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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTCTCAGTGCATGGTAGTGATGAAGAGATTGACGATCAACCAGAGGTGGGCAGTGATGAGGATTTTAGTGATGATGGCGGCAAACATGCCCTTGAAGAGgtagacttctgttttcatgttttaactcatttacctatctgtatatgttatgaaattttccctacagtttcaagtcttttgggttgattttggttttgtg...

Basic information

species Glycine max
transcript GLYMA11G20130.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G20130.1 (Glycine max), 5'ss of exon 6
lower sequence: Vv06s0061g00280.t01 (Vitis vinifera), 5'ss of exon 7
TTTCTCAGTGCATGGTAGTGATGAAGAGATTGACGATCAACCAGAGGTGGGCAGTGATGAGGATTTTAGTGATGATGGCGGCAAACATGCCCTTGAAGAGgtagacttctgttttcatgttttaactcatttacct--atctgtatatgttatgaaattttccctacagtttcaagtcttttgggttgattttggttttgtg
    ||||||  ||| |||||||||||| |||| |||| ||| ||||||| ||||||||||||| | || ||||| | |  ||| |    || ||| ||||||      ||  ||  || ||||| |  |     |  || ||  | || |||||| || |          || ||  ||| | |     ||  |       
ACATTCAGTGTTTGGCAGTGATGAAGAGGTTGATGATCCACCTGAGGTGGACAGTGATGAGGATCTCAGCGATGACGCCAACAAGCTGATCCATGAGGAGgtactaaaatggcttagtgatttaaattttgatgttgaatttgagtttgatatgaatttctggaatggtcctcgagaatttggtggactcttcaggccaa--
















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|9983348|gb|BE657456.1|BE657456
EST:     GCAGTGATGAGGATTTTAGTGATGATGNNGGCAAACATGCCCTTGAAGAG                         GTAGGATCAGTTGATGAGGAATCAACAAAATCCGACGAAGAGTATGATGAT
genomic: GCAGTGATGAGGATTTTAGTGATGATGGCGGCAAACATGCCCTTGAAGAGgtagacttct ... tgctttgcagGTAGGATCAGTTGATGAGGAATCAACAAAATCCGACGAAGAGTATGATGAT
EST: gi|51342988|gb|CO983721.1|CO983721
EST:     GCAGTGATGAGGATTTTAGTGATGATGGCGGCAAACATGCCCTTGAAGAG                         GTAGGATCAGTTGATGAGGAATCAACAAAATCCGACGAAGAGTATGATGAT
genomic: GCAGTGATGAGGATTTTAGTGATGATGGCGGCAAACATGCCCTTGAAGAGgtagacttct ... tgctttgcagGTAGGATCAGTTGATGAGGAATCAACAAAATCCGACGAAGAGTATGATGAT
EST: gi|10846412|gb|BF069315.1|BF069315
EST:     GCAGTGATGAGGATTTTAGTGATGATGGCGGCAAACATGCCCTTGAAGAG                         GTAGGATCAGTTGATGAGGAATCAACAAAATCCGACGAAGAGTATGATGAT
genomic: GCAGTGATGAGGATTTTAGTGATGATGGCGGCAAACATGCCCTTGAAGAGgtagacttct ... tgctttgcagGTAGGATCAGTTGATGAGGAATCAACAAAATCCGACGAAGAGTATGATGAT
EST: gi|6916259|gb|AW397789.1|AW397789
EST:     GCAGTGATGAGGATTTTAGTGATGATGGCGGCAAACATGCCCTTGAAGAG                         GTAGGATCAGTTGATGAGGAATCAACAAAATCCGACGAAGAGTATGATGAT
genomic: GCAGTGATGAGGATTTTAGTGATGATGGCGGCAAACATGCCCTTGAAGAGgtagacttct ... tgctttgcagGTAGGATCAGTTGATGAGGAATCAACAAAATCCGACGAAGAGTATGATGAT
EST: gi|151398828|gb|EV268699.1|EV268699
EST:     GCAGTGATGAGGATTTTAGTGATGATGGCGGCAAACATGCCCTTGAAGAG                         GTAGGATCAGTTGATGAGGAATCAACAAAATCCGACGAAGAGTATGATGAT
genomic: GCAGTGATGAGGATTTTAGTGATGATGGCGGCAAACATGCCCTTGAAGAGgtagacttct ... tgctttgcagGTAGGATCAGTTGATGAGGAATCAACAAAATCCGACGAAGAGTATGATGAT
EST: gi|151401672|gb|EV271485.1|EV271485
EST:     GCAGTGATGAGGATTTTAGTGATGATGGCGGCAAACATGCCCTTGAAGAG                         GTAGGATCAGTTGATGAGGAATCAACAAAATCCGACGAAGAGTATGATGAT
genomic: GCAGTGATGAGGATTTTAGTGATGATGGCGGCAAACATGCCCTTGAAGAGgtagacttct ... tgctttgcagGTAGGATCAGTTGATGAGGAATCAACAAAATCCGACGAAGAGTATGATGAT
EST: gi|209724198|gb|BW658104.1|BW658104
EST:     GCAGTGATGAGGATTTTAGTGATGATGGCGGCAAACATGCCCTTGAAGAG                         GTAGGATCAGTTGATGAGGAATCAACAAAATCCGACGAAGAGTATGATGAT
genomic: GCAGTGATGAGGATTTTAGTGATGATGGCGGCAAACATGCCCTTGAAGAGgtagacttct ... tgctttgcagGTAGGATCAGTTGATGAGGAATCAACAAAATCCGACGAAGAGTATGATGAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTCTCAGTGCATGGTAGTGATGAAGAGATTGACGATCAACCAGAGGTGGGCAGTGATGAGGATTTTAGTGATGATGGCGGCAAACATGCCCTTGAAGAGgtagacttctgttttcatgttttaactcatttacctatctgtatatgttatgaaattttccctacagtttcaagtcttttgggttgattttggttttgtg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA