General information for g3982.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as PH and SEC7 domain-containing protein.
Parent gene
- The parent gene g3982 is located on chr_3: 29373805..29377789 (+ 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 | g3982 | g3982.t1 | TSS | g3982.t1 | 29368735 | 29368735 |
| chr_3 | g3982 | g3982.t1 | isoform | g3982.t1 | 29369671 | 29377789 |
| chr_3 | g3982 | g3982.t1 | exon | g3982.t1.exon1 | 29369671 | 29369679 |
| chr_3 | g3982 | g3982.t1 | cds | g3982.t1.CDS1 | 29369671 | 29369679 |
| chr_3 | g3982 | g3982.t1 | exon | g3982.t1.exon2 | 29372984 | 29373050 |
| chr_3 | g3982 | g3982.t1 | cds | g3982.t1.CDS2 | 29372984 | 29373050 |
| chr_3 | g3982 | g3982.t1 | exon | g3982.t1.exon3 | 29373137 | 29373190 |
| chr_3 | g3982 | g3982.t1 | cds | g3982.t1.CDS3 | 29373137 | 29373190 |
| chr_3 | g3982 | g3982.t1 | exon | g3982.t1.exon4 | 29373257 | 29375441 |
| chr_3 | g3982 | g3982.t1 | cds | g3982.t1.CDS4 | 29373257 | 29375441 |
| chr_3 | g3982 | g3982.t1 | exon | g3982.t1.exon5 | 29375500 | 29375728 |
| chr_3 | g3982 | g3982.t1 | cds | g3982.t1.CDS5 | 29375500 | 29375728 |
| chr_3 | g3982 | g3982.t1 | exon | g3982.t1.exon6 | 29375792 | 29375949 |
| chr_3 | g3982 | g3982.t1 | cds | g3982.t1.CDS6 | 29375792 | 29375949 |
| chr_3 | g3982 | g3982.t1 | exon | g3982.t1.exon7 | 29376004 | 29376179 |
| chr_3 | g3982 | g3982.t1 | cds | g3982.t1.CDS7 | 29376004 | 29376179 |
| chr_3 | g3982 | g3982.t1 | exon | g3982.t1.exon8 | 29376353 | 29376453 |
| chr_3 | g3982 | g3982.t1 | cds | g3982.t1.CDS8 | 29376353 | 29376453 |
| chr_3 | g3982 | g3982.t1 | exon | g3982.t1.exon9 | 29376507 | 29376714 |
| chr_3 | g3982 | g3982.t1 | cds | g3982.t1.CDS9 | 29376507 | 29376714 |
| chr_3 | g3982 | g3982.t1 | exon | g3982.t1.exon10 | 29376769 | 29376836 |
| chr_3 | g3982 | g3982.t1 | cds | g3982.t1.CDS10 | 29376769 | 29376836 |
| chr_3 | g3982 | g3982.t1 | exon | g3982.t1.exon11 | 29376901 | 29377041 |
| chr_3 | g3982 | g3982.t1 | cds | g3982.t1.CDS11 | 29376901 | 29377041 |
| chr_3 | g3982 | g3982.t1 | exon | g3982.t1.exon12 | 29377101 | 29377291 |
| chr_3 | g3982 | g3982.t1 | cds | g3982.t1.CDS12 | 29377101 | 29377291 |
| chr_3 | g3982 | g3982.t1 | exon | g3982.t1.exon13 | 29377768 | 29377789 |
| chr_3 | g3982 | g3982.t1 | cds | g3982.t1.CDS13 | 29377768 | 29377789 |
| chr_3 | g3982 | g3982.t1 | TTS | g3982.t1 | NA | NA |
Sequences
>g3982.t1 Gene=g3982 Length=3609
ATGAGTTTTATTGAAGCTGGTGATGTGATTTTAAAGGTTAATGGAACAGACGTTCATCGT
TTTTCAACTAAAGAAGTATTGAAATGCCTTCGGCTCTCAGACGATCCTGTTACATTAGAG
TTAAAACGAGATCCAAATATAAAAGATCATGTAAGAAAATATTTAGCGTCAAACTCGAGT
CATCAAGATATAGGAATTTCATCGCCTTCATCACCAATTATTAATAACATTTCATCACAA
TATGGTCGTGGACATAGAATAAGTTCATCTGATTCATCAGCAACATGTCGAAAGTCTCGT
ATTCCAGTCAATAACACACGTATACCTTCATTAAGTGCACCACAATCTCCTCAAGCAATA
AAGCCTCGTTACTTATCACATATACCAGTCTCAAATGGTCAAACATCATCACCAACAACT
GTTGCTCCGAAAAAACAAAATCCTCGATTTGAGGCATACATGATGACTGGAGATTTAATT
TTAAATTTATCTAGAACATCTCAGAGCTCTAATTTGATTGCACCAGCACAAGTTAAAAAA
TCGACAATGGATAGTTTAAGAGATTCGCCAATGAGAAGTCTTAAAAGAAAGAATGGAATT
GCACCAAAGGCAATATATGATTCATCTCCTTCAGAATCATCTTCGGCTAGTGTAAGTGAA
TTAGGTTCATATGAAATTTGTGAAAACAACTATCATGATAGCAATATTGATGAGAGTAGA
AGAATCAGCAAACTCGGACGATATGCTGGCAATTCAAACACTAAAAACGAAAGCTTAGAT
GAAGAAGAAGAGCAATTGATAACAATTGAAGAATCTAATAATCCATCATCGTGTGGAGAT
GAACGGAAACTACAATACAATTTAAGTAAAGGCTGTGCAAATAATATTTCATCTTCTTCT
TCGACATCTTCGCCAACAAACACAAATTCATCCAATTCATCAACGAATAATAATAGTTAT
GATGGTGGTGGTGATGATAGATGCAGTAATAAGAACAATCAAGGACTCAATTCATTGCAG
CATAAAAAAAGCAAAATTTATACAGTTTTGCACAATGAAGAAATGCACCAAGATAATCTA
CAACAACATCATCAGCAAAAACAAGATAACAATTTAAATATTCGTAAAGAGATGACACCA
AGTGCTTCAATGTCCTCGACTACTACTTCTTCAGCATCAACGACAATAAATCGTAGTGAG
ACACTTTTAACCCCTAATTTAGATGTCTCTCGTTCAGTGCCCACATCACCGACTTCAATT
TCAACTCCTTTATTGGATGCAAATAAAAGACGAGAAAATGTTTGTTCCGTTCCTACAAGT
CCAGAATGTATACAACAAATGCAAGAAAGTACTTCAATGAGACATAATAGTAATAATGTT
CAGAATCATCAAAATGGAGTTTCATTGAGAAAATGTGATGCAAGTGGTTTTCGCACAAGT
CGATCTGAAGACCAACTTCAGCATTCTCAATGTGAAGGATTAATGGGGAATGCAATACCA
ATTGACATTGATGAAGACATTAATAGTTCATTAAATACACTCTTGGATACAAGACATGAT
TCTGAAGATTCTCAAAATTCTAATCGTGATAGAATAGTTTGGACCTATAATGCACCTGTT
ATGCAAAACTCAATAAATAACCAAACACAAGGTGTTATTTCACCAACCTCAAGCTCAATT
AGCACTTCGCCACAACACACTGATAGTCCTGCTTCGCCAACGTCTGTTTCTAGCTCAGTT
ATGTCCTCATCAGGTTCTAAAGGAAATGGCATAAATAATACAAATGGCAGTGCAGGACAA
AATATTATGTTTTTAAGTGGTGAACAGAGTGTCTCGGAAGCAATTTCAAATATTTCAAGT
CCTGACTATCAGGACGAGCATGATTTATTAAGCTCACGTGACTTATCAGCAGCAATGGCA
ATTAGTGATCCAAGTGATTCTGATTCAACGCTCATTGTTGATCAAGCAAAGAAAGAAAAG
GAACAAAAAGCTGTGATTCAAATGAATACGAAGACGACAACGACAACGAACGAAAGCTTT
AAATGTAATATTGCCAATGATGTTTTGAAAGAAATAGACGAAGAAGTTGCAACAACTTTT
ACCAATGAAACAATTACACAATCAGTATCAGAACATCAGGAAATTATTCGAGGTTCATCA
CCTATTTCAGATGATGGTTCAGATGTTGACTCACTTCATTCATTCCACTATTCTCCAAAA
GCAGTTGATTTGCCAAGTGCTGTGCGACTTGCAAAACGACTCTTTACTCTTGATGGTTTT
AAGAAAAGTGACGTTTCTAGACATTTAAGTAAAAATAACGAATTTAGTCGAGCAGTAGCC
GATGAGTATTTAAAATACTTTCAATTTGAGAAATTAACACTTGACGAAGCACTCCGACTT
TTTCTTAAACAATTTTCACTTTCTGGAGAAACACAAGAACGTGAACGCGTATTGGTACAT
TTTTCAAAAAGATATCTTGACTGCAACCCTGGAACATTCAACTCTCAAGATGCCGTACAC
ACTTTAACGTGTGCTATTATGTTGTTAAACACTGATCTTCATGGACAAAATATTGGCCGT
AAAATGACTTGCTCAGAATTTATAGAAAACCTAAGTGAACTAAATGATGGTGACAATTTT
CCAAAAGATGTCTTGAAGCATTTATATCAAGCAATAAAAGGCAATCCATTGGAATGGGCT
CTCGATGATGAACCGACTGATGCAAATCAAAAAACGAATCGTCAAGAGGGTAATAGTCTA
ACAGGTCCGCCAGTTGGTAACAATCCATTCCTTGATATTTCACAAAATGTAGCGACTGTT
GAATACAAGAAGGGCTATGTGATGCGAAAGTGCTGCTTCGATTCAAACAACAAAAAAACT
CCATTTGGTAAACGATCGTGGAAAATGTTTTATTGTACATTAAGGGACCCACTTGTAATG
TATTTGCACAAAGATGAAAGAGGATTTCATAAAAATCAACTTTCTGATAACGTTCATAAT
GCAATAAGAATACACCATGCGTTAGCAACCAAAGCTTCTGATTACACCAAAAAGCAACAC
GTCTTTCGTCTTCAAACATCTGATCAATCAGAATATTTGTTTCAAACAAGTGACTCGAAG
GAGCTTCAGTCATGGATTGACACAATAAATTTCGTGTGTGCCTCCTTTTCAGCACCAGCT
TTAGAAGGTGGTGTTGGTAGTCAAAAACGATTTCAACGTCCTTTATTACCATGTTCTCAA
ACAAGACTTATGCTCCGTGACCAATTAGCATCACATGAGGAACAAGTTACAAAATTAGAG
AATTCGTTAGCTGAACATAAACAAGGACAAACAGTGCCAATAAAGGGATTAGCTTTACAA
AACTATCGCGAAAAAGAGGCATATTTGCAATATGAATTAAAGCGATATAAAACCTATGTG
TATCTTTTGAGTTCGCATTTAAACTCAAATCAAACAGATCTTATTAATATAATTATAAGC
AGTGAAAGCACAACGACGAATGCGTCATCTAATTCAGTGTCATCGCCAACTGGAAATTCA
GGCGAAGAGGATGAATTAAGATCGTTGAATTCTCATGGAACTAACAGGAAGGATAAATTC
AAGTCATAG
>g3982.t1 Gene=g3982 Length=1202
MSFIEAGDVILKVNGTDVHRFSTKEVLKCLRLSDDPVTLELKRDPNIKDHVRKYLASNSS
HQDIGISSPSSPIINNISSQYGRGHRISSSDSSATCRKSRIPVNNTRIPSLSAPQSPQAI
KPRYLSHIPVSNGQTSSPTTVAPKKQNPRFEAYMMTGDLILNLSRTSQSSNLIAPAQVKK
STMDSLRDSPMRSLKRKNGIAPKAIYDSSPSESSSASVSELGSYEICENNYHDSNIDESR
RISKLGRYAGNSNTKNESLDEEEEQLITIEESNNPSSCGDERKLQYNLSKGCANNISSSS
STSSPTNTNSSNSSTNNNSYDGGGDDRCSNKNNQGLNSLQHKKSKIYTVLHNEEMHQDNL
QQHHQQKQDNNLNIRKEMTPSASMSSTTTSSASTTINRSETLLTPNLDVSRSVPTSPTSI
STPLLDANKRRENVCSVPTSPECIQQMQESTSMRHNSNNVQNHQNGVSLRKCDASGFRTS
RSEDQLQHSQCEGLMGNAIPIDIDEDINSSLNTLLDTRHDSEDSQNSNRDRIVWTYNAPV
MQNSINNQTQGVISPTSSSISTSPQHTDSPASPTSVSSSVMSSSGSKGNGINNTNGSAGQ
NIMFLSGEQSVSEAISNISSPDYQDEHDLLSSRDLSAAMAISDPSDSDSTLIVDQAKKEK
EQKAVIQMNTKTTTTTNESFKCNIANDVLKEIDEEVATTFTNETITQSVSEHQEIIRGSS
PISDDGSDVDSLHSFHYSPKAVDLPSAVRLAKRLFTLDGFKKSDVSRHLSKNNEFSRAVA
DEYLKYFQFEKLTLDEALRLFLKQFSLSGETQERERVLVHFSKRYLDCNPGTFNSQDAVH
TLTCAIMLLNTDLHGQNIGRKMTCSEFIENLSELNDGDNFPKDVLKHLYQAIKGNPLEWA
LDDEPTDANQKTNRQEGNSLTGPPVGNNPFLDISQNVATVEYKKGYVMRKCCFDSNNKKT
PFGKRSWKMFYCTLRDPLVMYLHKDERGFHKNQLSDNVHNAIRIHHALATKASDYTKKQH
VFRLQTSDQSEYLFQTSDSKELQSWIDTINFVCASFSAPALEGGVGSQKRFQRPLLPCSQ
TRLMLRDQLASHEEQVTKLENSLAEHKQGQTVPIKGLALQNYREKEAYLQYELKRYKTYV
YLLSSHLNSNQTDLINIIISSESTTTNASSNSVSSPTGNSGEEDELRSLNSHGTNRKDKF
KS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 18 | g3982.t1 | CDD | cd00992 | PDZ_signaling | 4 | 42 | 3.90766E-6 |
| 17 | g3982.t1 | CDD | cd00171 | Sec7 | 728 | 897 | 2.05383E-66 |
| 19 | g3982.t1 | CDD | cd13295 | PH_EFA6 | 940 | 1061 | 3.12634E-73 |
| 16 | g3982.t1 | Coils | Coil | Coil | 1082 | 1109 | - |
| 15 | g3982.t1 | Gene3D | G3DSA:2.30.42.10 | - | 2 | 61 | 2.8E-7 |
| 14 | g3982.t1 | Gene3D | G3DSA:1.10.1000.11 | - | 789 | 910 | 2.3E-42 |
| 13 | g3982.t1 | Gene3D | G3DSA:2.30.29.30 | - | 934 | 1060 | 3.2E-31 |
| 24 | g3982.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 176 | 214 | - |
| 26 | g3982.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 295 | 323 | - |
| 29 | g3982.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 379 | 419 | - |
| 23 | g3982.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 551 | 587 | - |
| 27 | g3982.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 906 | 926 | - |
| 28 | g3982.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 911 | 926 | - |
| 22 | g3982.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1165 | 1202 | - |
| 25 | g3982.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1165 | 1184 | - |
| 30 | g3982.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1185 | 1202 | - |
| 4 | g3982.t1 | PANTHER | PTHR10663:SF376 | EXCHANGE FACTOR FOR ARF 6, ISOFORM H | 145 | 546 | 1.3E-233 |
| 6 | g3982.t1 | PANTHER | PTHR10663 | GUANYL-NUCLEOTIDE EXCHANGE FACTOR | 145 | 546 | 1.3E-233 |
| 3 | g3982.t1 | PANTHER | PTHR10663:SF376 | EXCHANGE FACTOR FOR ARF 6, ISOFORM H | 545 | 1156 | 1.3E-233 |
| 5 | g3982.t1 | PANTHER | PTHR10663 | GUANYL-NUCLEOTIDE EXCHANGE FACTOR | 545 | 1156 | 1.3E-233 |
| 7 | g3982.t1 | PRINTS | PR00683 | Spectrin pleckstrin homology domain signature | 943 | 962 | 9.2E-9 |
| 8 | g3982.t1 | PRINTS | PR00683 | Spectrin pleckstrin homology domain signature | 1009 | 1026 | 9.2E-9 |
| 9 | g3982.t1 | PRINTS | PR00683 | Spectrin pleckstrin homology domain signature | 1029 | 1047 | 9.2E-9 |
| 2 | g3982.t1 | Pfam | PF01369 | Sec7 domain | 747 | 896 | 5.1E-43 |
| 1 | g3982.t1 | Pfam | PF15410 | Pleckstrin homology domain | 942 | 1054 | 6.2E-45 |
| 31 | g3982.t1 | ProSiteProfiles | PS50106 | PDZ domain profile. | 1 | 45 | 10.999 |
| 32 | g3982.t1 | ProSiteProfiles | PS50190 | SEC7 domain profile. | 729 | 895 | 24.871 |
| 33 | g3982.t1 | ProSiteProfiles | PS50003 | PH domain profile. | 940 | 1054 | 12.325 |
| 21 | g3982.t1 | SMART | SM00222 | sec7_5 | 708 | 897 | 2.1E-54 |
| 20 | g3982.t1 | SMART | SM00233 | PH_update | 941 | 1056 | 3.2E-12 |
| 11 | g3982.t1 | SUPERFAMILY | SSF50156 | PDZ domain-like | 4 | 48 | 1.17E-7 |
| 12 | g3982.t1 | SUPERFAMILY | SSF48425 | Sec7 domain | 736 | 901 | 1.57E-55 |
| 10 | g3982.t1 | SUPERFAMILY | SSF50729 | PH domain-like | 941 | 1057 | 4.29E-30 |
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 |
| GO:0032012 | regulation of ARF protein signal transduction | BP |
| GO:0005085 | guanyl-nucleotide exchange factor activity | MF |
| GO:0005543 | phospholipid binding | MF |
KEGG
Orthology
- This transcript has been annotated with K12494 (PH and SEC7 domain-containing protein)
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.
