Gene loci information

Transcript annotation

  • This transcript has been annotated as Structural maintenance of chromosomes protein 2.

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 g10517 g10517.t1 TTS g10517.t1 10312677 10312677
chr_1 g10517 g10517.t1 isoform g10517.t1 10312743 10316634
chr_1 g10517 g10517.t1 exon g10517.t1.exon1 10312743 10312918
chr_1 g10517 g10517.t1 cds g10517.t1.CDS1 10312743 10312918
chr_1 g10517 g10517.t1 exon g10517.t1.exon2 10312980 10315115
chr_1 g10517 g10517.t1 cds g10517.t1.CDS2 10312980 10315115
chr_1 g10517 g10517.t1 exon g10517.t1.exon3 10315175 10315322
chr_1 g10517 g10517.t1 cds g10517.t1.CDS3 10315175 10315322
chr_1 g10517 g10517.t1 exon g10517.t1.exon4 10315382 10315573
chr_1 g10517 g10517.t1 cds g10517.t1.CDS4 10315382 10315573
chr_1 g10517 g10517.t1 exon g10517.t1.exon5 10315638 10316152
chr_1 g10517 g10517.t1 cds g10517.t1.CDS5 10315638 10316152
chr_1 g10517 g10517.t1 exon g10517.t1.exon6 10316216 10316476
chr_1 g10517 g10517.t1 cds g10517.t1.CDS6 10316216 10316476
chr_1 g10517 g10517.t1 exon g10517.t1.exon7 10316541 10316634
chr_1 g10517 g10517.t1 cds g10517.t1.CDS7 10316541 10316634
chr_1 g10517 g10517.t1 TSS g10517.t1 10316726 10316726

Sequences

>g10517.t1 Gene=g10517 Length=3522
ATGTATATTAAGTCTATAGTTATTGATGGATTTAAATCATATGGTAGAAGAACAGAAGTC
AACGGTTTTGATAGAGAATTTAACGCTATTACAGGTTTAAATGGGACGGGAAAGTCAAAC
ATATTGGATAGTATTTGCTTTGTATTGGGAATATCAAATCTTTCTCATGTGCGCGCCAAT
TCTCTTCAAGATCTTGTTTATAAATCTGGTCAAGCCGGTGTAACAAAAGCGACAGTAACA
ATTAATTTTGACAACACTAACAAAAATCAATGTCCTATTGGATTTGAAAATTGTAAAGAG
ATTTCTGTTGCCCGACAAATTGTTGTAGGCGGCAAGGGAAAATATCTAATCAATGGAAAA
AATGCACAGTATAAACAAATTCAAGATCTTTTCTGCTCTGTACAATTGAATGTGAATAAT
CCAAATTTCTTAATTATGCAAGGAAGAATTACAAAAGTACTGAACATGAAACCACCAGAA
ATTTTATCAATGATAGAAGAAGCTGCTGGAACAAGTATGTATGAAACAAAGCGTGAAAAA
TCAATGGCATTGATTCAAAAGAAAGATGCAAAGCTTGATGAACTCAACTCTTTAATCAGA
GATGATATTCAACCAAAGCTTGATAAATTACGCAAAGACCAACAACAATATGTTGAATAC
CAACGAATATGTCGCGACGTTGAATATCTTACAAGAATTCACATTTCATATAAATATATT
CAGTGTCGTAAGAATATTGAACAATGTGAAACAACAATCACTAATCTTAATGATGACATT
GAAAAAAATAAGGAAACTATTGTCAAAAATAATGACGAAATCAAAGAAATTGAGATTAAA
ATTCAAGAAATTCAAGAGCAACTCAATGCACAATCTGGTGGTGATTTGAAAGAACTTGAA
AATGAACTTGATACGCTTAATCAGCAAGATGCAAAATTAAAAGCCTCTATAAGTGCTACA
AAAGAAGAAATGAATAGTGAACAGCGAAAATTAAAAACGTTAGAAAAAAACATTAAAATT
GATGAAACAGCTCTTTCAAAAAAAGAAGATGAAATGAATCAGATGGGTGACACATTTGAG
CAATTGAAACAAGAAGAGGCAAATGATTTAAAAGCTTTTAAAAATGCTCAAAAACGACTT
GAAGCAGTCAATATGGGTATGGCAATCAATGATGATGGCGAGGCAACTTCATATCAAGAT
CAGCTCATTACTGCAAACTCGAAAATCGCTGATGCCAAAAGTACAATTAAGAAAAGCGAA
ATGGAATTAAAATATTGTAAATCATCATTGGCAAAAAAAGAAAATGAATTAAAAACAAAT
GATTCTGCATACAACAAAGACCAAGATATTATCAAAAATACTGAGAAAGAAATAAAGAAT
CTTGAAAATCAATTAAACAAAATAAATTATCGCGATGGAGAACTTGAAGAGCTCATTCAG
AAAAGAGATGAGTTGACACGTGAATGTCGTGGAATTCGTAACAACATTGATCGTCAAAAT
GGTTCGAAATTTGATTTTCAATATACTGATCCCATTCCGAATTGGGATAAACGTCGAGTT
AAAGGTACAGTTGCAAATCATGTTCGTGTAAAAGATAATAAATATTCACGTGCATTATCG
AGCATTTTGGGAGGAAGTTGGAGAAGTGTGATTACTGACAATGATGAAACAGGCAAATTA
ATTTTAGAACGTGGAAATTTAGTGAATCGAGTGACACTTATTCCTCTCAATAAAATTTCT
GCTCGTACAATTGATCGTAATGTAGTGAATTTAGCACAGAAATTAGTTGGAAAGGAAAAT
GCAATTCCTGCTATCGATCTGATTGAATACGATAAAGAAGTTGAGCCAGCAATGCAATTC
ATTTTTGGAAATGCTTTTGTTTGTAAAGATATGGATGCTGCTAAGACTGTTACATATCAC
AAAGACATTTTGAAAAGATCATATACTCTTGATGGCGATGAAATGAGTCCGGATGGTGCG
TTAAGTGGTGGTGCAGTTCAATCTGGTCCTCCGATACTCGATGAAGTCTCTCGTATTTCA
CAAATGAAAAATGAAATTAATGCAAAGACTAGAGAAATTCAAGAAATTTCAAGACGTATT
GATGGCTTACAAAATGTTGCAACACAATATAAGCAGCTGAAAGACAAACTAGACACAATG
CAGTTACATCTGAAAACTGCTCAAGAACGTATTCAATCGACAACTTTCCAACAAGACCAA
AATGAAATTACTGAACTTAAAGAAAAAGTAAAAACATTAACTACTACCATCGAAGAATGT
CACAATATTTTGGCAACAAATGAGCAAAAAGTAAAAGAACTTACTGAAAAATTAAAAGAT
GCAAAAGGTAATCGAGAACGTGACTTGAAAAATGCTGAAGCTGATCTCAAAAAAGCTAAG
CAAAAACATGAGCAATCTCAGAAAAATTGGAAGAAACGTGAACAGCAATATGAGACAATG
AAGTTAGAAATTGAAGAACTCAAGAAAACAATAGCTGAAGGTAAAGAGCAAGTGATTCAA
ATGCAAACCAAAATAGAAGAATTCCAAAGGAAAATAGAAGAAACTAACAATGATGATGGA
AGTTTGAAAAAACGATCTGAAGAATTGCGAAGAAAAATTAAAGAACAAAAAGATTCAATC
GCTGCACAAAATAAAGAAGTCCGCACTAAAGCTGCACGAAAAGAAAAGCTTCAAAAACAC
ATTCAAGAATTAGAATTAGAAATAAAGAAAAAGGAAAATGAAATTGGTAAAGTGAAAGCT
GATAATGATGAAGGTTACAATAAGATTCAAGCACTTGAAGAAAAGTATCCTTGGATTCCA
GAAGATAAGGAGCACTTTGGTGCAAGAAATACTCGATATGATTACACAAAAGAAGATCCA
CAACAAGCAGGTCAAAAATTGACAAAATTGCAAGAAAATAAGGAAAAGCTCAGTCGAAAT
ATTAATCAAGAAGCAATGATGTTACTTGAAAAGGAAGAAGAACATTATAAAAAAATTATG
GATCGTCGTTCGAAAATTGAAAATGATAAGAAAAATATTCTGGATAGTATAAAGAATATG
GACACTAAAAAGATTGAAAATTTGAAAAAGGCATGGGAAGAAGTTAATAATAATTTTGGC
TCAATTTTTACAACTTTATTGCCTGGAGCACAAGCAAAACTTGATCCTCCAGAAGGACAA
AATTTCTTAAAAGGATTGGAAGTTAAAGTTGGTTTTAATGGCATATGGAAAGAATCTTTG
ACTGAATTAAGTGGTGGACAGAGATCACTTGTTGCACTTTCACTTATTTTGGCGATGCTA
AAGTATAAACCTGCACCTCTATACATTCTTGATGAAGTTGATGCTGCTCTTGATTTATCA
CATACACAAAATATTGGTGGCATGTTAAAAGCTCATTTTAAAAATTCTCAATTTATCATT
GTTTCTCTGAAAGATGGTATGTTCAATAATGCAAATGTTCTTTTTCGCACTAAGTTTGTT
GATGGTGTTTCTGGTGTGATTCGTACAGTTAACAAAAACTAA

>g10517.t1 Gene=g10517 Length=1173
MYIKSIVIDGFKSYGRRTEVNGFDREFNAITGLNGTGKSNILDSICFVLGISNLSHVRAN
SLQDLVYKSGQAGVTKATVTINFDNTNKNQCPIGFENCKEISVARQIVVGGKGKYLINGK
NAQYKQIQDLFCSVQLNVNNPNFLIMQGRITKVLNMKPPEILSMIEEAAGTSMYETKREK
SMALIQKKDAKLDELNSLIRDDIQPKLDKLRKDQQQYVEYQRICRDVEYLTRIHISYKYI
QCRKNIEQCETTITNLNDDIEKNKETIVKNNDEIKEIEIKIQEIQEQLNAQSGGDLKELE
NELDTLNQQDAKLKASISATKEEMNSEQRKLKTLEKNIKIDETALSKKEDEMNQMGDTFE
QLKQEEANDLKAFKNAQKRLEAVNMGMAINDDGEATSYQDQLITANSKIADAKSTIKKSE
MELKYCKSSLAKKENELKTNDSAYNKDQDIIKNTEKEIKNLENQLNKINYRDGELEELIQ
KRDELTRECRGIRNNIDRQNGSKFDFQYTDPIPNWDKRRVKGTVANHVRVKDNKYSRALS
SILGGSWRSVITDNDETGKLILERGNLVNRVTLIPLNKISARTIDRNVVNLAQKLVGKEN
AIPAIDLIEYDKEVEPAMQFIFGNAFVCKDMDAAKTVTYHKDILKRSYTLDGDEMSPDGA
LSGGAVQSGPPILDEVSRISQMKNEINAKTREIQEISRRIDGLQNVATQYKQLKDKLDTM
QLHLKTAQERIQSTTFQQDQNEITELKEKVKTLTTTIEECHNILATNEQKVKELTEKLKD
AKGNRERDLKNAEADLKKAKQKHEQSQKNWKKREQQYETMKLEIEELKKTIAEGKEQVIQ
MQTKIEEFQRKIEETNNDDGSLKKRSEELRRKIKEQKDSIAAQNKEVRTKAARKEKLQKH
IQELELEIKKKENEIGKVKADNDEGYNKIQALEEKYPWIPEDKEHFGARNTRYDYTKEDP
QQAGQKLTKLQENKEKLSRNINQEAMMLLEKEEEHYKKIMDRRSKIENDKKNILDSIKNM
DTKKIENLKKAWEEVNNNFGSIFTTLLPGAQAKLDPPEGQNFLKGLEVKVGFNGIWKESL
TELSGGQRSLVALSLILAMLKYKPAPLYILDEVDAALDLSHTQNIGGMLKAHFKNSQFII
VSLKDGMFNNANVLFRTKFVDGVSGVIRTVNKN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
21 g10517.t1 CDD cd03273 ABC_SMC2_euk 1 156 8.80563E-97
18 g10517.t1 Coils Coil Coil 246 287 -
17 g10517.t1 Coils Coil Coil 289 365 -
19 g10517.t1 Coils Coil Coil 444 495 -
16 g10517.t1 Coils Coil Coil 679 730 -
15 g10517.t1 Coils Coil Coil 736 921 -
14 g10517.t1 Coils Coil Coil 967 1009 -
11 g10517.t1 Gene3D G3DSA:3.40.50.300 - 1 183 1.2E-45
12 g10517.t1 Gene3D G3DSA:1.20.1060.20 - 518 672 2.6E-27
13 g10517.t1 Gene3D G3DSA:3.30.70.1620 - 577 667 2.6E-27
10 g10517.t1 Gene3D G3DSA:3.40.50.300 - 1020 1173 2.4E-43
4 g10517.t1 PANTHER PTHR43977 STRUCTURAL MAINTENANCE OF CHROMOSOMES PROTEIN 3 1 1172 0.0
5 g10517.t1 PANTHER PTHR43977:SF2 STRUCTURAL MAINTENANCE OF CHROMOSOMES PROTEIN 1 1172 0.0
20 g10517.t1 PIRSF PIRSF005719 SMC 1 1155 2.4E-176
2 g10517.t1 Pfam PF02463 RecF/RecN/SMC N terminal domain 2 518 2.0E-26
1 g10517.t1 Pfam PF06470 SMC proteins Flexible Hinge Domain 519 637 1.0E-20
3 g10517.t1 Pfam PF02463 RecF/RecN/SMC N terminal domain 821 1160 1.7E-30
22 g10517.t1 SMART SM00968 SMC_hinge_2 518 638 7.5E-26
7 g10517.t1 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 1 1153 1.13E-45
8 g10517.t1 SUPERFAMILY SSF75553 Smc hinge domain 475 686 2.48E-40
9 g10517.t1 SUPERFAMILY SSF57997 Tropomyosin 713 942 3.92E-6
6 g10517.t1 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 749 1152 8.52E-20

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

Orthology

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