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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTATGTTCCAAATCCTGTCTTGGTTATAATTGATGTTGAACCTAAGGAATTGGGAATCCCAACAAAAGCATATTATGCCGTTGAAGAGGTTAAAGAGgtacaaattaagtccgtcatatctttgatagaaatcttatatatctgttcttgctgatattttgcaaaagtaatcctgctgtatgtgatggtgggacgggagctagtgtttgctcaacactaaattagtactcaaagaaactaatatatagtttattctgagtacag

Basic information

species Glycine max
transcript GLYMA11G34980.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G34980.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G061745_T03 (Zea mays), 5'ss of exon 4
CTATGTTCCAAATCCTGTCTTGGTTATAATTGATGTTGAACCTAAGGAATTGGGAATCCCAACAAAAGCATATTATGCCGTTGAAGAGGTTAAAGAGgtacaaa-----ttaagtccgtcatatctttgatagaaatcttatatatctgttcttgctgatattttgcaaaagtaatcctgctgtatgtgatggtgggacgggagctagtgtttgctcaacactaaattagtactcaaagaaactaatatatagtttattctgagtacag
 |||||||| ||||| |||||||| || ||||||||  |||| |||||  |||| || || || ||||| || || || || || ||||||||||||||||| |      | |||   |    | ||| |      |  |   | | |  | |   |  |  ||| ||                                                                                                     
TTATGTTCCTAATCCAGTCTTGGTGATTATTGATGTCCAACCCAAGGAGCTGGGTATACCGACCAAAGCGTACTACGCTGTGGAGGAGGTTAAAGAGgtacataacttgctgagttgctggagtttttcacttgcttgctcagtgtttaatttgttttttcctttacag----------------------------------------------------------------------------------------------------

upper sequence: GLYMA11G34980.1 (Glycine max), 5'ss of exon 4
lower sequence: AT3G11270.2 (Arabidopsis thaliana), 5'ss of exon 4
CTATGTTCCAAATCCTGTCTTGGTTATAATTGATGTTGAACCTAAGGAATTGGGAATCCCAACAAAAGCATATTATGCCGTTGAAGAGGTTAAAGAGgtacaaattaagtccgtcatatctttgatagaaatcttatatatctg--ttcttgctgatattttgcaaaagtaatcctgctgtatgtgatggtgggacgggagctagtgtttgctcaacactaaattagtactcaaagaaactaatatatagtttattctgagtacag
||| ||||||||||| || ||||| || ||||||||  ||||||| ||| | |||||||| ||||||||||| ||||| ||||| ||||| ||||||||| | |  |     | ||  | | | |     || |||  |    |  |  |   |   || |  || |  | ||  | || | ||   | ||   |          |  ||||      |  || |  | |||   | |                            
CTACGTTCCAAATCCAGTGTTGGTCATTATTGATGTCCAACCTAAAGAACTTGGAATCCCCACAAAAGCATACTATGCGGTTGAGGAGgtgaaagaggtaaatacca-----gccaattttctaacc---attttacttgctcgactgttaagttgcatctgacatacttgatt-tactttctgcattagttatatccatatatctaattgccttgatccgaacttct-ctctctgcag---------------------------

upper sequence: GLYMA11G34980.1 (Glycine max), 5'ss of exon 4
lower sequence: AT5G05780.1 (Arabidopsis thaliana), 5'ss of exon 4
CTATGTTCCAAATCCTGTCTTGGTTATAATTGATGTTGAACCTAAGGAATTGGGAATCCCAACAAAAGCATATTATGCCGTTGAAGAGGTTAAAGAGgtacaaattaagtccgtcatatctttga-----tagaaatcttatatatctgttcttgctgatattttgcaaaagtaatcctgctgtatgtgatggtgggacgggagctagtgtttgctcaacactaaattagtactcaaagaaactaatatatagtttattctgagtacag
||||||||||||||| ||| |||| || ||||||||  | ||||| ||| | |||||||| || |||||||| ||||| || || |||||||| ||||||  |   ||  || ||  |   |||      | | ||  || |||   | || |       ||  ||   ||  | | ||  |       |                                                                               
CTATGTTCCAAATCCAGTCCTGGTCATTATTGATGTCCAGCCTAAAGAACTTGGAATCCCTACCAAAGCATACTATGCAGTGGAGGAGGTTAAGGAGgtaagatacaaacccttccaaatattgtcccttttgtaaagttgtatgcttattataatcag-atgctgattaaacacttctttttctctccag------------------------------------------------------------------------------

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|254323156|gb|GR835764.1|GR835764
EST:     AATTGGGAATCCCAACAAAAGCATATTATGCCGTTGAAGAGGTTAAAGAG                         AATGCCACTCAAAAAAGTCAAAAAGTGTTTGTGCATGTGCCATCAGAGATT
genomic: AATTGGGAATCCCAACAAAAGCATATTATGCCGTTGAAGAGGTTAAAGAGgtacaaatta ... ctgagtacagAATGCCACTCAAAAAAGTCAAAAAGTGTTTGTGCATGTGCCATCAGAGATT
EST: gi|207752168|gb|GD724525.1|GD724525
EST:     AATTGGGAATCCCAACAAAAGCATATTATGCCGTTGAAGAGGTTAAAGAG                         AATGCCACTCAAAAAAGTCAAAA-GTGTTTGTGCATGTGCCATCAGAGATT
genomic: AATTGGGAATCCCAACAAAAGCATATTATGCCGTTGAAGAGGTTAAAGAGgtacaaatta ... ctgagtacagAATGCCACTCAAAAAAGTCAAAAAGTGTTTGTGCATGTGCCATCAGAGATT
EST: gi|6071648|gb|AW101035.1|AW101035
EST:     AATTGGGAATCCCAACAAAAGCATATTATGCCGTTGAAGAGGTTAAAGAG                         AATGCCACTCATATAAGGCAAAAAGTGTTTGTGCATGTGCCATCAGAGATT
genomic: AATTGGGAATCCCAACAAAAGCATATTATGCCGTTGAAGAGGTTAAAGAGgtacaaatta ... ctgagtacagAATGCCACTCAAAAAAGTCAAAAAGTGTTTGTGCATGTGCCATCAGAGATT
EST: gi|193347090|gb|FK310960.1|FK310960
EST:     AATTGGGAATCCCAACAAAAGCATATTATGCCGTTGAAGAGGTTAAAGAG                         AATGCCACTCAAAAAAGTCAAAAAGTGTTTGTGCATGTGCCATCAG
genomic: AATTGGGAATCCCAACAAAAGCATATTATGCCGTTGAAGAGGTTAAAGAGgtacaaatta ... ctgagtacagAATGCCACTCAAAAAAGTCAAAAAGTGTTTGTGCATGTGCCATCAG
EST: gi|193562849|gb|FK518652.1|FK518652
EST:     AATTGGGAATCCCAACAAAAGCATATTATGCCGTTGAAGAGGTTAAAGAG                         AATGCCACTCAAAAAAGTCAAAAAGTGTTTGTGCATGTGCCATCAGAGATT
genomic: AATTGGGAATCCCAACAAAAGCATATTATGCCGTTGAAGAGGTTAAAGAGgtacaaatta ... ctgagtacagAATGCCACTCAAAAAAGTCAAAAAGTGTTTGTGCATGTGCCATCAGAGATT
EST: gi|58016090|gb|CX702832.1|CX702832
EST:     AATTGGGAATCCCAACAAAAGCATATTATGCCGTTGAAGAGGTTAAAGAG                         AATGCCACTCAAAAAAGTCAAAAAGTGTTTGTGCATGTGCCATCAGAGATT
genomic: AATTGGGAATCCCAACAAAAGCATATTATGCCGTTGAAGAGGTTAAAGAGgtacaaatta ... ctgagtacagAATGCCACTCAAAAAAGTCAAAAAGTGTTTGTGCATGTGCCATCAGAGATT
EST: gi|12774685|gb|BG239612.1|BG239612
EST:     GGAATCCCAACAAAAGCATATTATGCCGTTGAAGAGGTTAAAGAG                         AATGCCACTC-AAAAAGTCAAAAAGTGTTTGTGCATGTGCCATCAGAGATT
genomic: GGAATCCCAACAAAAGCATATTATGCCGTTGAAGAGGTTAAAGAGgtacaaatta ... ctgagtacagAATGCCACTCAAAAAAGTCAAAAAGTGTTTGTGCATGTGCCATCAGAGATT
EST: gi|193630911|gb|FK585066.1|FK585066
EST:     GGAATCCCAACAAAAGCATATTATGCCGTTGAAGAGGTTAAAGAG                         AATGCCACTC-AAAAAGTCAAAAAGTGTTTGTGCATGTGCCATCAGAGATT
genomic: GGAATCCCAACAAAAGCATATTATGCCGTTGAAGAGGTTAAAGAGgtacaaatta ... ctgagtacagAATGCCACTCAAAAAAGTCAAAAAGTGTTTGTGCATGTGCCATCAGAGATT
EST: gi|254323157|gb|GR835765.1|GR835765
EST:     GAATCCC-ACAAAAGCATA-TATGCCGTTGAAGA-GTTAAAGAG                         AATGCCACTCAAAAAAGTCAAAAAGTGTTTGTGCATGTGCCATCAGAGATT
genomic: GAATCCCAACAAAAGCATATTATGCCGTTGAAGAGGTTAAAGAGgtacaaatta ... ctgagtacagAATGCCACTCAAAAAAGTCAAAAAGTGTTTGTGCATGTGCCATCAGAGATT
EST: gi|207836671|gb|GD806668.1|GD806668
EST:     AATTGGGAATCCCAACAAAAGCATATTATGCCGTTGAAGAGGTTAAAGAG                         AATGCCACTCAAAAAAGTCAAAAAGTGTTTGTGCATGTGCCATCAGAGATT
genomic: AATTGGGAATCCCAACAAAAGCATATTATGCCGTTGAAGAGGTTAAAGAGgtacaaatta ... ctgagtacagAATGCCACTCAAAAAAGTCAAAAAGTGTTTGTGCATGTGCCATCAGAGATT
EST: gi|58017218|gb|CX703960.1|CX703960
EST:     AATTGGGAATCCCAACAAAAGCATATTATGCCGTTGAAGAGGTTAAAGAG                         AATGCCACTCAAAAAAGTCAAAAAGTGTTTGTGCATGTGCCATCAGAGATT
genomic: AATTGGGAATCCCAACAAAAGCATATTATGCCGTTGAAGAGGTTAAAGAGgtacaaatta ... ctgagtacagAATGCCACTCAAAAAAGTCAAAAAGTGTTTGTGCATGTGCCATCAGAGATT
EST: gi|208165655|gb|GD959443.1|GD959443
EST:     AATTGGGAATCCCAACAAAAGCATATTATGCCGTTGAAGAGGTTAAAGAG                         AATGCCACTCAAAAAAGTCAAAAAGTGTTTGTGCATGTGCCATCAGAGATT
genomic: AATTGGGAATCCCAACAAAAGCATATTATGCCGTTGAAGAGGTTAAAGAGgtacaaatta ... ctgagtacagAATGCCACTCAAAAAAGTCAAAAAGTGTTTGTGCATGTGCCATCAGAGATT
EST: gi|207759617|gb|GD733976.1|GD733976
EST:     AATTGGGAATCCCAACAAAAGCATATTATGCCGTTGAAGAGGTTAAAGAG                         AATGCCACTCAAAAAAGTCAAAAAGTGTTTGTGCATGTGCCATCAGAGATT
genomic: AATTGGGAATCCCAACAAAAGCATATTATGCCGTTGAAGAGGTTAAAGAGgtacaaatta ... ctgagtacagAATGCCACTCAAAAAAGTCAAAAAGTGTTTGTGCATGTGCCATCAGAGATT
EST: gi|58017413|gb|CX704155.1|CX704155
EST:     AATTGAGAATCCCAACAAAAGCATATTATGCCGTTGAAGAGGTTAAAGAG                         AATGCCACTCAAAAAAGTCAAAAAGTGTTTGTGCATGTGCCATCAGAGATT
genomic: AATTGGGAATCCCAACAAAAGCATATTATGCCGTTGAAGAGGTTAAAGAGgtacaaatta ... ctgagtacagAATGCCACTCAAAAAAGTCAAAAAGTGTTTGTGCATGTGCCATCAGAGATT
EST: gi|58023179|gb|CX709920.1|CX709920
EST:     AATTGGGAATCCCAACAAAAGCATATTATGCCGTAGAAGAGGTTAAAGAG                         AATGCCACTCAAAAAAGTCAAAAAGTGTTTGTGCATGTGCCATCAGAGATT
genomic: AATTGGGAATCCCAACAAAAGCATATTATGCCGTTGAAGAGGTTAAAGAGgtacaaatta ... ctgagtacagAATGCCACTCAAAAAAGTCAAAAAGTGTTTGTGCATGTGCCATCAGAGATT
EST: gi|208056626|gb|GD850343.1|GD850343
EST:     AATTGGGAATCCCAACAAAAGCATATTATGCCGTTGAAGAGGTTAAAGAG                         AATGCTACTCAAAAAAGTCAAAAAGTGTTTGTGCATGTGCCATCAGAGATT
genomic: AATTGGGAATCCCAACAAAAGCATATTATGCCGTTGAAGAGGTTAAAGAGgtacaaatta ... ctgagtacagAATGCCACTCAAAAAAGTCAAAAAGTGTTTGTGCATGTGCCATCAGAGATT
EST: gi|151411180|gb|EV280991.1|EV280991
EST:     AATTGGGAATCCCAACAAAAGCATATTATGCCGTTGAAGAGGTTAAAGAG                         AATGCCACTCAAAAAAGTCAAAAAGTGTTTGTGCATGTGCCATCAGAGATT
genomic: AATTGGGAATCCCAACAAAAGCATATTATGCCGTTGAAGAGGTTAAAGAGgtacaaatta ... ctgagtacagAATGCCACTCAAAAAAGTCAAAAAGTGTTTGTGCATGTGCCATCAGAGATT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTATGTTCCAAATCCTGTCTTGGTTATAATTGATGTTGAACCTAAGGAATTGGGAATCCCAACAAAAGCATATTATGCCGTTGAAGAGGTTAAAGAGgtacaaattaagtccgtcatatctttgatagaaatcttatatatctgttcttgctgatattttgcaaaagtaatcctgctgtatgtgatggtgggacgggagctagtgtttgctcaacactaaattagtactcaaagaaactaatatatagtttattctgagtacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG