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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcttcttccataaccctactaaacctataattctttacggctatatgacttatgaccattttttttatgtcgtcaccccttgaattcataatctctctagCCTCCTGAGGTATGGGATGGTGGTGAAGGATTTGTGTCAAAGGAGATGATTCAAACCCATTGCCCTGCTCCAGCACAAGATATTAAG

Basic information

species Glycine max
transcript GLYMA03G00920.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G00920.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os05g40990.1 (Oryza sativa), 3'ss of exon 7
---------------------------------------------------------------------------------tcttcttccataacc--ctactaaacctataattctttacggctatat-gacttatgaccattttttttatgtcgtcaccccttgaattcataatctctctagCCTCCTGAGGTATGGGATGGTGGTGAAGGATTTGTGTCAAAGGAGATGATTCAAACCCATTGCCCTGCTCCAGCACAAGATATTAAG
                                                                                  | ||||| |  ||   || ||||  |||  ||  | |  |  |  ||  | ||   |||||     |||   | ||| |  |||  ||||| | |     ||||||| ||  | ||| |||||||||  || |||||||||| ||| ||||| |||||||||||||| || || ||    || ||| ||
gtttgttttctgttctgaggtctagtactttgtactgtggtgtgcaataatttcatgcctgaactgtctactttggtagtcccatcttctactacttactgctaatactactatattatg-gcttgcattaaattcctaccatgcaccttacaccatcagct-ttgttttcatgagc-----agCCTCCAGAAATCTGGAATGGTGGTGTTGGGTTTGTGTCAATGGAAATGATCCAAACCCATTGCCCGGCACCTGCTGCTGACATTCAG

upper sequence: GLYMA03G00920.1 (Glycine max), 3'ss of exon 7
lower sequence: AT5G17770.1 (Arabidopsis thaliana), 3'ss of exon 7
--------------tcttcttccataaccctactaaacctataattctttacggctatatgacttatgac-cattttttttatgtcgtcaccccttga-attcataatctctctagCCTCCTGAGGTATGGGATGGTGGTGAAGGATTTGTGTCAAAGGAGATGATTCAAACCCATTGCCCTGCTCCAGCACAAGATATTAAG
              ||  |||   |  |  | || ||     ||| | | |       |    || |||  | |||| ||  ||| ||       |    |  || |      |||||||| || ||||||||||||||||  |||||||| |||||||| |||||||| || ||||||||||| || |||   |||||| ||
gttagccacaacattcaactttttttgcgtttctcaaatgtaaatacctaaaaaaagaactctttctgataccttttgttcttgttgtttttgtatatcgtctatgacaatattagCCTCCGGAAGTATGGGATGGTGGTGTTGGATTTGTATCAAAGGAAATGATTCAGACTCATTGCCCTGCACCTGCATCTGATATTCAG
















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|192301598|gb|FG994782.1|FG994782
EST:     TTGCTTCTAACTATCCAGATCGATTCAAAATATACTATGTGTTAAATCAG                         CCTCCTGAG-TATGG
genomic: TTGCTTCTAACTATCCAGATCGATTCAAAATATACTATGTGTTAAATCAGgttagtttcc ... atctctctagCCTCCTGAGGTATGG
EST: gi|209728695|gb|BW655402.1|BW655402
EST:     TTGCTTCTAACTATCCAGATCGATTCAAAATATACTATGTGTTAAATCAG                         CCTCCTGAGGTATGGGATGGTGGTGAAGGATTTGTGTCAAAGGAGATGATT
genomic: TTGCTTCTAACTATCCAGATCGATTCAAAATATACTATGTGTTAAATCAGgttagtttcc ... atctctctagCCTCCTGAGGTATGGGATGGTGGTGAAGGATTTGTGTCAAAGGAGATGATT
EST: gi|208315309|gb|GE113133.1|GE113133
EST:     TTGCTTCTAACTATCCAGATCGATTCAAAATATACTATGTGTTAAATCAG                         CCTCCTGAGGTATGGGATGGTGGTGAAGG
genomic: TTGCTTCTAACTATCCAGATCGATTCAAAATATACTATGTGTTAAATCAGgttagtttcc ... atctctctagCCTCCTGAGGTATGGGATGGTGGTGAAGG
EST: gi|151407227|gb|EV277042.1|EV277042
EST:     TTGCTTCTAACTATCCAGATCGATTCAAAATATACTATGTGTTAAATCAG                         CCTCCTGAGGTATGGGATGGGTGGTG
genomic: TTGCTTCTAACTATCCAGATCGATTCAAAATATACTATGTGTTAAATCAGgttagtttcc ... atctctctagCCTCCTGAGGTATGGGATGG-TGGTG
EST: gi|151394787|gb|EV264658.1|EV264658
EST:     TTGCTTCTAACTATCCAGATCGATTCAAAATATGCTATGTGTTAAATCAG                         CCTCCTGAGGTATGGGATGG
genomic: TTGCTTCTAACTATCCAGATCGATTCAAAATATACTATGTGTTAAATCAGgttagtttcc ... atctctctagCCTCCTGAGGTATGGGATGG
EST: gi|13251953|gb|BG362856.1|BG362856
EST:     TTGCTTCTAACTATCCAGATCGATTCAAAATATACTATGTGTTAAATCAG                         CCTCCTGAGGTATGGGATGGTGGTGAAGGATTTGTGTCAAAGGAGATGATT
genomic: TTGCTTCTAACTATCCAGATCGATTCAAAATATACTATGTGTTAAATCAGgttagtttcc ... atctctctagCCTCCTGAGGTATGGGATGGTGGTGAAGGATTTGTGTCAAAGGAGATGATT
EST: gi|58021619|gb|CX708360.1|CX708360
EST:     TTGCTTCTAACTATCCAGATCGATTCAAAATATACTATGTGTTAAATCAG                         CCTCCTGAGGTATGGGATGGTGGTGAAGGATTTGTGTCAAAGGAGATGATT
genomic: TTGCTTCTAACTATCCAGATCGATTCAAAATATACTATGTGTTAAATCAGgttagtttcc ... atctctctagCCTCCTGAGGTATGGGATGGTGGTGAAGGATTTGTGTCAAAGGAGATGATT
EST: gi|151401464|gb|EV271278.1|EV271278
EST:     TTGCTTCTAACTATCCAGATCGATTCAAA-TATACTATGTGTTAAATCA-                         CCTCCTGAGGTAT
genomic: TTGCTTCTAACTATCCAGATCGATTCAAAATATACTATGTGTTAAATCAGgttagtttcc ... atctctctagCCTCCTGAGGTAT
EST: gi|298184687|gb|HO029900.1|HO029900
EST:     TTGCTTCTAACTATCCAGATCGATTCAAAATATACTATGTGTTAAATCAG                         CCTCCTGAGGTATGGGATGGTGGTGAAGGATTTGTGTCAAAGGAGATGATT
genomic: TTGCTTCTAACTATCCAGATCGATTCAAAATATACTATGTGTTAAATCAGgttagtttcc ... atctctctagCCTCCTGAGGTATGGGATGGTGGTGAAGGATTTGTGTCAAAGGAGATGATT
EST: gi|193684767|gb|FK622291.1|FK622291
EST:     TGTCTTCTAACTATCCAGATCGATTCAAAATATACTATGTGTTAAATCAG                         CCTCCTGAGGTATGGGATGGTGGTGAAGGATTTGTGTCAAAGGAGATGATT
genomic: TG-CTTCTAACTATCCAGATCGATTCAAAATATACTATGTGTTAAATCAGgttagtttcc ... atctctctagCCTCCTGAGGTATGGGATGGTGGTGAAGGATTTGTGTCAAAGGAGATGATT
EST: gi|193434756|gb|FK403736.1|FK403736
EST:     TGCTTCTAACTATCCAGATCGATTACAAAATATACTATGTGTTAAATCAG                         CCTCCTGAGGTATGGGATGGTGGTGAA
genomic: TGCTTCTAACTATCCAGATCGATT-CAAAATATACTATGTGTTAAATCAGgttagtttcc ... atctctctagCCTCCTGAGGTATGGGATGGTGGTGAA
EST: gi|151403993|gb|EV273803.1|EV273803
EST:     TTGCTTCTAACTATCCAGATCGATTCAAAATATACTATGTGTTAAATCAG                         CCTCCTGAGGTATGGGATGGGTGGGTGAAAGGATTTGTGTCAAAGGAGATG
genomic: TTGCTTCTAACTATCCAGATCGATTCAAAATATACTATGTGTTAAATCAGgttagtttcc ... atctctctagCCTCCTGAGGTATGGGATGG-TGG-TGAA-GGATTTGTGTCAAAGGAGATG
EST: gi|56173100|gb|CV997226.1|CV997226
EST:     TTGCTTCTAACTATCCAGATCGATTCAAAATATACTATGTGTTAAATCAG                         CCTCCTGAGGTATGGGATGGTGGTGAAGGATTTGTGTCAAAGGAGATGATT
genomic: TTGCTTCTAACTATCCAGATCGATTCAAAATATACTATGTGTTAAATCAGgttagtttcc ... atctctctagCCTCCTGAGGTATGGGATGGTGGTGAAGGATTTGTGTCAAAGGAGATGATT
EST: gi|37995436|gb|CF807025.1|CF807025
EST:     TTGCTTCTAACTATCCAGATCGATTCAAAATATACTATGTGTTAAATCAG                         CCTCCTGAGGTATGGGATGGTGGTGAAGGATTTGTGTCAAAGGAGATGATT
genomic: TTGCTTCTAACTATCCAGATCGATTCAAAATATACTATGTGTTAAATCAGgttagtttcc ... atctctctagCCTCCTGAGGTATGGGATGGTGGTGAAGGATTTGTGTCAAAGGAGATGATT
EST: gi|207830162|gb|GD804570.1|GD804570
EST:     TTGCTTCTAACTATCCAGATCGATTCAAAATATACTATGTGTTAAATCAG                         CCTCCTGAGGTATGGGATGGTGGTGAAGGATTTGTGTCAAAGGAG
genomic: TTGCTTCTAACTATCCAGATCGATTCAAAATATACTATGTGTTAAATCAGgttagtttcc ... atctctctagCCTCCTGAGGTATGGGATGGTGGTGAAGGATTTGTGTCAAAGGAG
EST: gi|151399348|gb|EV269219.1|EV269219
EST:     TTGCTTCTAACTATCCAGATCGATTCAAAATATACTATGTGTTAAATCAG                         CCTCCTGAGGTATGGGATGGTGGTGAAGGATTTGTGTCAAAGGAGATGATT
genomic: TTGCTTCTAACTATCCAGATCGATTCAAAATATACTATGTGTTAAATCAGgttagtttcc ... atctctctagCCTCCTGAGGTATGGGATGGTGGTGAAGGATTTGTGTCAAAGGAGATGATT
EST: gi|193576645|gb|FK533728.1|FK533728
EST:     GATCGATTCAAAATATACTATGTGTTAAATCAG                         CCTCCTGAGGTATGGGATGGTGGTGAAGGATTTGTGTCAAAGGAGATGATT
genomic: GATCGATTCAAAATATACTATGTGTTAAATCAGgttagtttcc ... atctctctagCCTCCTGAGGTATGGGATGGTGGTGAAGGATTTGTGTCAAAGGAGATGATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgacttatgaccattttttttatgtcgtcaccccttgaattcataatctctctagCCTCCTGAGGTATGGGATGGTGGTGAAGGATTTGTGTCAAAGGAGATGATTCAAACCCATTGCCCTGCTCCAGCACAAGATATTAAG
                                              tctctct  CT-rich tract
            attttttttatgt  TA-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcttcttccataaccctactaaacctataattctttacggctatatgacttatgaccattttttttatgtcgtcaccccttgaattcataatctctctagCCTCCTGAGGTATGGGATGGTGGTGAAGGATTTGTGTCAAAGGAGATGATTCAAACCCATTGCCCTGCTCCAGCACAAGATATTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- ttcttcc
- - - - - - - - - ctaaacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcacccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgaattc