General information for g3117.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Structural maintenance of chromosomes protein 1A.
Parent gene
- The parent gene g3117 is located on chr_3: 22913836..22914697 (- 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 | g3117 | g3117.t1 | TTS | g3117.t1 | 22910835 | 22910835 |
| chr_3 | g3117 | g3117.t1 | isoform | g3117.t1 | 22910908 | 22914697 |
| chr_3 | g3117 | g3117.t1 | exon | g3117.t1.exon1 | 22910908 | 22912825 |
| chr_3 | g3117 | g3117.t1 | cds | g3117.t1.CDS1 | 22910908 | 22912825 |
| chr_3 | g3117 | g3117.t1 | exon | g3117.t1.exon2 | 22912882 | 22914526 |
| chr_3 | g3117 | g3117.t1 | cds | g3117.t1.CDS2 | 22912882 | 22914526 |
| chr_3 | g3117 | g3117.t1 | exon | g3117.t1.exon3 | 22914586 | 22914697 |
| chr_3 | g3117 | g3117.t1 | cds | g3117.t1.CDS3 | 22914586 | 22914697 |
| chr_3 | g3117 | g3117.t1 | TSS | g3117.t1 | 22914819 | 22914819 |
Sequences
>g3117.t1 Gene=g3117 Length=3675
ATGGCTGCGTTTTTGGAATTCATTGAAATCGAGAATTTCAAGAGTTATAAAGGAAAAGTT
GTTATTGGCCCATTGAAAAAATTTACTGCAGTTATTGGACCTAATGGAAGCGGTAAATCT
AATTTCATGGATGCAATATCTTTTGTAATGGGTGAAAAAACAACTTCCCTTCGTGTAAAG
AAACTTGGTGATTTGATTCATGGAGCTTCAATCTCTCGTCCTATATCAAGACATGCTTCA
GTTACAGCTAAATTTAAATTACCCGATGGAACTGATATGAGTTTCCAACGAGCTGTATCT
GGATCATCATCAGATTATAAAATTAACAATCAAAATGTTTCTAGCAACACATATTTATCT
GAACTCGAGAAAATGGGCATTAATGTAAAAGCAAAAAACTTTTTAGTGTTTCAAGGTGCT
GTTGAGAATATTGCTATGAAAAATGCAAAAGAACGCACACAATTATTTGAAGAAATCAGT
ACATCTGGATTATTGAAAGAAGAATACAACACTCTTAAACAAGAAATGATGAGTGCAGAA
GAAGAAACACAATTTACTTATCAGAAAAAGAAAGGTGTTGCTGCAGAGAGAAAGGAAGCA
AAATTGGAAAAACAAGAAGCTGATCGTTATTCACGTTTGCGAGAAGAATATACAGAGAAG
CAAATAATATATCAACTCTACAAGCTGTATCACAATGAAAAGGACATTCAAAGATACAAT
GACGAATTAAAATCAAAACAACAAGAATCAAAGAAGTTGGAAGATAAAAAGAGCCGTGCT
GATGAAGTATTACGAGATAAAAAGAAAGAAGGTGGAAAAATTAGTAGAGATTTGGCTAAA
ATTGAGCAAGACATTCGTGAAGCTGAAAGTGACATGAACAAGAAGCATCCACTTTATATC
AAAGCTAAAGAAAAAGTTGCACATACGCAAAAGAAACTCGATGGAGCAATGAAAACTCTT
GAGCAAGCAAGAAAAGCAGATGAAGCTCATCAATCCGACATTCGTAAATTGGAAGATGAA
TTACAGAGCATTCTTGATAAAAAGAAATCATTTGAATCAGAAATCGCAATGGACTCGAAG
AAACGCGGTAGCAATGTTCATCTTGAGCAAGATTTTCTTAAGGAATATGATCGTTTGAAG
CAACAAGCTGATTTAAAATCTGCAAAATATCTCGCTAAACTGGATAGTATTAATCGTGAG
CAAAAATCTGAACAAGATCTGCTTGATTCTGAAATGAATAAGAAAACTCAATTAGAAGAA
ACGCTCAAGAAATACAGTAGTGAGAAAGAAGAAGCAATAAAACGTAAAGAAAAACTGTAT
GAGCATATTAGATCGAGTGAGGCACAACTTGCAGAGCAAATGCGTAATAAAGAAGAATTG
AGTAAAGATGTTGGATGCTCAAAAGAACGTCAAATGGAGTTACAGCGTGAAATTTATGAT
GTAAATGAACAGCTTGGAGATGCCAAAAATGATAAACATGAAGATGCACGACGTAAAAAG
AAGCAAGAAGTTGTCGAAATGTTTAAGCGCGAAATTCCTGGCGTTTATGATCGAATGATT
AACATGTGTCAACCAACAAATAAACGCTACAACGTAGCGGTTACTAAAGTGCTTGGAAAA
TATATGGAAGCTATCATTGTTGACACTGAAAAAACTGCTCGAAAATGCATTCAAATGTTG
AAAGATCAAAAGCTTGAAGTTGAAACTTTTCTACCATTGGATTACCTACAAGCCAAGCCT
TTGAAAGAGAGATTAAGAACTATTCAAAATCCAAAAGGCGTCCATTTGATCTATGATGTT
TTGCGATTTGATCCACCGGATATTGAGAGAGCTGTACTTTTTGCAACAAACAATGCACTT
GTTTGTGAATCACCAGAAGATGCAATGAAAGTTGCATATGAAATGGATAGAAGTCGCTAT
GACGCTCTTGCTCTAGACGGTACATTTTATCAAAAATCTGGTATTATTTCTGGCGGCTCT
CATGATTTAGCTCGAAAAGCAAAACGATGGGATGAGAAACACATGAATCAATTGAAATTA
CAAAAGGAACGACTCAATGAAGAATTGAAAGAGGTCACAAAGAAAACTCGCAAACAGAGT
GAATTAACTACCATTGAGTCTCAGATTAAGGGCATTGAAAATCGTTTAAGATACAGTCGC
AATGATTTAGCAAATAGCGACAAAGCTATTCGAGATTTTGAACGTTCAATGAATGATTTG
AGGAAAGAACTTGATTTGATTGGACCTAATATTAGCGAAATTGAACGTCGTATGATGAGT
CGAGATGCTAAAATTCAAGAAATTAAGGGCAAGATGAACACAGTCGAAGACGAATATTTT
AAAAATTTCTGCAAGAAAATTGGTGTTGCAAACATTCGTCAATATGAAGATCGTGAATTA
GTTTTGCAACAAGAACGCGATAAGAAACTTGCTGAATTTGAGCAGCAAATTGATCGTATC
AACACAAACCTTGATTTTGAACGCAGCAAAGATACTTCAAAGAATGTTCAACGTTGGGAA
CGTACTGTTCAAGACGATGAAGATTCTTTGGAGTCATTAAAGCAAGCTGAAAAGAGACAT
CGTGATGACATTGAGAAAGATAAAGAGAAAATTGAAAGTCTTAAACTAGAAAAACAAAAT
AAGAAAAAACTCGTTGATGAGATGGAAGAGGACACTGCAAAAGCACGAAGAGATGTGGCA
TCATTAGCAAAAGATATTGCTACAATATCACATCAGATTTCATCTATTGAGAATAAAATT
GACTCAAAGAGAAACGATCGTTTAAACATGTTGAGGCAGTGTAAAATGGACGATATTCAA
ATACCCATGCTCGGTCATTCGAGCTTAGATGATATTTTAGCAGAACAAGAAACAAATGAC
CCTTCATCATCAGCAACAATGTCAAACAGCATGTTATCAAAAATCAATGAAATTCAACTT
GATTACAGAAGTATTCCGAGAAATTTGAAAGATATTGATGAACCTGATCAAGTGAAAAAA
TCAGGTGATGGTTTGAATAAAGAACTTCAACAAAAACTAGATACTCTTGAGAAAATTCAA
ACGCCTAATATGAAAGCATTACAAAAACTTGATGCTGTTGCAGAAAAGATTCAATCTACA
AACGAAGAATTTGAAAATGCTAAGAAAAAGGCGAAGAAAGCAAAAGCTGCATTTGAAAAA
GTTAAAAATGAACGAATTGCTCGATTCAACAAGTGTCTAAATCACATTTCGGAAGCAATT
GATGGTATTTACAAAGCACTCTCGCGCAATGATGCTGCACAAGCTTTTCTTAATCCCGAT
AATCCAGAAGAATCTTATCTCGATGGTATCAACTATAATTGCGTTGCACCAGGTAAACGT
TTTCAACCGATGAGCAATCTTAGTGGTGGTGAAAAGACAATTGCAGCTTTAGCATTACTT
TTTGCTATTCATAGCTATCAGCCTGCTCCGTTTTTTGTACTTGATGAGATTGATGCCGCT
CTTGATAATACTAACATTGGAAAAGTTGCAAAATATATTCGTGAACAGCAAGATCTTCAG
ACAATTGTCATTTCATTAAAAGAAGAATTTTATGGTCATGCTGATATTTTAATTGGTATT
ACACCACAACCTGCCGATTGTTTGGTCTCACGCACATACCTTTATGATTTGACTAACTTT
GAGAGTAACGATTAA
>g3117.t1 Gene=g3117 Length=1224
MAAFLEFIEIENFKSYKGKVVIGPLKKFTAVIGPNGSGKSNFMDAISFVMGEKTTSLRVK
KLGDLIHGASISRPISRHASVTAKFKLPDGTDMSFQRAVSGSSSDYKINNQNVSSNTYLS
ELEKMGINVKAKNFLVFQGAVENIAMKNAKERTQLFEEISTSGLLKEEYNTLKQEMMSAE
EETQFTYQKKKGVAAERKEAKLEKQEADRYSRLREEYTEKQIIYQLYKLYHNEKDIQRYN
DELKSKQQESKKLEDKKSRADEVLRDKKKEGGKISRDLAKIEQDIREAESDMNKKHPLYI
KAKEKVAHTQKKLDGAMKTLEQARKADEAHQSDIRKLEDELQSILDKKKSFESEIAMDSK
KRGSNVHLEQDFLKEYDRLKQQADLKSAKYLAKLDSINREQKSEQDLLDSEMNKKTQLEE
TLKKYSSEKEEAIKRKEKLYEHIRSSEAQLAEQMRNKEELSKDVGCSKERQMELQREIYD
VNEQLGDAKNDKHEDARRKKKQEVVEMFKREIPGVYDRMINMCQPTNKRYNVAVTKVLGK
YMEAIIVDTEKTARKCIQMLKDQKLEVETFLPLDYLQAKPLKERLRTIQNPKGVHLIYDV
LRFDPPDIERAVLFATNNALVCESPEDAMKVAYEMDRSRYDALALDGTFYQKSGIISGGS
HDLARKAKRWDEKHMNQLKLQKERLNEELKEVTKKTRKQSELTTIESQIKGIENRLRYSR
NDLANSDKAIRDFERSMNDLRKELDLIGPNISEIERRMMSRDAKIQEIKGKMNTVEDEYF
KNFCKKIGVANIRQYEDRELVLQQERDKKLAEFEQQIDRINTNLDFERSKDTSKNVQRWE
RTVQDDEDSLESLKQAEKRHRDDIEKDKEKIESLKLEKQNKKKLVDEMEEDTAKARRDVA
SLAKDIATISHQISSIENKIDSKRNDRLNMLRQCKMDDIQIPMLGHSSLDDILAEQETND
PSSSATMSNSMLSKINEIQLDYRSIPRNLKDIDEPDQVKKSGDGLNKELQQKLDTLEKIQ
TPNMKALQKLDAVAEKIQSTNEEFENAKKKAKKAKAAFEKVKNERIARFNKCLNHISEAI
DGIYKALSRNDAAQAFLNPDNPEESYLDGINYNCVAPGKRFQPMSNLSGGEKTIAALALL
FAIHSYQPAPFFVLDEIDAALDNTNIGKVAKYIREQQDLQTIVISLKEEFYGHADILIGI
TPQPADCLVSRTYLYDLTNFESND
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 22 | g3117.t1 | CDD | cd03275 | ABC_SMC1_euk | 5 | 149 | 5.24524E-74 |
| 21 | g3117.t1 | CDD | cd03275 | ABC_SMC1_euk | 1116 | 1217 | 2.46893E-58 |
| 16 | g3117.t1 | Coils | Coil | Coil | 162 | 182 | - |
| 10 | g3117.t1 | Coils | Coil | Coil | 200 | 220 | - |
| 18 | g3117.t1 | Coils | Coil | Coil | 229 | 270 | - |
| 13 | g3117.t1 | Coils | Coil | Coil | 306 | 354 | - |
| 14 | g3117.t1 | Coils | Coil | Coil | 408 | 463 | - |
| 17 | g3117.t1 | Coils | Coil | Coil | 668 | 702 | - |
| 11 | g3117.t1 | Coils | Coil | Coil | 723 | 743 | - |
| 12 | g3117.t1 | Coils | Coil | Coil | 810 | 830 | - |
| 15 | g3117.t1 | Coils | Coil | Coil | 836 | 905 | - |
| 19 | g3117.t1 | Coils | Coil | Coil | 1023 | 1064 | - |
| 6 | g3117.t1 | Gene3D | G3DSA:3.40.50.300 | - | 5 | 208 | 2.2E-40 |
| 8 | g3117.t1 | Gene3D | G3DSA:1.20.1060.20 | - | 500 | 573 | 1.4E-32 |
| 9 | g3117.t1 | Gene3D | G3DSA:3.30.70.1620 | - | 574 | 662 | 1.4E-32 |
| 7 | g3117.t1 | Gene3D | G3DSA:3.40.50.300 | - | 940 | 1222 | 5.7E-44 |
| 24 | g3117.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 245 | 269 | - |
| 25 | g3117.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 844 | 863 | - |
| 3 | g3117.t1 | PANTHER | PTHR18937 | STRUCTURAL MAINTENANCE OF CHROMOSOMES SMC FAMILY MEMBER | 5 | 1221 | 0.0 |
| 20 | g3117.t1 | PIRSF | PIRSF005719 | SMC | 3 | 1212 | 1.0E-214 |
| 2 | g3117.t1 | Pfam | PF02463 | RecF/RecN/SMC N terminal domain | 5 | 1203 | 4.5E-56 |
| 1 | g3117.t1 | Pfam | PF06470 | SMC proteins Flexible Hinge Domain | 513 | 631 | 1.6E-18 |
| 23 | g3117.t1 | SMART | SM00968 | SMC_hinge_2 | 513 | 632 | 1.9E-26 |
| 4 | g3117.t1 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 8 | 1200 | 5.95E-41 |
| 5 | g3117.t1 | SUPERFAMILY | SSF75553 | Smc hinge domain | 474 | 682 | 8.63E-45 |
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:0005524 | ATP binding | MF |
| GO:0005515 | protein binding | MF |
| GO:0051276 | chromosome organization | BP |
| GO:0005694 | chromosome | CC |
| GO:0007064 | mitotic sister chromatid cohesion | BP |
| GO:0016887 | ATP hydrolysis activity | MF |
| GO:0008278 | cohesin complex | CC |
KEGG
Orthology
- This transcript has been annotated with K06636 (structural maintenance of chromosome 1)
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.
