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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgaacgataagaaagagcaatgatttttttatgacatgtcattagatgcatttgtgttgtggttagtttgtattcgggatggtgcttaactgtttctagATACGAGGAGGCGAAAGCAAAGGGGACCGATAATTATGACAGGGAGTTGGAGGATGTAATAGATAAGCTTATTGGTGAGTGTGATAGGAAAATTGGCAGG

Basic information

species Glycine max
transcript GLYMA09G38430.1
intron # 2
splice site 3'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G38430.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G17440.1 (Arabidopsis thaliana), 3'ss of exon 2
----------ttgaacgataagaaagagcaatgatttttttatgacatgtcatt----agatgcatttgtgttgtg---------gttagtttgtattcgggatggtgc---ttaact-gtttctagATACGAGGAGGCGAAAGCAAAGGGGACCGATAATTATGACAGGGAGTTGGAGGATGTAATAGATAAGCTTATTGGTGAGTGTGATAGGAAAATTGGCAGG
          || || || | | ||   |  |   || ||  ||   ||| |||    |  | ||     ||| |          |||| || |         || |     |||||| || | ||||||  | || || || ||||| ||    || || ||||| ||||| ||||| ||||  ||||||| |||||||| ||||||||||||||| ||||| |||
gtatcctttttttaatga-atgtaaagtctttttcttcttcgtgtgttgttatttctaaagtccacactagttattcagtaggatgttatttcgctcctctactgttttgctttaactcgtctttagATATAAAGATGCAAAGGCAAAAGGTGTTGACAACTATGATAGGGAATTGGAAGATGCGATAGATAGGCTTATTGTTGAGTGTGATAGGAAGATTGGTAGG

upper sequence: GLYMA09G38430.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv04s0023g00800.t01 (Vitis vinifera), 3'ss of exon 2
-ttgaacgataagaaagagcaatgattttt-ttatgacatgtcattagatgcatttgtgttgtggttagtttgtattcgggatggtgcttaactgtttctagATACGAGGAGGCGAAAGCAAAGGGGACCGATAATTATGACAGGGAGTTGGAGGATGTAATAGATAAGCTTATTGGTGAGTGTGATAGGAAAATTGGCAGG
  |   | | || | |    |   ||     | | |       || | ||   ||  | |  ||   | ||  |   |  ||  |   |||||| |||||||||| || || || |||||||| ||   | |||||||||||||||| ||||||||||| ||||||| ||| |||| |||||||||||| |||||||  || 
tatttgcaagaatatatcttatccatgcaaatcaaggtcacctataaaatatgttgatat-atgaaaatttgtttcacttgactgc-tttaactctttctagATATGAAGAAGCCAAAGCAAAAGGTGTCCATAATTATGACAGGGACTTGGAGGATGTTATAGATAGGCTCATTGTTGAGTGTGATAGAAAAATTGCTAGA
















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|18717489|gb|BM522947.1|BM522947
EST:     ATGGATATGGGCCCTTGCCCTAAGGTCCACTCCTTGCAGCTCCGGAAAGA                         ATACGAGGAGGCGAAAGCAAAGGGGACCGATAATTATGACAGGGAGTTGGA
genomic: ATGGATATGGGCCCTTGCCCTAAGGTCCACTCCTTGCAGCTCCGGAAAGAgtatccttcg ... ctgtttctagATACGAGGAGGCGAAAGCAAAGGGGACCGATAATTATGACAGGGAGTTGGA
EST: gi|213611014|gb|DB970941.1|DB970941
EST:     ATGGATATGGGCCCTTGCCCTAAGGTCCACTCCTTGCAGCTCCGGAAAGA                         ATACGAGGAGGCGAAAGCAAAGGGGACCGATAATTATGACAGGGAGTTGGA
genomic: ATGGATATGGGCCCTTGCCCTAAGGTCCACTCCTTGCAGCTCCGGAAAGAgtatccttcg ... ctgtttctagATACGAGGAGGCGAAAGCAAAGGGGACCGATAATTATGACAGGGAGTTGGA
EST: gi|8282927|gb|BE020488.1|BE020488
EST:     ATGGATATGGGCCCTTGCCCTAAGGTCCACTCCTTGCAGCTCCGGAAAGA                         ATACGAGGAGGCGAAAGCAAAGGGGACCGATAATTATGACAGGGAGTTGGA
genomic: ATGGATATGGGCCCTTGCCCTAAGGTCCACTCCTTGCAGCTCCGGAAAGAgtatccttcg ... ctgtttctagATACGAGGAGGCGAAAGCAAAGGGGACCGATAATTATGACAGGGAGTTGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatgcatttgtgttgtggttagtttgtattcgggatggtgcttaactgtttctagATACGAGGAGGCGAAAGCAAAGGGGACCGATAATTATGACAGGGAGTTGGAGGATGTAATAGATAAGCTTATTGGTGAGTGTGATAGGAAAATTGGCAGG
                                     gtgcttaac  putative branch site 
                                             ctgtttct  CT-rich tract
                      tttgtatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgaacgataagaaagagcaatgatttttttatgacatgtcattagatgcatttgtgttgtggttagtttgtattcgggatggtgcttaactgtttctagATACGAGGAGGCGAAAGCAAAGGGGACCGATAATTATGACAGGGAGTTGGAGGATGTAATAGATAAGCTTATTGGTGAGTGTGATAGGAAAATTGGCAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - -ataagaaa
- - - - - - - - agcaatg
- - - - - - - - - - - - - - - - - acatgtc
- - - - - - - - - - - - - - - - - - - - - - - -tgcattt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - gttgtgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtattc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gatggtg