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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaagccttcccttgagttggataactcttgcaaaacaaataatctgtttttggagaactctgtcagtggattcatgtttcatcttctatccttctttcagGGAAGCGCTAGGAGGCTGGTAAAAGCTGCGCTTCAAGAAGCTGCAAAGAAGAGAGAAATGAGATATTCAGATTTAAAGAAAATTGATCGCGGAGTTCGTC

Basic information

species Glycine max
transcript GLYMA20G24100.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G24100.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os06g50380.1 (Oryza sativa), 3'ss of exon 5
aaagccttcccttgagttggataactct---tgcaaaacaaataatctgtttttggagaactctgtcagtggattc-atgtttcatcttctatccttctttcagGGAAGCGCTAGGAGGCTGGTAAAAGCTGCGCTTCAAGAAGCTGCAAAGAAGAGAGAAATGAGATATTCAGATTTAAAGAAAATTGATCGCGGAGTTCGTC
   ||| ||  | ||     | |    |     |||||   | |  ||   | | ||       || |  | ||   ||| ||  |  ||| |   ||||||||||||| |||||||||||  |||| || ||  | |||||||| || ||||| ||||||||||| || |||||| | ||||| ||||| || || ||||| |
---gccctcagtggaaggcaacatgcatgaaaacaaaatggacacgctaagtgttgattgtgaagtgaaagaatctgatgatttgtgctct-ttgatctttcagGGAAGTGCTAGGAGGCTCATAAAGGCAGCTTTGCAAGAAGCAGCCAAGAAAAGAGAAATGAGGTACTCAGATCTCAAGAAGATTGACCGTGGTGTTCGCC

upper sequence: GLYMA20G24100.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv03s0038g02650.t01 (Vitis vinifera), 3'ss of exon 4
-----aaagccttcccttgagttggataactcttgcaaaacaaataatctgtttttggagaactctgtcagtggattcatgtttcatcttctatccttctttcagGGAAGCGCTAGGAGGCTGGTAAAAGCTGCGCTTCAAGAAGCTGCAAAGAAGAGAGAAATGAGATATTCAGATTTAAAGAAAATTGATCGCGGAGTTCGTC
     |||       || | |   ||    | |        ||| |||||   ||     ||||  |  |    | | |  ||| || | || ||  || | |||||||| || | ||||||||| ||||||||  | |||||||| ||||| |||||||||||||| ||||||||  | ||||| ||||| || || |||||||
ctgttaaatgtgatactagtggcagaggcatgtcatggggaaaaaaatctccatt----aaactaaggaacaaaacttac-ttttatttgctttctctcatgcagGGAAGTGCAAAGAGGCTGGTGAAAGCTGCTTTACAAGAAGCAGCAAAAAAGAGAGAAATGAGGTATTCAGACCTGAAGAAGATTGACCGAGGGGTTCGTC
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|18725738|gb|BM523643.1|BM523643
EST:     ACCTCAGCAATCAAGAAGCAGTTGATATAGTTCAAAACAGTCCCCGCAGT                         GGAAGCGCTAGGAGGCTGGTAAAAGCTGCGCTTCAAGAAGCTGCAAAGAAG
genomic: ACCTTAGCAATCAAGAAGCAGTTGATATAGTTCAAAACAGTCCCCGCAGTgtaagataca ... cttctttcagGGAAGCGCTAGGAGGCTGGTAAAAGCTGCGCTTCAAGAAGCTGCAAAGAAG
EST: gi|6341594|gb|AW164418.1|AW164418
EST:     ACCTTAGCAATCAAGAAGCAGTTGATATAGTTCAAAACAGTCCCCGCAGT                         GGAAGCGCTAGGAGGCTGGTAAAAGCTGCGCTTCAAGAAGCTGCAAAGAAG
genomic: ACCTTAGCAATCAAGAAGCAGTTGATATAGTTCAAAACAGTCCCCGCAGTgtaagataca ... cttctttcagGGAAGCGCTAGGAGGCTGGTAAAAGCTGCGCTTCAAGAAGCTGCAAAGAAG
EST: gi|308098935|gb|HO760776.1|HO760776
EST:     CCTTTAGCAATCAAGAAGCAGTTGATATAGTTCAAAACAGTCCCCGCAGT                         GGAAGCGCTAGGAGGCTGGTAAAAGCTGCGCTTCTAGAAGCTGCAAAGAAG
genomic: CCTT-AGCAATCAAGAAGCAGTTGATATAGTTCAAAACAGTCCCCGCAGTgtaagataca ... cttctttcagGGAAGCGCTAGGAGGCTGGTAAAAGCTGCGCTTCAAGAAGCTGCAAAGAAG
EST: gi|308098964|gb|HO760805.1|HO760805
EST:     ACCTCAGCAATCAAGAAGCAGTTGATATAGTTCAAAACAGTCCCCGCAGT                         GGAAGCGCTAGGAGGCTGGTAAAAGCTGCGCTTCAAGAAGCTGCAAAGAAG
genomic: ACCTTAGCAATCAAGAAGCAGTTGATATAGTTCAAAACAGTCCCCGCAGTgtaagataca ... cttctttcagGGAAGCGCTAGGAGGCTGGTAAAAGCTGCGCTTCAAGAAGCTGCAAAGAAG
EST: gi|193497542|gb|FK460788.1|FK460788
EST:     ACCTTAGCAATCAAGAAGCAGTTGATATAGTTCAAAACAGTCCCCGCAGT                         GGAAGCGCTAGGAGGCTGGTAAAAGCTGCGCTTCAAGAAGCTGCAAAGAAG
genomic: ACCTTAGCAATCAAGAAGCAGTTGATATAGTTCAAAACAGTCCCCGCAGTgtaagataca ... cttctttcagGGAAGCGCTAGGAGGCTGGTAAAAGCTGCGCTTCAAGAAGCTGCAAAGAAG
EST: gi|208135415|gb|GD938360.1|GD938360
EST:     CAAGAAGCAGTTGATATAGTTCAAAACAGTCCCCGCAGT                         GGAAGCGCTAGGAGGCTGGTAAAAGCTGCGCTTCAAGAAGCTGCAAAGAAG
genomic: CAAGAAGCAGTTGATATAGTTCAAAACAGTCCCCGCAGTgtaagataca ... cttctttcagGGAAGCGCTAGGAGGCTGGTAAAAGCTGCGCTTCAAGAAGCTGCAAAGAAG
EST: gi|208086498|gb|GD879812.1|GD879812
EST:     ACCTCAGCAATCAAGAAGCAGTTGATATAGTTCAAAACAGTCCCCGCAGT                         GGAAGCGCTAGGAGGCTGGTAAAAGCTGCGCTTCAAGAAGCTGCAAAGAAG
genomic: ACCTTAGCAATCAAGAAGCAGTTGATATAGTTCAAAACAGTCCCCGCAGTgtaagataca ... cttctttcagGGAAGCGCTAGGAGGCTGGTAAAAGCTGCGCTTCAAGAAGCTGCAAAGAAG
EST: gi|192294523|gb|FG987452.1|FG987452
EST:     ACCTTAGCAATCAAGAAGCAGTTGATATAGTTCAAAACAGTCCCCGCAGT                         GGAAGCGCTAGGAGGCTGGTAAAAGCTGCGCTTCAAGAAGCTGCAAAGAAG
genomic: ACCTTAGCAATCAAGAAGCAGTTGATATAGTTCAAAACAGTCCCCGCAGTgtaagataca ... cttctttcagGGAAGCGCTAGGAGGCTGGTAAAAGCTGCGCTTCAAGAAGCTGCAAAGAAG
EST: gi|151412759|gb|EV282571.1|EV282571
EST:     ACCTTAGCAATCAAGAAGCAGTTGATATAGTTCAAAACAGTCCCCGCAGT                         GGAAGCGCTAGGAGGCTGGTAAAAGCTGCGCTTCAAGAAGCTGCAAAGAAG
genomic: ACCTTAGCAATCAAGAAGCAGTTGATATAGTTCAAAACAGTCCCCGCAGTgtaagataca ... cttctttcagGGAAGCGCTAGGAGGCTGGTAAAAGCTGCGCTTCAAGAAGCTGCAAAGAAG
EST: gi|31471392|gb|CD413420.1|CD413420
EST:     ACCTTAGCAATCAAGAAGCAGTTGATATAGTTCAAAACAGTCCCCGCAGT                         GGAAGCGCTAGGAGGCTGGTAAAAGCTGCGCTTCAAGAAGCAGCAAAGAAG
genomic: ACCTTAGCAATCAAGAAGCAGTTGATATAGTTCAAAACAGTCCCCGCAGTgtaagataca ... cttctttcagGGAAGCGCTAGGAGGCTGGTAAAAGCTGCGCTTCAAGAAGCTGCAAAGAAG
EST: gi|207730397|gb|GD708853.1|GD708853
EST:     ATATAGTTCAAAACAGTCCCCGCAGT                         GGAAGCGCTAGGAGGCTGGTAAAAGCTGCGCTTCAAGAAGCTGCAAAGAAG
genomic: ATATAGTTCAAAACAGTCCCCGCAGTgtaagataca ... cttctttcagGGAAGCGCTAGGAGGCTGGTAAAAGCTGCGCTTCAAGAAGCTGCAAAGAAG
EST: gi|207691136|gb|GD673172.1|GD673172
EST:     ATATAGTTCAAAACTAGTTCCCCGTCAGT                         GGAAGCGCTAGGAGGCTGGTAAAAGCTGCGCTTCAAGAAGCTGCAAAGAA
genomic: ATATAGTTCAAAAC-AG-TCCCCG-CAGTgtaagataca ... cttctttcagGGAAGCGCTAGGAGGCTGGTAAAAGCTGCGCTTCAAGAAGCTGCAAAGAA
EST: gi|208160921|gb|GD960883.1|GD960883
EST:     TAGTTCAAAACAGTCCCCGCAGT                         GGAAGCGCTAGGAGGCTGGTAAAAGCTGCGCTTCAAGAAGCTGCAAAGAAG
genomic: TAGTTCAAAACAGTCCCCGCAGTgtaagataca ... cttctttcagGGAAGCGCTAGGAGGCTGGTAAAAGCTGCGCTTCAAGAAGCTGCAAAGAAG
EST: gi|193546740|gb|FK500453.1|FK500453
EST:     ACCTCAGCAATCAAGAAGCAGTTGATATAGTTCAAAACAGTCCCCGCAGT                         GGAAGCGCTAGGAGGCTGG
genomic: ACCTTAGCAATCAAGAAGCAGTTGATATAGTTCAAAACAGTCCCCGCAGTgtaagataca ... cttctttcagGGAAGCGCTAGGAGGCTGG
EST: gi|254340610|gb|GR854338.1|GR854338
EST:     ACCTCAGCAATCAAGAAGCAGTTGATATAGTTCAAAACAGTCCCCGCAGT                         GGAAGCGCTAGGAGGCTGGTAAAAGCTGCGCTTCAAGAAGCTGCAAAGAAG
genomic: ACCTTAGCAATCAAGAAGCAGTTGATATAGTTCAAAACAGTCCCCGCAGTgtaagataca ... cttctttcagGGAAGCGCTAGGAGGCTGGTAAAAGCTGCGCTTCAAGAAGCTGCAAAGAAG
EST: gi|23729680|gb|BU762942.1|BU762942
EST:     ACCTCAGCAATCAAGAAGCAGTTGATATAGTTCAAAACAGTCCCCGCAGT                         GGAAGCGCTAGGAGGCTGGTAAAAGCTGCGCTTCAAGAAGCTGCAAAGAAG
genomic: ACCTTAGCAATCAAGAAGCAGTTGATATAGTTCAAAACAGTCCCCGCAGTgtaagataca ... cttctttcagGGAAGCGCTAGGAGGCTGGTAAAAGCTGCGCTTCAAGAAGCTGCAAAGAAG
EST: gi|18038853|gb|BM307147.1|BM307147
EST:     ACCTTAGCAATCAAGAAGCAGTTGATATAGTTCAAAACAGTCCCCGCAGT                         GGAAGCGCTAGGAGGCTGGTAAAAGCTGCGCTTCAAGAAGCAGCAAAGAAG
genomic: ACCTTAGCAATCAAGAAGCAGTTGATATAGTTCAAAACAGTCCCCGCAGTgtaagataca ... cttctttcagGGAAGCGCTAGGAGGCTGGTAAAAGCTGCGCTTCAAGAAGCTGCAAAGAAG
EST: gi|298165586|gb|HO011635.1|HO011635
EST:     ACCTTAGCAATCAAGAAGCAGTTGATATAGTTCAAAACAGTCCCCGCAGT                         GGAAGCGCTAGGTGGCTGGTAAAAGCTGCGCTTCAAGAAGCTGCAAAGAAG
genomic: ACCTTAGCAATCAAGAAGCAGTTGATATAGTTCAAAACAGTCCCCGCAGTgtaagataca ... cttctttcagGGAAGCGCTAGGAGGCTGGTAAAAGCTGCGCTTCAAGAAGCTGCAAAGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttttggagaactctgtcagtggattcatgtttcatcttctatccttctttcagGGAAGCGCTAGGAGGCTGGTAAAAGCTGCGCTTCAAGAAGCTGCAAAGAAGAGAGAAATGAGATATTCAGATTTAAAGAAAATTGATCGCGGAGTTCGTC
                         ttcatgtttcatcttc  CT-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaagccttcccttgagttggataactcttgcaaaacaaataatctgtttttggagaactctgtcagtggattcatgtttcatcttctatccttctttcagGGAAGCGCTAGGAGGCTGGTAAAAGCTGCGCTTCAAGAAGCTGCAAAGAAGAGAGAAATGAGATATTCAGATTTAAAGAAAATTGATCGCGGAGTTCGTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - -cttccct
- - - - - - - - - - - - ctcttgc
- - - - - - - - - - - - - - - - aaacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - tctgtca