General information for g2860.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as IQ motif and SEC7 domain-containing protein 1.
Parent gene
- The parent gene g2860 is located on chr_3: 20731829..20732803 (- 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 | g2860 | g2860.t3 | TTS | g2860.t3 | 20723154 | 20723154 |
| chr_3 | g2860 | g2860.t3 | isoform | g2860.t3 | 20723641 | 20726487 |
| chr_3 | g2860 | g2860.t3 | exon | g2860.t3.exon1 | 20723641 | 20724726 |
| chr_3 | g2860 | g2860.t3 | cds | g2860.t3.CDS1 | 20724536 | 20724726 |
| chr_3 | g2860 | g2860.t3 | exon | g2860.t3.exon2 | 20724791 | 20725126 |
| chr_3 | g2860 | g2860.t3 | cds | g2860.t3.CDS2 | 20724791 | 20725126 |
| chr_3 | g2860 | g2860.t3 | exon | g2860.t3.exon3 | 20725181 | 20725358 |
| chr_3 | g2860 | g2860.t3 | cds | g2860.t3.CDS3 | 20725181 | 20725358 |
| chr_3 | g2860 | g2860.t3 | exon | g2860.t3.exon4 | 20725460 | 20725549 |
| chr_3 | g2860 | g2860.t3 | cds | g2860.t3.CDS4 | 20725460 | 20725549 |
| chr_3 | g2860 | g2860.t3 | exon | g2860.t3.exon5 | 20725624 | 20725833 |
| chr_3 | g2860 | g2860.t3 | cds | g2860.t3.CDS5 | 20725624 | 20725833 |
| chr_3 | g2860 | g2860.t3 | exon | g2860.t3.exon6 | 20725916 | 20726487 |
| chr_3 | g2860 | g2860.t3 | cds | g2860.t3.CDS6 | 20725916 | 20726422 |
| chr_3 | g2860 | g2860.t3 | TSS | g2860.t3 | NA | NA |
Sequences
>g2860.t3 Gene=g2860 Length=2472
CAAACAATGGAAGTCTACAGTCAGTTCAGTCATCGGGTAGTGAGAGTAGTGCATCATTGG
AGAAAATGCATTATGAAAACCTAACAGAGCGAGGAACATCGCCACTTTGGAAACACAAAA
ACGATGATGATGATCAATCACATCGAAAAAACGCTGCAAATGAGAATTACAAATATTCTG
AAATCATACGTAAACGAAAATACCGTCTTGGTCTAAATTTATTCAATAAGAAACCAGAGA
AAGGCATTGAATTTTTGGTGAAAAATGGTTTTCTCGATAATACACATTCAGGTGTTGCCA
AATTCCTGATCTCACGAAAAGGTTTATCGCGTCAAATGATTGGCGAATATTTGGGAATGA
TTCAGAATTCTTTCAATATGGCAGTTCTTGATGCATTCTGTGATGAATTGGATTTAAGTG
GTATGGCTGTGGATGTTGCATTACGAAAATTCCAAAGTTATTTTCGAATGCCAGGCGAGG
CACAAAAAATTGAAAGGCTTATACAAGCATTTAGTCATCGCTATGCAAAATGTAATCCGG
AAGTTGTGGGAAAACTTCGCTCATCGGAAACTATATTCATACTAGCTTTTGCAATTATAA
TGCTAAATACTGATTTACATACACAAGCACTAAAACCAGAAAAGCGAATGCGATGTGAAG
ATTTTATAAAAAATTTACGCGGTGTTGATGATTGTTCGGACATTGATAGAGATATTCTTG
TGGGAATATATGAGCGAATTAAAGTGAACGAATTCAAACCAGCATCAGATCATGTGACTC
AAGTTATGAAGGTACAAGCGACAATCATTGGTAAAAAACCCAATTTGGCATTGCCACATC
GACGCTTAGTTTGTTATTGTCGGCTATATGAAGTGCCGGATTTAAATCGTAAAGAACGGC
CTGGCGTTCATCAACGAGAAGTGTTTCTATTCAACGACATTTTAGTGATCACAAAAATAT
TTAAAAAGATTTCTAAAACTTCCGTGACTTATTCATTCCGTACAAGTTATGCATTACCTG
GAATGGTCGTTACATTATTGAAATCTTCAAATTATCCTCATGCAATACAACTTTCAAATA
GAGTTGATAATAAAGTGCTTATAACATTTAATGCACGAAATGAACATGATAGATGCAAAT
TTGCTCAAGATTTAGAAGAGAGCATCGCTGAAATGGATGAAATGGAACAAATACGAATAG
AGTCAGAATTAGAAAAACAGAAAAATTCGAGGAATTCAAGAAATTCAAAATCTACTTCGA
GTGAACATCATCGTGATAGCGGCTATGCTGAAATTAAACACAAACATAAAACAAAATCAT
CTCCTACAGCAAATCACGCACAAAATAATAAACTTAGCAATTCTCTGTTAAATATCAATG
AACAATTTACCGGTGATAATAAATATGATAAAAATAGACGTGCATCAGTTTGTTCATTAG
ACAGTGGAACATCACTATCGTTTTTATCTTCAAATGGAACAAGAGCTAGTGATAACAATA
ATAATGTCAATAATAAACCTCCAACAACACAAAAATTAATTCTCATGCCAAATTCACCGA
GATCAACAGAGGTCTAAAAACATACGTACACTGATTCTTTAAATATTGTGTATTTGAATA
AGAGATATTTTTATCAACCAAAACAGAAACTGCTACAAACTACTTGAATGTGTGTTATTT
TTTTTATATATCTATAAAAATAGTGATGATAATCATGCACAAATGAAAGGAAAAATTCTT
TTTAAAAGATTATTATAGAATGTAATTTCTCGATATTTACATACTTCACAAAATAACGAA
AACTAAAGAAACTTTTCAAAGATACATAAATAATATATTTTTTGTTCTAGTCGAATAACA
AAATTAATGAAAGAAATTAGTAATGATGAATGAGAAAAAAGATGAAAGTGAGAGCAATTA
CAGTATTTAATATTGATTAAATAATAAAAATGTTAATATGAAACCTACATATTTGAAAGA
CATACTTAGGGGATAAAAAATAAAATCTTGTTCATGTGAATGATAAAAAAATTCTTTTAA
AAAAACTAATCTACGAAAGCAATCACTACCTACAAAACTTTTCCTTTTCATATCTATCTA
TGTGGCCTATAGCTAGTTACAAAAAATGTTTATTAAGTCTATAATATAGAGATTTAAATT
ATTCTGACTGTTATAGTTTTTTCAAATTTGATGACTTGATAGTTTTTTCTTAAAAATAAA
TAAAAATAAAATTGAAACGAAAATTTATTCAATTCTCAACATGTTGCATTTTCAATAATG
TTTCAGAATTCTTTTTTCACATGTATAGCAGGATCACACGTTTAATGTCAATAAAGGAGA
AAAACTTTACATTTTTGCCTAAAGCTATAAAATATAAATGCAAAGCAAGTCGAATAACGT
TTGGAACGAGAATTTTTTCTCATGTTCTCAACGAGTTTCATTTTCAGCAAAAAGGAGCCC
GCTTCAGTTTCA
>g2860.t3 Gene=g2860 Length=503
MHYENLTERGTSPLWKHKNDDDDQSHRKNAANENYKYSEIIRKRKYRLGLNLFNKKPEKG
IEFLVKNGFLDNTHSGVAKFLISRKGLSRQMIGEYLGMIQNSFNMAVLDAFCDELDLSGM
AVDVALRKFQSYFRMPGEAQKIERLIQAFSHRYAKCNPEVVGKLRSSETIFILAFAIIML
NTDLHTQALKPEKRMRCEDFIKNLRGVDDCSDIDRDILVGIYERIKVNEFKPASDHVTQV
MKVQATIIGKKPNLALPHRRLVCYCRLYEVPDLNRKERPGVHQREVFLFNDILVITKIFK
KISKTSVTYSFRTSYALPGMVVTLLKSSNYPHAIQLSNRVDNKVLITFNARNEHDRCKFA
QDLEESIAEMDEMEQIRIESELEKQKNSRNSRNSKSTSSEHHRDSGYAEIKHKHKTKSSP
TANHAQNNKLSNSLLNINEQFTGDNKYDKNRRASVCSLDSGTSLSFLSSNGTRASDNNNN
VNNKPPTTQKLILMPNSPRSTEV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g2860.t3 | CDD | cd00171 | Sec7 | 42 | 230 | 5.26147E-74 |
| 12 | g2860.t3 | CDD | cd13318 | PH_IQSEC | 257 | 385 | 6.94101E-74 |
| 10 | g2860.t3 | Coils | Coil | Coil | 363 | 383 | - |
| 9 | g2860.t3 | Gene3D | G3DSA:1.10.220.20 | - | 22 | 116 | 2.9E-32 |
| 8 | g2860.t3 | Gene3D | G3DSA:1.10.1000.11 | - | 117 | 233 | 7.6E-43 |
| 7 | g2860.t3 | Gene3D | G3DSA:2.30.29.30 | - | 250 | 386 | 8.8E-55 |
| 16 | g2860.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 29 | - |
| 14 | g2860.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 381 | 428 | - |
| 15 | g2860.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 381 | 416 | - |
| 17 | g2860.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 469 | 488 | - |
| 3 | g2860.t3 | PANTHER | PTHR10663:SF342 | FI21420P1 | 21 | 472 | 2.0E-196 |
| 4 | g2860.t3 | PANTHER | PTHR10663 | GUANYL-NUCLEOTIDE EXCHANGE FACTOR | 21 | 472 | 2.0E-196 |
| 1 | g2860.t3 | Pfam | PF01369 | Sec7 domain | 42 | 230 | 2.4E-60 |
| 2 | g2860.t3 | Pfam | PF16453 | PH domain | 250 | 385 | 1.5E-61 |
| 18 | g2860.t3 | ProSiteProfiles | PS50190 | SEC7 domain profile. | 42 | 228 | 38.981 |
| 13 | g2860.t3 | SMART | SM00222 | sec7_5 | 39 | 230 | 8.4E-76 |
| 6 | g2860.t3 | SUPERFAMILY | SSF48425 | Sec7 domain | 42 | 235 | 1.03E-63 |
| 5 | g2860.t3 | SUPERFAMILY | SSF50729 | PH domain-like | 239 | 374 | 5.95E-18 |
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:0032012 | regulation of ARF protein signal transduction | BP |
| GO:0005085 | guanyl-nucleotide exchange factor activity | MF |
KEGG
Orthology
- This transcript has been annotated with K12495 (IQ motif 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.
