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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTCCTGGGGTTGACCCAAATGACCCTTCTGTCAAGGATTTGCTGGCGTCCATGCAAAATCAGTCTGAGgttagtctttctatgaaaaagaatatattggatttgaaaggaatttcttttagaaaatttcagtgcaggccagtaaacgttaaccttgaacacctttccc...

Basic information

species Glycine max
transcript GLYMA11G08290.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G08290.1 (Glycine max), 5'ss of exon 9
lower sequence: Vv04s0023g03620.t01 (Vitis vinifera), 5'ss of exon 9
CTTCCTGGGGTTGACCCAAATGACCCTTCTGTCAAGGATTTGCTGGCGTCCATGCAAAATCAGTCTGAGgttagtctttctatgaaaaagaatatattggatttgaaaggaatttcttt----tagaaaatttcagtgcaggccagt---aaacgttaaccttgaacacctttccc-----
||||| || |||||||| ||||| ||||| ||||| |||||||| || |||||||||||| |||| |||||  || | |  |   | ||   ||| |||  |   | ||| ||||  ||         |||| |     | | |||    | | ||| |   |  |    ||||       
CTTCCAGGAGTTGACCCCAATGATCCTTCAGTCAAAGATTTGCTAGCATCCATGCAAAATGAGTCAGAGgtgggtttgttaacttacaatt-tatgttgattacaagaggcattttcttgcctccactaattgcccaatatgtcaggcagagatgttgattgtataattgtttcttctcag
















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|58019852|gb|CX706594.1|CX706594
EST:     ATGACCCTTCTGTCAAGGATTTGCTGGCGTCCATGCAAAATCAGTCTGAG                         CCTCAACAGAAGAATGACGACAAGCCATCAAACGAGGAGGAGAAGAAGTAA
genomic: ATGACCCTTCTGTCAAGGATTTGCTGGCGTCCATGCAAAATCAGTCTGAGgttagtcttt ... gtttatccagCCTCAACAGAAGAATGACGACAAGCCATCAAACGAGGAGGAGAAGAAGTAA
EST: gi|58023403|gb|CX710144.1|CX710144
EST:     ATGACCCTTCTGTCAAGGATTTGCTGGCGTCCATGCAAAATCAGTCTGAG                         CCTCAACAGAAGAATGACGACAAGCCATCAAACGAGGAGGAGAAGAAGTAA
genomic: ATGACCCTTCTGTCAAGGATTTGCTGGCGTCCATGCAAAATCAGTCTGAGgttagtcttt ... gtttatccagCCTCAACAGAAGAATGACGACAAGCCATCAAACGAGGAGGAGAAGAAGTAA
EST: gi|57574672|gb|CX547647.1|CX547647
EST:     ATGACCCTTCTGTCAAGGATTTGCTGGCGTCCATGCAAAATCAGTCTGAG                         CCTCAACAGAAGAATGACGACAAGCCATCAAACGAGGAGGAGAAGAAGTAA
genomic: ATGACCCTTCTGTCAAGGATTTGCTGGCGTCCATGCAAAATCAGTCTGAGgttagtcttt ... gtttatccagCCTCAACAGAAGAATGACGACAAGCCATCAAACGAGGAGGAGAAGAAGTAA
EST: gi|6847457|gb|AW349818.1|AW349818
EST:     ATGACCCTTCTGTCAAGGATTTGCTGGCGTCCATGCAAAATCAGTCTGAG                         CCTCAACAGAAGAATGACGACAAGCCATCAAACGAGGAGGAGAAGAAGTAA
genomic: ATGACCCTTCTGTCAAGGATTTGCTGGCGTCCATGCAAAATCAGTCTGAGgttagtcttt ... gtttatccagCCTCAACAGAAGAATGACGACAAGCCATCAAACGAGGAGGAGAAGAAGTAA
EST: gi|213602700|gb|DB978115.1|DB978115
EST:     ATGACCCTTCTGTCAAGGATTTGCTGGCGTCCATGCAAAATCAGTCTGAG                         CCTCAACAGAAGAATGACGACAAGCCATCAAACGAGGAGGAGAAGAAGTAA
genomic: ATGACCCTTCTGTCAAGGATTTGCTGGCGTCCATGCAAAATCAGTCTGAGgttagtcttt ... gtttatccagCCTCAACAGAAGAATGACGACAAGCCATCAAACGAGGAGGAGAAGAAGTAA
EST: gi|213597471|gb|DB981639.1|DB981639
EST:     ATGACCCTTCTGTCAAGGATTTGCTGGCGTCCATGCAAAATCAGTCTGAG                         CCTCAACAGAAGAATGACGACAAGCCATCAAACGAGGAGGAGAAGAAGTAA
genomic: ATGACCCTTCTGTCAAGGATTTGCTGGCGTCCATGCAAAATCAGTCTGAGgttagtcttt ... gtttatccagCCTCAACAGAAGAATGACGACAAGCCATCAAACGAGGAGGAGAAGAAGTAA
EST: gi|193591118|gb|FK546909.1|FK546909
EST:     GGCGTCCATGCAAAATCAGTCTGAG                         CCTCAACAGAAGAATGACGACAAGCCATCAAACGAGGAGGAGAAGAAGTAA
genomic: GGCGTCCATGCAAAATCAGTCTGAGgttagtcttt ... gtttatccagCCTCAACAGAAGAATGACGACAAGCCATCAAACGAGGAGGAGAAGAAGTAA
EST: gi|214006796|gb|DB987664.1|DB987664
EST:     ATGAGCCTTCTGTCAAGGATTTGCTGGCGTCCATGCAAAATCAGTCTGAG                         CCTCAACAGAAGAATGACGACAAGCCATCAAACGAGGAGGAGAAGAAGTAA
genomic: ATGACCCTTCTGTCAAGGATTTGCTGGCGTCCATGCAAAATCAGTCTGAGgttagtcttt ... gtttatccagCCTCAACAGAAGAATGACGACAAGCCATCAAACGAGGAGGAGAAGAAGTAA
EST: gi|254318748|gb|GR830312.1|GR830312
EST:     ATGACCCTTCTGTCAAGGATTTGCTGGCGTCCATGCAAAATCAGTCTGAG                         CCTCAACAGAAGAATGACGACAAGCCATCAAACGAGGAGGAGAAGAAGTAA
genomic: ATGACCCTTCTGTCAAGGATTTGCTGGCGTCCATGCAAAATCAGTCTGAGgttagtcttt ... gtttatccagCCTCAACAGAAGAATGACGACAAGCCATCAAACGAGGAGGAGAAGAAGTAA
EST: gi|207826324|gb|GD800653.1|GD800653
EST:     TCCATGCAAAATCAGTCTGAG                         CCTCAACAGAAGAATGACGACAAGCCATC-AACGAGGAGGAGAAGAAGTAA
genomic: TCCATGCAAAATCAGTCTGAGgttagtcttt ... gtttatccagCCTCAACAGAAGAATGACGACAAGCCATCAAACGAGGAGGAGAAGAAGTAA
EST: gi|21602391|gb|BQ612722.1|BQ612722
EST:     ATGACCCTTCTGTCAAGGATTTGCTGGCGTCCATGCAAAATCAGTCTGAG                         CCTCAACAGAAGAATGACGACAAGCCATCAAACGAGGAGGAGAAGAAGTAA
genomic: ATGACCCTTCTGTCAAGGATTTGCTGGCGTCCATGCAAAATCAGTCTGAGgttagtcttt ... gtttatccagCCTCAACAGAAGAATGACGACAAGCCATCAAACGAGGAGGAGAAGAAGTAA
EST: gi|193361745|gb|FK327719.1|FK327719
EST:     CAAAATCAGTCTTGTAG                         CCTCAACAGAAGAACGACGACAAGCCATCAAACGAGGAGGAGAAGAAGTA
genomic: CAAAATCAGTC-TG-AGgttagtcttt ... gtttatccagCCTCAACAGAAGAATGACGACAAGCCATCAAACGAGGAGGAGAAGAAGTA
EST: gi|13479589|gb|BG508932.1|BG508932
EST:     ATGACCCTTCTGTCAAGGATTTGCTGGCGTCCATGCAAAATCAGTCTGAG                         CCTCAACAGAAGAATGACGACAAGCCATCAAACGAGGAGGAGAAGAAGTAA
genomic: ATGACCCTTCTGTCAAGGATTTGCTGGCGTCCATGCAAAATCAGTCTGAGgttagtcttt ... gtttatccagCCTCAACAGAAGAATGACGACAAGCCATCAAACGAGGAGGAGAAGAAGTAA
EST: gi|208307682|gb|GE109278.1|GE109278
EST:     ATGACCCTTCTGTCAAGGATTTGCTGGCTTCCATGCAAAATCAGTCTGAG                         CCTCAACAGAAGAATGACGACAAGCCATCAAACGAGGAGGAGAAGAAGTAA
genomic: ATGACCCTTCTGTCAAGGATTTGCTGGCGTCCATGCAAAATCAGTCTGAGgttagtcttt ... gtttatccagCCTCAACAGAAGAATGACGACAAGCCATCAAACGAGGAGGAGAAGAAGTAA
EST: gi|208301073|gb|GE097338.1|GE097338
EST:     ATGACCCTTCTGTCAAGGATTTGCTGGCGTCCATGCAAAATCAGTCTGAG                         CCTCAACAGAAGAATGACGACAAGCCATCAAACGAGGAGGAGAAGAAGTAA
genomic: ATGACCCTTCTGTCAAGGATTTGCTGGCGTCCATGCAAAATCAGTCTGAGgttagtcttt ... gtttatccagCCTCAACAGAAGAATGACGACAAGCCATCAAACGAGGAGGAGAAGAAGTAA
EST: gi|22931412|gb|BU548551.1|BU548551
EST:     ATGACCCTTCTGTCAAGGATTTGCTGGCGTCCATGCAAAATCAGTCTGAG                         CCTCAACAGAAGAATGACGACAAGCCATCAAACGAGGAGGAGAAGAAGTAA
genomic: ATGACCCTTCTGTCAAGGATTTGCTGGCGTCCATGCAAAATCAGTCTGAGgttagtcttt ... gtttatccagCCTCAACAGAAGAATGACGACAAGCCATCAAACGAGGAGGAGAAGAAGTAA
EST: gi|207736145|gb|GD711268.1|GD711268
EST:     TTCTGTCAAGGATTTGCTGGCGTCCATGCAAAATCAGTCTGAG                         CCTCAACAGAAGAATGACGACAAGCCATCAAACGAGGAGGAGAAGAAGTAA
genomic: TTCTGTCAAGGATTTGCTGGCGTCCATGCAAAATCAGTCTGAGgttagtcttt ... gtttatccagCCTCAACAGAAGAATGACGACAAGCCATCAAACGAGGAGGAGAAGAAGTAA
EST: gi|6069956|gb|AW099536.1|AW099536
EST:     ATGACCCTTCTGTCAAGGATTTGCTGGCGTCCATGCAAAATCAGTCTGAG                         CCTCAACAGAAGAATGACGACAAGCCATCAAACGAGGAGGAGAAGAAGTAA
genomic: ATGACCCTTCTGTCAAGGATTTGCTGGCGTCCATGCAAAATCAGTCTGAGgttagtcttt ... gtttatccagCCTCAACAGAAGAATGACGACAAGCCATCAAACGAGGAGGAGAAGAAGTAA
EST: gi|27426751|gb|CA938271.1|CA938271
EST:     ATGACCCTTCTGTCAAGGATTTGCTGGCGTCCATGCAAAATCAGTCTGAG                         CCTCAACAGAAGAATGACGACAAGCCATCAAACGAGGAGGAGAAGAAGTAA
genomic: ATGACCCTTCTGTCAAGGATTTGCTGGCGTCCATGCAAAATCAGTCTGAGgttagtcttt ... gtttatccagCCTCAACAGAAGAATGACGACAAGCCATCAAACGAGGAGGAGAAGAAGTAA
EST: gi|209715415|gb|BW684699.1|BW684699
EST:     ATGACCCTTCTGTCAAGGATTTGCTGGCGTCCATGCAAAATCAGTCTGAG                         CCTCAACAGAAGAATGACGACAAGCCATCAAACGAGGAGGAGAAGAAGTAA
genomic: ATGACCCTTCTGTCAAGGATTTGCTGGCGTCCATGCAAAATCAGTCTGAGgttagtcttt ... gtttatccagCCTCAACAGAAGAATGACGACAAGCCATCAAACGAGGAGGAGAAGAAGTAA
EST: gi|37995492|gb|CF807081.1|CF807081
EST:     ATGACCCTTCTGTCAAGGATTTGCTGGCGTCCATGCAAAATCAGTCTGAG                         CCTCAACAGAAGAATGACGACAAGCCATCAAACGAGGAGGAGAAGAAGTAA
genomic: ATGACCCTTCTGTCAAGGATTTGCTGGCGTCCATGCAAAATCAGTCTGAGgttagtcttt ... gtttatccagCCTCAACAGAAGAATGACGACAAGCCATCAAACGAGGAGGAGAAGAAGTAA
EST: gi|31459111|gb|CD401139.1|CD401139
EST:     AGGATTTGCTGGCGTCCATGCAAAATCAGTCTGAG                         CCTCAACAGAAGAATGACGACAAGCCATCAAACGAGGAGGAGAAGAAGTAA
genomic: AGGATTTGCTGGCGTCCATGCAAAATCAGTCTGAGgttagtcttt ... gtttatccagCCTCAACAGAAGAATGACGACAAGCCATCAAACGAGGAGGAGAAGAAGTAA
EST: gi|193554701|gb|FK515538.1|FK515538
EST:     ATGACCCTTCTGTCAAGGATTTGCTGGCGTCCATGCAAAATCAGTCTGAG                         CCTCAACAGAAGAATGACGACAAGCCATCAAACGAGGAGGAGAAGAAGTAA
genomic: ATGACCCTTCTGTCAAGGATTTGCTGGCGTCCATGCAAAATCAGTCTGAGgttagtcttt ... gtttatccagCCTCAACAGAAGAATGACGACAAGCCATCAAACGAGGAGGAGAAGAAGTAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTCCTGGGGTTGACCCAAATGACCCTTCTGTCAAGGATTTGCTGGCGTCCATGCAAAATCAGTCTGAGgttagtctttctatgaaaaagaatatattggatttgaaaggaatttcttttagaaaatttcagtgcaggccagtaaacgttaaccttgaacacctttccc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaagaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cctttcc