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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattgaatacaaatacaataataatcgttcattctattgaataagaagtaaataaatggttggtgcaatgcagGGAACGTTGGGGCTGATCATGCTGTGTTTGAGCAAGGTGCTTCCGCTGGAAATGTCGGAAAGGAAAAGATGGTGGAGCAGAAGAAGGCAAATCCTGTTGC

Basic information

species Glycine max
transcript GLYMA14G00500.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G00500.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os04g40310.2 (Oryza sativa), 3'ss of exon 3
------------------------gtaattgaatacaaatacaataataatcgttcattctat-tgaataagaagtaaata-aatggttggtgcaatgcagGGAACGTTGGGGCTGATCATGCTGTGTTTGAGCAAGGTGCTTCCGCTGGAAATGTCGGAAAGGAAAAGATGGTGGAGCAGAAGAAGGCAAATCCTGTTGC
                          | |||  | ||  |      |  ||  || |||| |  ||  | |  | |   || | | |         |||||| || || ||    || |||||||| ||||||||||||||||| || ||||| |||||||| || || ||  | ||||||||||| ||||| ||| ||||
acccattttatatgtttggaccacccagttggtt-catttttgtataccataattaattcaacgtggtttactaatccttatattcgccatcctgttgcagGTAATGTGGGTCAGGACCATGCTGTCTTTGAGCAAGGTGCTTCTGCAGGAAACGTCGGAAACGAGAACATCTTAGAGCAGAAGAAAGCAAACCCTATTGC
















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|22928993|gb|BU546132.1|BU546132
EST:     GGCTAATACGGCAGCTGGAATTGCCGGTGGCACTGGGGTCATGCCCGGAG                         GGAACGTTGGGGCTGATCATGCTGTGTTTGAGCAAGGTGCTTCCGCTGGAA
genomic: GGCTAATACGGCAGCTGGAATTGCCGGTGGCACTGGGGTCATGCCCGGAGgtaattgaat ... tgcaatgcagGGAACGTTGGGGCTGATCATGCTGTGTTTGAGCAAGGTGCTTCCGCTGGAA
EST: gi|193522206|gb|FK478201.1|FK478201
EST:     AATTGCCGGTGGCACTGGGGTCATGCCCGGAG                         GGAACGTTGGGGCTGATCATGCTGTGTTTGAGCAAGGTGCTTCCGCTGGAA
genomic: AATTGCCGGTGGCACTGGGGTCATGCCCGGAGgtaattgaat ... tgcaatgcagGGAACGTTGGGGCTGATCATGCTGTGTTTGAGCAAGGTGCTTCCGCTGGAA
EST: gi|7924578|gb|AW830604.1|AW830604
EST:     GGCTAATACGGCAGCTGGAATTGCCGGTGGCACTGGGGTCATGCCCGGAT                         GGAACGTTGGGGCTGATCATGCTGTGTTTGAGCAAAGTGCT
genomic: GGCTAATACGGCAGCTGGAATTGCCGGTGGCACTGGGGTCATGCCCGGAGgtaattgaat ... tgcaatgcagGGAACGTTGGGGCTGATCATGCTGTGTTTGAGCAAGGTGCT
EST: gi|193555830|gb|FK516443.1|FK516443
EST:     AATTGCCGGTGGCACTGGGGTCATGCCCGGAG                         GGAACGTTAGGGGCTGATCATGCTGTGTTTGAGCAAGGTGCTTCCGCTGGA
genomic: AATTGCCGGTGGCACTGGGGTCATGCCCGGAGgtaattgaat ... tgcaatgcagGGAACGTT-GGGGCTGATCATGCTGTGTTTGAGCAAGGTGCTTCCGCTGGA
EST: gi|193457614|gb|FK424906.1|FK424906
EST:     AATTGCCGGTGGCACTGGGGTCATGCCCGGAG                         GGAACGTTGGGGCTGATCATGCTGTGTTTGAGCAAGGTGCTTCCGC
genomic: AATTGCCGGTGGCACTGGGGTCATGCCCGGAGgtaattgaat ... tgcaatgcagGGAACGTTGGGGCTGATCATGCTGTGTTTGAGCAAGGTGCTTCCGC
EST: gi|207790179|gb|GD762688.1|GD762688
EST:     AATTGCCGGTGGCACTGGGGTCATGCCCGGAG                         GGAACGTTGGGGCTGATCATGCTGTGTTTGAGCAAGGTGCTTCCGCTGGAA
genomic: AATTGCCGGTGGCACTGGGGTCATGCCCGGAGgtaattgaat ... tgcaatgcagGGAACGTTGGGGCTGATCATGCTGTGTTTGAGCAAGGTGCTTCCGCTGGAA
EST: gi|207824679|gb|GD793829.1|GD793829
EST:     AATTGCCGGTGGCACTGGGGTCATGCCCGGAG                         GGAACGTTGGGGCTGATCATGCTGTGTTTGAGCAAGGTGCTTCCGCTGGAA
genomic: AATTGCCGGTGGCACTGGGGTCATGCCCGGAGgtaattgaat ... tgcaatgcagGGAACGTTGGGGCTGATCATGCTGTGTTTGAGCAAGGTGCTTCCGCTGGAA
EST: gi|193612976|gb|FK565079.1|FK565079
EST:     GGCTAATACGGCAGCTGGAATTGCCGGTGGCACTGGGGTCATGCCCGGAG                         GGAACGTTGGGGCTGATCATGCTGTGTTTGAGCAAGGTGCTTCCGCTGGAA
genomic: GGCTAATACGGCAGCTGGAATTGCCGGTGGCACTGGGGTCATGCCCGGAGgtaattgaat ... tgcaatgcagGGAACGTTGGGGCTGATCATGCTGTGTTTGAGCAAGGTGCTTCCGCTGGAA
EST: gi|22927386|gb|BU544525.1|BU544525
EST:     GGCTAATACGGCAGCTGGAATTGCCGGTGGCACTGGGGTCATGCCCGGAG                         GGAACGTTGGGGCTGATCATGCTGTGTTTGAGCAAGGTGCTTCCGCTGGAA
genomic: GGCTAATACGGCAGCTGGAATTGCCGGTGGCACTGGGGTCATGCCCGGAGgtaattgaat ... tgcaatgcagGGAACGTTGGGGCTGATCATGCTGTGTTTGAGCAAGGTGCTTCCGCTGGAA
EST: gi|208163744|gb|GD963272.1|GD963272
EST:     GGCTAATACGGCAGCTGGAATTGCCGGTGGCACTGGGGTCATGCCCGGAG                         GGAACGTTGGGGCNGATCATGCTGTGTTTGAGCAAAGGTGCTTCCGCT
genomic: GGCTAATACGGCAGCTGGAATTGCCGGTGGCACTGGGGTCATGCCCGGAGgtaattgaat ... tgcaatgcagGGAACGTTGGGGCTGATCATGCTGTGTTTGAGCAA-GGTGCTTCCGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taataatcgttcattctattgaataagaagtaaataaatggttggtgcaatgcagGGAACGTTGGGGCTGATCATGCTGTGTTTGAGCAAGGTGCTTCCGCTGGAAATGTCGGAAAGGAAAAGATGGTGGAGCAGAAGAAGGCAAATCCTGTTGC
            attctattgaataaga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattgaatacaaatacaataataatcgttcattctattgaataagaagtaaataaatggttggtgcaatgcagGGAACGTTGGGGCTGATCATGCTGTGTTTGAGCAAGGTGCTTCCGCTGGAAATGTCGGAAAGGAAAAGATGGTGGAGCAGAAGAAGGCAAATCCTGTTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG