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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtatgctttaactgacatgataaaggtatctctatttcaagttggatgttgtcctaaatcctaataagttgtaaaattgcagGTTGCTATCAAGAAAATGAAGAAGAAATATTACTCTTGGGAGGAGTGTGTAAACCTGAGAGAAGTCAAG

Basic information

species Glycine max
transcript GLYMA01G35190.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G35190.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os06g02555.1 (Oryza sativa), 3'ss of exon 2
-----gtaag-tatgct-ttaactgacatgataaaggt---atctctatttcaagttggatgttgtcctaa-atcctaataagttgtaaaa---ttgcagGTTGCTATCAAGAAAATGAAGAAGAAATATTACTCTTGGGAGGAGTGTGTAAACCTGAGAGAAGTCAAG
      | |  |||  | | ||  ||  ||| |  |     ||||   ||   | | | ||  | |  | | ||  || |||  | |       |  |||||||| ||||||||||||||||| |||||||| || |||||||||||  | || ||  | ||||| |||
ccgtcatgatctatcttatgaaaagaagtgacagtgacttgatctgccttatcaatggcataattttttgacatattattaacatatctggccttgacagGTTGCAATCAAGAAAATGAAGAAAAAATATTATTCATGGGAGGAGTGCATCAATCTCCGTGAAGTGAAG

upper sequence: GLYMA01G35190.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv02s0033g01110.t01 (Vitis vinifera), 3'ss of exon 2
gtaagta-tgctttaactgacatgataaaggtatctctatttcaagttggatgttgtcctaaatcctaataagttgtaaaatt---gcagGTTGCTATCAAGAAAATGAAGAAGAAATATTACTCTTGGGAGGAGTGTGTAAACCTGAGAGAAGTCAAG
||||| |     || |  |   | ||     |    ||     || ||| ||  | |  ||| ||    |  ||| |    ||    ||||||||||| || || ||||||| ||||||||| || ||||| || ||| |||| |||||||||||||||
gtaagcagcatgttcatagtttttattgctttgaaactgaaggaaattg-attctata-taagtcagggtttgttcttttgtttcaacagGTTGCTATAAAAAAGATGAAGAGGAAATATTATTCCTGGGAAGAATGTTTAAATCTGAGAGAAGTCAAG
















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|254336468|gb|GR842647.1|GR842647
EST:     GGACTTTTGGGAGTGTCTGGAGAGCTATTAATAAGCAAACCGGTGAAGTT                         GTTGCTATCAAGAAAATGAAGAAGAAATATTACTCTTGGGAGGAGTGTGTA
genomic: GGACTTTTGGGAGTGTCTGGAGAGCTATTAATAAGCAAACCGGTGAAGTTgtaagtatgc ... aaaattgcagGTTGCTATCAAGAAAATGAAGAAGAAATATTACTCTTGGGAGGAGTGTGTA
EST: gi|254345622|gb|GR855958.1|GR855958
EST:     GGACTTTTGGGAGTGTCTGGAGAGCTATTAATAAGCAAACCGGTGAAGTT                         GTTGCTATCAAGAAAATGAAGAAGAAATATTACTCTTGGGAGGAGTGTGTA
genomic: GGACTTTTGGGAGTGTCTGGAGAGCTATTAATAAGCAAACCGGTGAAGTTgtaagtatgc ... aaaattgcagGTTGCTATCAAGAAAATGAAGAAGAAATATTACTCTTGGGAGGAGTGTGTA
EST: gi|14205773|gb|BG839451.1|BG839451
EST:     GGACTTTTGGGAGTGTCTGGAGAGCTATTAATAAGCAAACCGGTGAAGTT                         GTTGCTATCAAGAAAATGAAGAAGAAATATTACTCTTGGGAGGAGTGTGTA
genomic: GGACTTTTGGGAGTGTCTGGAGAGCTATTAATAAGCAAACCGGTGAAGTTgtaagtatgc ... aaaattgcagGTTGCTATCAAGAAAATGAAGAAGAAATATTACTCTTGGGAGGAGTGTGTA
EST: gi|208067113|gb|GD862205.1|GD862205
EST:     GGACTTTTGGGAGTGTCTGGAGAGCTATTAATAAGCAAACCGGTGAAGTT                         GTTGCTATCAAGAAAATGAAGAAGAAATATTACTCTTGGGAGGAGTGTGTA
genomic: GGACTTTTGGGAGTGTCTGGAGAGCTATTAATAAGCAAACCGGTGAAGTTgtaagtatgc ... aaaattgcagGTTGCTATCAAGAAAATGAAGAAGAAATATTACTCTTGGGAGGAGTGTGTA
EST: gi|22522544|gb|BU081355.1|BU081355
EST:     GGACTTTTGGGAGTGTCTGGAGAGCTATTAATAAGCAAACCGGTGAAGTT                         GTTGCTATCAAGAAAATGAAGAAGAAATATTACTCTTGGGAGGAGTGTGTA
genomic: GGACTTTTGGGAGTGTCTGGAGAGCTATTAATAAGCAAACCGGTGAAGTTgtaagtatgc ... aaaattgcagGTTGCTATCAAGAAAATGAAGAAGAAATATTACTCTTGGGAGGAGTGTGTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atctctatttcaagttggatgttgtcctaaatcctaataagttgtaaaattgcagGTTGCTATCAAGAAAATGAAGAAGAAATATTACTCTTGGGAGGAGTGTGTAAACCTGAGAGAAGTCAAG
                               tcctaat  putative branch site (score: 2)
                                  taataagttgtaaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtatgctttaactgacatgataaaggtatctctatttcaagttggatgttgtcctaaatcctaataagttgtaaaattgcagGTTGCTATCAAGAAAATGAAGAAGAAATATTACTCTTGGGAGGAGTGTGTAAACCTGAGAGAAGTCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT