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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGGGCAGGTCAGGCTTTGTTTGGAACTCTTACACCAGATATAATTGTTCTCACACTCCTATACAGCATAGCTGGAgtatgtaatattctacatggcactttgttggatatgaatatgataatatgccaaataagaatggttattaatactgttgttgtatcacattgcag

Basic information

species Glycine max
transcript GLYMA07G18470.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G18470.1 (Glycine max), 5'ss of exon 10
lower sequence: GRMZM2G162672_T02 (Zea mays), 5'ss of exon 10
GTGGGCAGGTCAGGCTTTGTTTGGAACTCTTACACCAGATATAATTGTTCTCACACTCCTATACAGCATAGCTGGAgtatgtaatattctacatggcactttgttggatatgaatatgataatatgccaaataaga-atggttattaatactgttgttgtatcacattgcag
|||||| || ||||| || ||||||||||||||||||||||| |||||  | ||     | |||||||||||||| |||| |  | | |       ||   ||||  || |   | |||| ||    || | | |  ||| | ||| |   | ||  |  || |  | |   
GTGGGCTGGCCAGGCGTTATTTGGAACTCTTACACCAGATATCATTGTCTTGACTACTTTGTACAGCATAGCTGGGgtatttcgtctcc------acatcctgttccatttcggtttgatcat---tcatacatgtcatgatgattgacctttttacttgattatgtag---

upper sequence: GLYMA07G18470.1 (Glycine max), 5'ss of exon 10
lower sequence: AT3G51820.1 (Arabidopsis thaliana), 5'ss of exon 10
GTGGGCAGGTCAGGCTTTGTTTGGAACTCTTACACCAGATATAATTGTTCTCACACTCCTATACAGCATAGCTGGAgtatgtaatattctacatggcactttgttggatatgaatatgataatatgccaaataagaatggttattaatactgttgttgtatcacattgcag
|||||| || || || |||||||| |||||||| |||||| |  ||||||| |||||| | |||||||||||||| |||     | || |      |  ||| |  | |     | |  | || ||    |  |   |  |  || ||  |||   | | | | | |||||
GTGGGCTGGCCAAGCATTGTTTGGCACTCTTACGCCAGATGTTGTTGTTCTAACACTCTTGTACAGCATAGCTGGGgtac----tcttttggcaaaccttttat--gttgcttttttcgttatctgttgtaatatgctcttgcttcatgttgtacctttgtgataatgcag

upper sequence: GLYMA07G18470.1 (Glycine max), 5'ss of exon 10
lower sequence: Vv08s0105g00590.t01 (Vitis vinifera), 5'ss of exon 10
GTGGGCAGGTCAGGCTTTGTTTGGAACTCTTACACCAGATATAATTGTTCTCACACTCCTATACAGCATAGCTGGAgtatgtaatattctacatggcactttgttggatatgaatatgataatatgccaaataagaatggttattaatactgttgttgtatcacattgcag
|||||| ||||| ||||||||||| |||||||  || ||||||||||||||||| ||| | |||||||||||||| ||||    | ||  ||| |        |   ||||| ||   |||||     ||  |   |     | ||||    || ||| ||  |||  |||
GTGGGCTGGTCAAGCTTTGTTTGGGACTCTTAATCCTGATATAATTGTTCTCACCCTCTTGTACAGCATAGCTGGGgtat----tctttcaca-gatgtgccttaacatatgtattgcataat-----aagaaccgacaaacaataatttattttttgcatttcatgccag

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|15589810|gb|BI674426.1|BI674426
EST:     CTCTTACACCAGATATAATTGTTCTCACACTCCTATACAGCATAGCTGGA                         TTGGGAATTGCTATTGTCAATGACTTCAAAAGTGTTGAAGGGGATAGGGCT
genomic: CTCTTACACCAGATATAATTGTTCTCACACTCCTATACAGCATAGCTGGAgtatgtaata ... cacattgcagTTGGGAATTGCTATTGTCAATGACTTCAAAAGTGTTGAAGGGGATAGGGCT
EST: gi|16276808|gb|BI942055.1|BI942055
EST:     TCTTACACCAGATATAATTGTTCTCACCCTCCTATACCGCATTAGCTTGA                         TTGGGAATTGCTATTGTCAATGACTTCAAAAGTGTTGAAGGGGATAGGGC
genomic: TCTTACACCAGATATAATTGTTCTCACACTCCTATACAGCAT-AGCTGGAgtatgtaata ... cacattgcagTTGGGAATTGCTATTGTCAATGACTTCAAAAGTGTTGAAGGGGATAGGGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGGGCAGGTCAGGCTTTGTTTGGAACTCTTACACCAGATATAATTGTTCTCACACTCCTATACAGCATAGCTGGAgtatgtaatattctacatggcactttgttggatatgaatatgataatatgccaaataagaatggttattaatactgttgttgtatcacattgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA