Gene loci information

Transcript annotation

  • This transcript has been annotated as Structural maintenance of chromosomes protein 3.

Parent gene

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_1 g12247 g12247.t1 TSS g12247.t1 21983136 21983136
chr_1 g12247 g12247.t1 isoform g12247.t1 21983276 21987095
chr_1 g12247 g12247.t1 exon g12247.t1.exon1 21983276 21983290
chr_1 g12247 g12247.t1 cds g12247.t1.CDS1 21983276 21983290
chr_1 g12247 g12247.t1 exon g12247.t1.exon2 21983387 21983552
chr_1 g12247 g12247.t1 cds g12247.t1.CDS2 21983387 21983552
chr_1 g12247 g12247.t1 exon g12247.t1.exon3 21983607 21986260
chr_1 g12247 g12247.t1 cds g12247.t1.CDS3 21983607 21986260
chr_1 g12247 g12247.t1 exon g12247.t1.exon4 21986323 21986474
chr_1 g12247 g12247.t1 cds g12247.t1.CDS4 21986323 21986474
chr_1 g12247 g12247.t1 exon g12247.t1.exon5 21986534 21987095
chr_1 g12247 g12247.t1 cds g12247.t1.CDS5 21986534 21987095
chr_1 g12247 g12247.t1 TTS g12247.t1 21987266 21987266

Sequences

>g12247.t1 Gene=g12247 Length=3549
ATGCATATTAAACAGGTCATTATTCACGGTTTCAAGTCATATCGCGAACAAACTGTCGTC
GATCCGTTCCATAAAAAGCATAATGTAGTCGTCGGAAGAAATGGTAGTGGCAAGAGCAAT
TTTTTCTCAGCAATTCAATTTGTTCTTAGTGATGAATTTACACATCTACGCCCAGAACAG
CAAATTATATTTGACAATTCTGATAATCGTGTTCCAATTGATAAAGAAGAAATTTCTTTA
AAGCGAGTTATTGGTGCAAAAAAAGATCAATATTTCCTCAACAAAAAGAATGTTCCAAGA
TCAGAAGTTGTCAATTTGCTTGAATCAGCAGGTTTTTCAAATTCAAATCCTTATTACATT
GTAAAACAAGGTAAAATCAATCAAATGGCCACAGCTCCAGATGCACATCGATTGAAATTA
TTAAGAGAAGTTGCTGGTACAAGAGTATATGATGAACGCAAAGAAGAATCCAAGACAATT
TTGAAAGATACAGATTCAAAAGTGGAAAAAATTACAGAATTTTTAAAAACTATCGAAGAA
CGTTTAAAAACTCTTGAAGAAGAAAAGGAAGAATTGAAAGAATATCAAAAATGGGACAAG
CTTCGAAGAATGCTTGAATATATAATTTACGAGACAGAGTTAAAAGAGAATCGTAAACAG
CTTGATGATCTTGAAAATCATCGTAAAAATTCAGGAGATCAGCAAAAGAAACTAACAAAT
GAGATTCAAAAAATACAAGATAAAATCAAAAACATACAGAAGAATCTCAAAGATGCTAAG
AAAGAAGTGACTACTTGTAAAGAAGAACGATCTGTATTAGTTGCTGAACAACAGCAATTG
TTGCGTGAGAAAACTAAATTGGATCTAACAATTAATGATTTGAATGATGAAGTTCAAGGT
GACAATAAGTCAAAAGAAAGAGCAGAACAAGAATTGAAACGACTCGAAATAACTATTGCT
GAAAAAGAAAAGGAATTGAAACAAGTTAAGCCACAATATGAAGAAATGAAACGAAAAGAA
GAAGAGTACAGTCGTGAGTTGGCATTGAAAGAACAGAAGCGCAAAGAACTTTATGCAAAG
CAAGGACGTGGTTCTCAATTTTCATCACGTGAAGAACGAGACAAATGGATTCAAACAGAA
TTAAAATCATTGACTAAACAAATTAAGGATAAAATTTCACATCAAACTAAATTGACAGAG
GACTTGAGACGTGATGCTGCTAAACAAACAGAACTTGAAAAAAAGATTGAAGATTCTTCT
GGTGGAACAGATCAATTACGTCAACAAATTGACGAGCATAATAAAAACTTTTATGAACTG
AAGAAAACAAAGGACCATGAACAAAGTATTCGAAACGATTTGTGGCGTCAAGAGACTCAA
CTAACTCAAACTTTAACATCACACAAAGATGAACTCTCAAAAGCAGATCAAGCTCTTAGA
TCAATGGCAGGCAAACCAATTTTGAATGGTCGTGATTCTGTTCGTAAAGTTCTTGACATG
TTTCAAGAGCGTGGCGGTGAATATGCAAAAATCGCAAATTCTTATTATGGGCCAGTAATC
GAAAATTTCAATTGCGATAAAACAATCTATACAGCTGTGGAAGTAACTGCAGGAAATCGT
CTCTTTCATCATATTGTTGAATCAGATCGTGTTGGTACGCAAATATTGAAGGAAATGAAT
AAACAAAAGCTTCCAGGTGAAGTCACATTTATGCCATTGAATCGTCTTCAATTTAAAATT
CATGATTATCCAGATAACAATGATTCAATTCCAATGATTAGTAAATTGAAATATGAAGAA
AAGTATGATAAAGCACTTCGATATATTTTTGGAAAGACACTCATTTGTCGTAATCTTGAG
CGTGCTACAGAATTAGCTAAAACAACTGGTTTAGATTGTGTAACGCTAGAAGGTGATCAA
GTTTCATCAAAAGGATGCTTAACTGGTGGTTTCTTCAACACTTCACGTTCTCGTCTTGAA
ATGCAAAAGAAACGTTCTGAATATATGCAAATGATTCAAGATTTTGAAGATCAACTTCAT
GAAATTCGTACTAAATTGAAAGCTACAGAGCAACGGATTAATGAGATTGTAAGTGACATG
CAAAAGACGGAAACAAAACTTGGAAAATCGAAAGATGCATTTGAAAAAGTTCAAGCTGAC
ATTCGTTTAATGAAAGAAGAATTAACTCGTATAGAACGCTATCGATCACCAAAAGAACGT
TCACTAGCTCAATGCAAATCTAGTTTAGAAGCAATGAACACTACAAAATCGGGCTTAGAA
AGTGAACTTCATCAAGAATTAATGGCACAACTATCAGTTCAAGATCAACAAGAAGTTGAT
CAATTAAATGATGATATTCGTCGTTTGAATCAAGAAAATAAAGCAGCATTCAGTTCTAGA
ATGAGTTTGGAAGTTACTAAAAATAAACTTGAAAACCTACTTACTAACAATCTCATTCGT
CGTCGTGATGAATTGCAACAAGCATTGCAAGAAATTTCAGTTGAAGATCGTAAGCGTCAA
TTAACAAATTGTCAAGCAGATTTGACAGCTGTCGCTGAACGAATTCGCAAAGTGAATACA
GATGTTGAAGATATGGATCGTAAGTTTGATAAAGCAGCAAAAACTCAAAAATCATTACAA
AAAGAATTAGAAGCATTAGTGCAAAAGGAAAAAGATCTGCAAGATAAAATTGATCAAGAT
TCAAAATTAACTGAGAAATGGGCAGCAAAAGAAAATTTATTCCGTCAAAAGATTGATGAA
AGCACTGAGAAAATTGCCAATCTCGGAGCACTGCCACAAGTAGAACCACAATATATGAAA
ATGTCATTGAAAAAACTATTTCAAGAATTGGAAAAAGCGAATCATCATTTGAAAAAGTAC
AATCATGTTAACAAGAAAGCTCTTGATCAATTCTTGAGCTTCTCTGAACAAAAGGAGAAA
TTGTATAAGCGCAAAGAAGAGTTGGATATTGGTAGTGAAAAAATTAAAGAATTGATGCAT
AATCTTGAGATGCGAAAAGTAGAAGCAATTCAAAATACTTTCAAACAAGTTGCTACTAAT
TTCACAAAAGTATTTAAGAAACTTGTACCACATGGTAGTGGTCATTTAGTTTTGCGAACG
TCAAAAGATCATGAAGAGAAAGGTGATGGAGAAATTTCAACATCGGATGATTTCACTGGT
ATTGGTATTCGAGTATCGTTTACGGGAAGTGATTCAGAAATGCGTGAAATGAATCAACTT
AGTGGAGGACAAAAATCACTTGTTGCGCTTGCATTGATTTTTGCTATCCAAAAATGTGAT
CCTGCCCCTTTCTATTTGTTTGACGAAATTGACCAAGCTCTTGATGCACAACATCGAAAA
GCAGTTGCTGATATGATTCATGAATTAAGTGACAATGCACAATTCATTACAACAACCTTC
AGACCAGAGTTACTCGAGAAAGCTCACAAATTTTATGGTGTGAGATTTCGAAATAAAGTC
AGCCATGTTGATTGTGTGACAAGAGAAATTGCAAGAGATTTCGTTGAAGATGATAACACT
CATGGTTAA

>g12247.t1 Gene=g12247 Length=1182
MHIKQVIIHGFKSYREQTVVDPFHKKHNVVVGRNGSGKSNFFSAIQFVLSDEFTHLRPEQ
QIIFDNSDNRVPIDKEEISLKRVIGAKKDQYFLNKKNVPRSEVVNLLESAGFSNSNPYYI
VKQGKINQMATAPDAHRLKLLREVAGTRVYDERKEESKTILKDTDSKVEKITEFLKTIEE
RLKTLEEEKEELKEYQKWDKLRRMLEYIIYETELKENRKQLDDLENHRKNSGDQQKKLTN
EIQKIQDKIKNIQKNLKDAKKEVTTCKEERSVLVAEQQQLLREKTKLDLTINDLNDEVQG
DNKSKERAEQELKRLEITIAEKEKELKQVKPQYEEMKRKEEEYSRELALKEQKRKELYAK
QGRGSQFSSREERDKWIQTELKSLTKQIKDKISHQTKLTEDLRRDAAKQTELEKKIEDSS
GGTDQLRQQIDEHNKNFYELKKTKDHEQSIRNDLWRQETQLTQTLTSHKDELSKADQALR
SMAGKPILNGRDSVRKVLDMFQERGGEYAKIANSYYGPVIENFNCDKTIYTAVEVTAGNR
LFHHIVESDRVGTQILKEMNKQKLPGEVTFMPLNRLQFKIHDYPDNNDSIPMISKLKYEE
KYDKALRYIFGKTLICRNLERATELAKTTGLDCVTLEGDQVSSKGCLTGGFFNTSRSRLE
MQKKRSEYMQMIQDFEDQLHEIRTKLKATEQRINEIVSDMQKTETKLGKSKDAFEKVQAD
IRLMKEELTRIERYRSPKERSLAQCKSSLEAMNTTKSGLESELHQELMAQLSVQDQQEVD
QLNDDIRRLNQENKAAFSSRMSLEVTKNKLENLLTNNLIRRRDELQQALQEISVEDRKRQ
LTNCQADLTAVAERIRKVNTDVEDMDRKFDKAAKTQKSLQKELEALVQKEKDLQDKIDQD
SKLTEKWAAKENLFRQKIDESTEKIANLGALPQVEPQYMKMSLKKLFQELEKANHHLKKY
NHVNKKALDQFLSFSEQKEKLYKRKEELDIGSEKIKELMHNLEMRKVEAIQNTFKQVATN
FTKVFKKLVPHGSGHLVLRTSKDHEEKGDGEISTSDDFTGIGIRVSFTGSDSEMREMNQL
SGGQKSLVALALIFAIQKCDPAPFYLFDEIDQALDAQHRKAVADMIHELSDNAQFITTTF
RPELLEKAHKFYGVRFRNKVSHVDCVTREIARDFVEDDNTHG

Protein features from InterProScan

Transcript Database ID Name Start End E.value
22 g12247.t1 CDD cd03272 ABC_SMC3_euk 3 140 1.57341E-74
15 g12247.t1 Coils Coil Coil 168 195 -
18 g12247.t1 Coils Coil Coil 207 269 -
14 g12247.t1 Coils Coil Coil 277 360 -
16 g12247.t1 Coils Coil Coil 658 706 -
19 g12247.t1 Coils Coil Coil 772 799 -
20 g12247.t1 Coils Coil Coil 815 835 -
13 g12247.t1 Coils Coil Coil 862 899 -
17 g12247.t1 Coils Coil Coil 943 963 -
10 g12247.t1 Gene3D G3DSA:3.40.50.300 - 1 224 1.8E-38
11 g12247.t1 Gene3D G3DSA:1.20.1060.20 - 512 660 3.7E-28
12 g12247.t1 Gene3D G3DSA:3.30.70.1620 - 574 653 3.7E-28
9 g12247.t1 Gene3D G3DSA:3.40.50.300 - 1003 1181 1.9E-53
4 g12247.t1 PANTHER PTHR43977 STRUCTURAL MAINTENANCE OF CHROMOSOMES PROTEIN 3 1 1167 0.0
5 g12247.t1 PANTHER PTHR43977:SF1 STRUCTURAL MAINTENANCE OF CHROMOSOMES PROTEIN 3 1 1167 0.0
21 g12247.t1 PIRSF PIRSF005719 SMC 1 1172 4.2E-147
3 g12247.t1 Pfam PF02463 RecF/RecN/SMC N terminal domain 2 60 2.8E-18
2 g12247.t1 Pfam PF02463 RecF/RecN/SMC N terminal domain 61 1161 2.4E-22
1 g12247.t1 Pfam PF06470 SMC proteins Flexible Hinge Domain 514 626 2.7E-24
23 g12247.t1 SMART SM00968 SMC_hinge_2 513 626 6.2E-29
6 g12247.t1 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 1 1154 3.11E-40
8 g12247.t1 SUPERFAMILY SSF75553 Smc hinge domain 462 670 6.54E-44
7 g12247.t1 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 816 1163 4.72E-32

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:0016887 ATP hydrolysis activity MF

KEGG

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.

Raw TPM values