641.t1.exon6 | 10817224 | 10818238 |
| chr_2 | g5641 | g5641.t1 | cds | g5641.t1.CDS6 | 10817224 | 10818238 |
| chr_2 | g5641 | g5641.t1 | exon | g5641.t1.exon7 | 10818304 | 10818402 |
| chr_2 | g5641 | g5641.t1 | cds | g5641.t1.CDS7 | 10818304 | 10818402 |
| chr_2 | g5641 | g5641.t1 | exon | g5641.t1.exon8 | 10819262 | 10820149 |
| chr_2 | g5641 | g5641.t1 | cds | g5641.t1.CDS8 | 10819262 | 10820149 |
| chr_2 | g5641 | g5641.t1 | exon | g5641.t1.exon9 | 10820212 | 10820283 |
| chr_2 | g5641 | g5641.t1 | cds | g5641.t1.CDS9 | 10820212 | 10820283 |
| chr_2 | g5641 | g5641.t1 | exon | g5641.t1.exon10 | 10820354 | 10820651 |
| chr_2 | g5641 | g5641.t1 | cds | g5641.t1.CDS10 | 10820354 | 10820651 |
| chr_2 | g5641 | g5641.t1 | exon | g5641.t1.exon11 | 10820729 | 10820834 |
| chr_2 | g5641 | g5641.t1 | cds | g5641.t1.CDS11 | 10820729 | 10820834 |
| chr_2 | g5641 | g5641.t1 | TTS | g5641.t1 | 10821320 | 10821320 |
Sequences
>g5641.t1 Gene=g5641 Length=3753
ATGGGACAATCTTCAAGCATTCTTCAGCAGTCATCATCGCTAAAAAGAAGATTCTTTCTT
GTTACACCCAAAAAATTGATCAGGCTACGTAGACAAACATCATGCGAAAATTCAGGAGCT
GTATCGAGCCATCAAAATGAATTTACGCAAGCGCTAAATGAAGGAGAAGATGATATTCAG
AAAACAGCTGATTCACGAGACCGGCATAAAGATACTCAACAACAAACACACACAGATGAA
AATGTTGAGACAGCAAAGCACAACCACGATGACAAAGTGGCAGCAACGTTCAGTCGTGAT
CCAACAGCGCGAGACGAGAGTTTGATTGAAGAAAATTTATTGCAACAGTTGCGTGAATTA
ATTGAAAATTTATTGTGCGGCGGAGATCGAATTGATGGCGATATTGTACTTGAGATTGAT
ACAATTGAGAAAACTTTAAAAATTTTACCACAGCAAACGAGTTCATTGGTCAAGGAAGAT
CAGGAAGAGAATTGTATAGAATTTCAGTCGCCGCAGCCACTATATCAAGGCAATGGACTG
ATAATAATTCGCGAACACGCTACACCGTCGAGTTGTGATACATATTTTACTGATGCCGCT
TCATCGTCTATTTGTGAAAAAGTGAACTTTCAAAATTTAACAGTTACAAAATTAGAGCAA
TTCGATATTTTTGGTGATAAAAAAACACTTCAAATTATACGTAATGAGTCAATAAATCTT
GATAGTGAATGTGTAGAGGAAGTAGGCGGAAAAATGCCAATCGTAAGAAACGGCTCTTCG
AGCAACGGTCGAAAATTGCATACTGATGCAAGTGACAAAGATAAAGGAATGTTTAATGTG
TCGCGAGTTAAGAAGATTGAATTATCGGAAATTCCTCTGGCAACGGATATATGTACTTCA
TCTTTAACTTCAGTTGCGTCAACAACATCATCTGAACAACAAAAAGTTACACATTCGTCA
AATGGAAGTAAAGTACTTCATCGTGTTATTACTTTGACGACTGCTAATCATAATGACAAC
AGTAATTATGTGAAACAAACAAAACCCGCATTTATTCCTGAGAAATTGCAATTTTCTGCA
TATGAAAAATTCGAAGGTCAAATGCTATTGAATTGGTTTATTCAATCGATTCCTTCGTCT
CTCTCACAAACTTTAAATGAAAATGATTTGAACGCCCTCACGATGCAGTATTGTACGAAT
TTATTAATTGCCGGTATTATTAAGCCATTGTTGGATACGCCTAGTAGTAACAGTAATAGC
AATGAAGTTTTCAAGTCAAATTTAATGTATCAATGGACATTTAAAGAGCCGACAATAATA
TCAAATTTACCTGGAAAATTGGAGACAAATGTTTGGCCTTATAATAATAGTAATATTAAT
AATAACAATAACTCATCGGCGTCATTATCAACAGCTACAATATCAAGTCCTAAACGTGAT
GGAGAATCAAAAATACCTAAATTAGTATCAAATTTCACATCAACGCCAAAACCTCGCATT
CAAACATCACTTGCAAGCCTGTGCACACCTGAAAATTCAATTTTGCTCAATGGAACTGAA
TTCGATCAACATAGTAAGATCACTGAACTGAAAAATAAGTTGAGCAAGTGTGAAACTGTA
CAGGAGACATTGATATTAATAAGAGGATTTTTAAGCGATGTAATGCAGTCATCTGAGTCA
AGCACAAATAGTAGTGGAGGTGCAGCTATTTTAACAAATTCTATTTTAAATGGGTCTGAT
ACAACAATTTTTGATAAAAGTTGTGATACTTCGCTCAATACTATTGTGAATAATAATAAT
CAAATACAAAAATCCCCGATCCGTAAAGGAACAGCATCACCCTCTCGAAGTCCACCCAAA
TCGAGAACATTACCCAGCACACCAACAGGATTAGCTGCAAGACAGCGACTACGTAAAAAT
AATTCAGCTGATTCTGTTTCATCAACACCTGTCAGTAATAATTTGTCATCGTCACCGTGC
AAAAAGTGTATGCTTAATTCGAAAACTAAGAAGCGCTTGGTTGATAAGGCAACAGTTATG
GATGTTGAGCCAATTACTTTTCCTAAAATACCCGAGAAAAAATCTGTCGAGATTCAGACT
GATCCTATTACTATTACTAATGTTAGTGACAAATCTAATGAAAATGAAGAAAAACATGAG
AACAAAGAAGAAGAAAAAGAAAAAGTAGCAAATGTACCTCCACCACCTCCAATGCCAAAC
TCAAACTCAATATCAACTTCTCCAATTCCTCCGCCTCCACCATTATCAAATATTCCAAAA
GCTCCACCAGGACCACCACCGCCACCAAATGGACCAATTCCGCCGCCAATTCCAAATTCG
AATAAAGGACCTTGTCCTTTGCCTCCGCCTCTTTTGTTAAACACTCCAGCTTTACGTAAA
AGCGCAGTAAATCCACCAAAACCCATGAGACCGCTTTATTGGACGAGAATTGTGACTCCG
ATAATTCAATCTCAAGATTCAGTTGACGGTAGTGGAAATAACGCATCATCTGAGGAGATT
CATGATAAGGATGAATTGTGGAAGGAAATTGACGAAACAAAACTCGACAATCTCGATGAA
TTTACGGAACTTTTTTCTCGGCAATGTGTTGTGCCTAAAACGAAGGAACAAACGCCCCTG
CCAAAAGTTAAGACGATCAAAGTATTAGATAGTAAACGATCACAAAATGTAGGAATATTT
GTTCGAAGTATTCATGTAGATTTCGCTGAAATTGAGCATGCCATTTATGAATGTGACACC
TCAGTAGTGAGTCAAGAGACCTTGCAAAATATTATGGCAATAAAAGCCACAAACGATGAA
TTAGCAATGATAAAAGAGGCAGTCGAGGCTCATAATAGCAGCGATAATTCTATTCCTTTA
GACACACCCGAACGTTTTCTTTTAAAACTTTCACAAATTTCATCATCGACTGAAAGAATT
GCGTGCATTGTGTTTCAGGATGAATTTGAAGAACAATGTCTAATGGTAACACGAAAAGTT
ATTATTGTTAGAGACCTTTGTGAATTTTTGCTCGAAAGTGAAGATCTGAAAGAAGTATTT
TCAATTATTCTTACACTTGGAAATTTTATGAATGGTGGTAACAGACAGCGAGGTCAGGCT
GATGGATTTGGACTTGAAATTTTAGGAAAACTTAAAGATGTAAAATCAAAAGATCCAAAA
ATTACATTATTGCATTTTATTGTGAAAACATATATTGCAAGGTCACGTCAAAACGGAATT
GCAATAACTGATTTAAAATTGCCTGTACCAAATGATGTTGATAAAAGTCTTTCGATTGAT
TTCGAAGAATGTAAGCAGCAATTGAATGCACTCAAGAACAAACTTGAAGAATGTAAAAAG
ACGACAGAGAAAGTCATAGAGGCATCATCAGAAGAACATGTTCAACCATTTAAAGATAAG
ATGGAAGCATTCTTAAATATGGCTGCACAGCGAATTGAAAGTCGTTTTCATAAAGTTGAA
GAGTGTAAAACGCTCTTCATTAAAACACTAAGATTTTATAAGTTTATGCCTAAAGGTGGT
GCTCTCGAAGAAACAACGCCCGCACAATTTTTCGAATATTGGACATCATTTACTAGTGAT
TTCAGTGGAATCTTTAAGAAGGAACTTATGATACTCACCAATGAGCTTTACAAGAAATCA
CGCCAAGTGACAAAACCACAGTCAAAACCAACTTCGCTTGGTGAGAACAATCTAAAAGCA
CGCATCAATCGTCTTAAAAATCGTGATAAGTAA
>g5641.t1 Gene=g5641 Length=1250
MGQSSSILQQSSSLKRRFFLVTPKKLIRLRRQTSCENSGAVSSHQNEFTQALNEGEDDIQ
KTADSRDRHKDTQQQTHTDENVETAKHNHDDKVAATFSRDPTARDESLIEENLLQQLREL
IENLLCGGDRIDGDIVLEIDTIEKTLKILPQQTSSLVKEDQEENCIEFQSPQPLYQGNGL
IIIREHATPSSCDTYFTDAASSSICEKVNFQNLTVTKLEQFDIFGDKKTLQIIRNESINL
DSECVEEVGGKMPIVRNGSSSNGRKLHTDASDKDKGMFNVSRVKKIELSEIPLATDICTS
SLTSVASTTSSEQQKVTHSSNGSKVLHRVITLTTANHNDNSNYVKQTKPAFIPEKLQFSA
YEKFEGQMLLNWFIQSIPSSLSQTLNENDLNALTMQYCTNLLIAGIIKPLLDTPSSNSNS
NEVFKSNLMYQWTFKEPTIISNLPGKLETNVWPYNNSNINNNNNSSASLSTATISSPKRD
GESKIPKLVSNFTSTPKPRIQTSLASLCTPENSILLNGTEFDQHSKITELKNKLSKCETV
QETLILIRGFLSDVMQSSESSTNSSGGAAILTNSILNGSDTTIFDKSCDTSLNTIVNNNN
QIQKSPIRKGTASPSRSPPKSRTLPSTPTGLAARQRLRKNNSADSVSSTPVSNNLSSSPC
KKCMLNSKTKKRLVDKATVMDVEPITFPKIPEKKSVEIQTDPITITNVSDKSNENEEKHE
NKEEEKEKVANVPPPPPMPNSNSISTSPIPPPPPLSNIPKAPPGPPPPPNGPIPPPIPNS
NKGPCPLPPPLLLNTPALRKSAVNPPKPMRPLYWTRIVTPIIQSQDSVDGSGNNASSEEI
HDKDELWKEIDETKLDNLDEFTELFSRQCVVPKTKEQTPLPKVKTIKVLDSKRSQNVGIF
VRSIHVDFAEIEHAIYECDTSVVSQETLQNIMAIKATNDELAMIKEAVEAHNSSDNSIPL
DTPERFLLKLSQISSSTERIACIVFQDEFEEQCLMVTRKVIIVRDLCEFLLESEDLKEVF
SIILTLGNFMNGGNRQRGQADGFGLEILGKLKDVKSKDPKITLLHFIVKTYIARSRQNGI
AITDLKLPVPNDVDKSLSIDFEECKQQLNALKNKLEECKKTTEKVIEASSEEHVQPFKDK
MEAFLNMAAQRIESRFHKVEECKTLFIKTLRFYKFMPKGGALEETTPAQFFEYWTSFTSD
FSGIFKKELMILTNELYKKSRQVTKPQSKPTSLGENNLKARINRLKNRDK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 12 | g5641.t1 | Coils | Coil | Coil | 705 | 732 | - |
| 11 | g5641.t1 | Coils | Coil | Coil | 1101 | 1131 | - |
| 10 | g5641.t1 | Coils | Coil | Coil | 1235 | 1250 | - |
| 9 | g5641.t1 | Gene3D | G3DSA:1.20.58.2220 | - | 839 | 1238 | 6.2E-90 |
| 17 | g5641.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 58 | 91 | - |
| 15 | g5641.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 597 | 657 | - |
| 14 | g5641.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 698 | 736 | - |
| 16 | g5641.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 711 | 730 | - |
| 2 | g5641.t1 | PANTHER | PTHR13037:SF11 | FORMIN-1 | 717 | 1222 | 4.8E-111 |
| 3 | g5641.t1 | PANTHER | PTHR13037 | FORMIN | 717 | 1222 | 4.8E-111 |
| 7 | g5641.t1 | PRINTS | PR00828 | Formin signature | 842 | 865 | 4.7E-8 |
| 6 | g5641.t1 | PRINTS | PR00828 | Formin signature | 1010 | 1029 | 4.7E-8 |
| 4 | g5641.t1 | PRINTS | PR00828 | Formin signature | 1092 | 1113 | 4.7E-8 |
| 5 | g5641.t1 | PRINTS | PR00828 | Formin signature | 1189 | 1208 | 4.7E-8 |
| 1 | g5641.t1 | Pfam | PF02181 | Formin Homology 2 Domain | 800 | 1202 | 4.5E-72 |
| 18 | g5641.t1 | ProSiteProfiles | PS51444 | Formin homology-2 (FH2) domain profile. | 799 | 1227 | 46.515 |
| 13 | g5641.t1 | SMART | SM00498 | it6_source | 799 | 1216 | 1.7E-77 |
| 8 | g5641.t1 | SUPERFAMILY | SSF101447 | Formin homology 2 domain (FH2 domain) | 812 | 1211 | 2.75E-81 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5641/g5641.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5641.t1.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0005884 | actin filament | CC |
| GO:0008017 | microtubule binding | MF |
| GO:0045010 | actin nucleation | BP |
KEGG
Orthology
- This transcript has been annotated with K02184 (formin 2)
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.
