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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttattttgcctctgttgaagtattaagcttttgctgtattgcatctctcttttctaacttggatttcgcttcagTGTTAGATTCATTGGTTGATCCTCTCCAGAAGACTATTAATTTTAAGCCAAAGCAAGACGCTGTCAAGCAAGAAGTAGATCGCAATGAAGACATGATTCG

Basic information

species Glycine max
transcript GLYMA07G40230.2
intron # 28
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G40230.2 (Glycine max), 3'ss of exon 28
lower sequence: LOC_Os02g07120.1 (Oryza sativa), 3'ss of exon 27
------------------gtttattttgcctctgttgaagtattaagcttttgctgtattgc-atctctcttttctaa----cttgg-atttcgcttcagTGTTAGATTCATTGGTTGATCCTCTCCAGAAGACTATTAATTTTAAGCCAAAGCAAGACGCTGTCAAGCAAGAAGTAGATCGCAATGAAGACATGATTCG
                  | |  ||  |    ||||  | ||  | ||   |||  || |   |  ||| ||| ||||    |||   ||   |  ||||| || || ||||| ||||| ||  |  |||| ||||| |||   || || |||   || || || |||||||| || |||||||||||||||||||||||
gtttgttgccttaatctaggtccttacggggatgtttca-tacgatgcaaatgccctactctgagttctttttgctaatattcttactatgctgtctcagTTTTGGACTCATTAGTTGACCCCATTGAGAAAACTATAAATCACAAACCCAAGGGCGATGCAGTGAAGCAAGAGGTTGATCGCAATGAAGACATGATTCG

upper sequence: GLYMA07G40230.2 (Glycine max), 3'ss of exon 28
lower sequence: Vv12s0035g01840.t01 (Vitis vinifera), 3'ss of exon 28
gtttattttgcctctgttgaagtattaagcttttgctgtattgcatctctcttttctaacttggatttc-----gcttcagTGTTAGATTCATTGGTTGATCCTCTCCAGAAGACTATTAATTTTAAGCCAAAGCAAGACGCTGTCAAGCAAGAAGTAGATCGCAATGAAGACATGATTCG
|||   ||    |||| |    | |  |   | || || ||   |  | || ||||| |     |||         |||||| || || |||||||| ||||| || | |||||||||||||||||| ||||||||||| ||||||||||||||||||||||| |||||||||||||||||
gttagcttaatatctgattttatttctacaatgtggtgcataataattttcatttctcatgcaaattatttgaaatttcagTATTGGACTCATTGGTGGATCCCCTTCTGAAGACTATTAATTTTAAACCAAAGCAAGATGCTGTCAAGCAAGAAGTAGATCGTAATGAAGACATGATTCG
















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|208219503|gb|GE020587.1|GE020587
EST:     GCTGACAAGTGTCCTTCTGCAGTCTTGGCAG                         TGTTAGATTCATTGGTTGATCCTCTCCAGAAGACTATTAATTTTAAGCCAA
genomic: GCTGACAAGTGTCCTTCTGCAGTCTTGGCAGgtttattttg ... ttcgcttcagTGTTAGATTCATTGGTTGATCCTCTCCAGAAGACTATTAATTTTAAGCCAA
EST: gi|207681336|gb|GD661411.1|GD661411
EST:     CCAAACTAGTTGACAAGTGTCCTTCTGCAGTCTTGGCAG                         TGTTAGATTCATTGGTTGATCCTCTCCAGAAGACTATTAATTTTAAGCCAA
genomic: CCAAACTAGCTGACAAGTGTCCTTCTGCAGTCTTGGCAGgtttattttg ... ttcgcttcagTGTTAGATTCATTGGTTGATCCTCTCCAGAAGACTATTAATTTTAAGCCAA
EST: gi|15199998|gb|BI424117.1|BI424117
EST:     CCTGATACTCTCCAAACTAGCTGACAAGTGTCCTTCTGCAGTCTTGGCAG                         TGTTAGATTCATTGGTTGATCCTCTCCAGAAGACTATTAATTTTAAGCCAA
genomic: CCTGATACTCTCCAAACTAGCTGACAAGTGTCCTTCTGCAGTCTTGGCAGgtttattttg ... ttcgcttcagTGTTAGATTCATTGGTTGATCCTCTCCAGAAGACTATTAATTTTAAGCCAA
EST: gi|7285013|gb|AW597500.1|AW597500
EST:     CCTGATACTCTCCAAACTAGCTGACAAGTGTCCTTCTGCAGTCTTGGCAG                         TGTTAGATTCATTGGTTGATCCTCTCCAGAAGACTATTAATTTTAAGCCAA
genomic: CCTGATACTCTCCAAACTAGCTGACAAGTGTCCTTCTGCAGTCTTGGCAGgtttattttg ... ttcgcttcagTGTTAGATTCATTGGTTGATCCTCTCCAGAAGACTATTAATTTTAAGCCAA
EST: gi|151410822|gb|EV280637.1|EV280637
EST:     CCTGATACTCTCCAAACTAGCTGACAAGTGTCCTTCTGCAGTCTTGGCAG                         TGTTAGATTCATTGGTTGATCCTCTCCAGAAGACTATTAATTTTAAGCCAA
genomic: CCTGATACTCTCCAAACTAGCTGACAAGTGTCCTTCTGCAGTCTTGGCAGgtttattttg ... ttcgcttcagTGTTAGATTCATTGGTTGATCCTCTCCAGAAGACTATTAATTTTAAGCCAA
EST: gi|20812570|gb|BQ297048.1|BQ297048
EST:     CCTGATACTCTCCAAACTAGCTGACAAGTGTCCTTCTGCAGTCTTGGCAG                         TGATAGATTCATTGGTTGATCCTCTCCAGAAGACTATTAATTTTAAGCCAA
genomic: CCTGATACTCTCCAAACTAGCTGACAAGTGTCCTTCTGCAGTCTTGGCAGgtttattttg ... ttcgcttcagTGTTAGATTCATTGGTTGATCCTCTCCAGAAGACTATTAATTTTAAGCCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtattaagcttttgctgtattgcatctctcttttctaacttggatttcgcttcagTGTTAGATTCATTGGTTGATCCTCTCCAGAAGACTATTAATTTTAAGCCAAAGCAAGACGCTGTCAAGCAAGAAGTAGATCGCAATGAAGACATGATTCG
                                ttctaac  putative branch site (score: 1)
                                            tttcgcttc  putative PPT
                              ttttctaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttattttgcctctgttgaagtattaagcttttgctgtattgcatctctcttttctaacttggatttcgcttcagTGTTAGATTCATTGGTTGATCCTCTCCAGAAGACTATTAATTTTAAGCCAAAGCAAGACGCTGTCAAGCAAGAAGTAGATCGCAATGAAGACATGATTCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA