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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTAAGTATGTTGGAAACCGTCCTATAAAACTACGCAAGAGTAAGTGGAGGGAGAGGACAGATTATGAAGCACTGGAGAAACAGAAGgtagcaattttctttgtcaatgatttgaaattatgctgttaaatgtaaccttttgtatgaccaacttaattcttctattgtttacatggcag

Basic information

species Glycine max
transcript GLYMA10G30900.2
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G30900.2 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G068255_T01 (Zea mays), 5'ss of exon 4
GTAAGTATGTTGGAAACCGTCCTATAAAACTACGCAAGAGTAAGTGGAGGGAGAGGACAGATTATGAAGCACTGGAGAAACAGAAGgtagcaattttctttgtcaatgatttgaaattatgctgttaaatgtaaccttttgtatgaccaacttaattcttctattgtttacatggcag
| ||||||||||| ||||| ||||| ||| | || |||||||| |||| |||||||||||||  ||| || ||||| | ||| ||||||    | |  ||  |      ||| ||  | | || |    |||  |||||  | |   | |      | ||| || ||| |        
GAAAGTATGTTGGGAACCGCCCTATTAAATTGCGTAAGAGTAACTGGAAGGAGAGGACAGATGTTGAGGCTCTGGAAAGACAAAAGgtacttgtctatttccttc----tttaaatgttttctctc---tgtgtcctttaatttcgtctat---gcttttccatcgttcag-------

upper sequence: GLYMA10G30900.2 (Glycine max), 5'ss of exon 5
lower sequence: AT3G04500.1 (Arabidopsis thaliana), 5'ss of exon 5
GTAAGTATGTTGGAAACCGTCCTATAAAACTACGCAAGAGTAAGTGGAGGGAGAGGACAGATTATGAAGCACTGGAGAAACAGAAGgtagcaattttctttgtcaatgatttga-aattatgctgttaaatgtaaccttttgtatgaccaacttaattctt--ctattgtttacatggcag-------------------
|||||||||||||||| ||||| ||||||||||| |||||||  ||||  ||||| |||||| | || ||    || | ||| |||| |   || ||   |   || | ||||| |  ||   |   ||| |      ||| |||||  | || |||||||   |||   | |     |                     
GTAAGTATGTTGGAAATCGTCCGATAAAACTACGAAAGAGTAGCTGGAAAGAGAGAACAGATCAGGAGGCTGCTGAAAGACAAAAGgcaagtatcttgact-cgaacgttttgatagatacatttgcaaaggattttatttttatgagtatct-aattcttgattataactgatggttctctgtttgattgtaaatgcag

upper sequence: GLYMA10G30900.2 (Glycine max), 5'ss of exon 5
lower sequence: Vv09s0018g01710.t01 (Vitis vinifera), 5'ss of exon 5
GTAAGTATGTTGGAAACCGTCCTATAAAACTACGCAAGAGTAAGTGGAGGGAGAGGACAGATTATGAAGCACTGGAGAAACAGAAGgtag---caattttctttgtcaatgatttgaaattatgctgttaaatgtaaccttttgtatg---accaacttaattcttctattg-tttacatggcag
| ||||||||||||||  | || || |||||||| ||||| || |||| |||||||||||||| ||||||  |||| | ||| ||||||    ||   || | |||  | |  ||  |  | |  || |     |  | ||  ||  |   ||  |||| || | |||  ||  | || ||||||
GCAAGTATGTTGGAAATAGGCCAATCAAACTACGGAAGAGCAATTGGAAGGAGAGGACAGATTCTGAAGCCTTGGAAAGACAAAAGgtatattcacacttttgtgtttacggcttccatgttta-tgctttgccttcctttgggtgggtatacttactttatccatctcctgactcacttggcag

upper sequence: GLYMA10G30900.2 (Glycine max), 5'ss of exon 5
lower sequence: Vv14s0036g00630.t01 (Vitis vinifera), 5'ss of exon 5
GTAAGTATGTTGGAAACCGTCCTATAAAACTACGCAAGAGTAAGTGGAGGGAGAGGACAGATTATGAAGCACTGGAGAAACAGAAGgtagcaattttctttgtcaatgatttgaaattatgct---gttaaatgtaaccttttgtatgaccaacttaattcttctattgtttacatggcag
| || |||||||||||  | || || |||||||| ||||| || ||||||||||||||||||| ||||||  |||| | ||| ||||||      |||||||    ||  | |     ||| |   | |     | || ||  |||||   |  ||   | |    |   | || ||||||
GAAAATATGTTGGAAATAGGCCAATCAAACTACGTAAGAGCAATTGGAGGGAGAGGACAGATTTTGAAGCCTTGGAAAGACAAAAGgtacattaattctttggtgttgtatggcttccatgtttatgctttgccttactttgggtatgcttactttgggtgtctcctgactcacttggcag

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|208150188|gb|GD950247.1|GD950247
EST:     AGAGTAAGTGGAGGGAGAGGACAGATTATGAAGCACTGGAGAAACAGAAG                         AATCACATTCAAAAGAAACCGAAAATGGCAAGGAAAGGTGTGCTGCACAAG
genomic: AGAGTAAGTGGAGGGAGAGGACAGATTATGAAGCACTGGAGAAACAGAAGgtagcaattt ... tacatggcagAATCACATTCAAAAGAAACCGAAAATGGCAAGGAAAGGTGTGCTGCACAAG
EST: gi|7284795|gb|AW597220.1|AW597220
EST:     GTGGAGGGAGAGGACAGATTATGAAGCACTGGAGAAACAGAAG                         AATCACATTCAAAAGAAACCGAAAATGGCAAGGAAAGGTGTGCTGCACAAG
genomic: GTGGAGGGAGAGGACAGATTATGAAGCACTGGAGAAACAGAAGgtagcaattt ... tacatggcagAATCACATTCAAAAGAAACCGAAAATGGCAAGGAAAGGTGTGCTGCACAAG
EST: gi|15664653|gb|BI702024.1|BI702024
EST:     AGAGTAAGTGGAGGGAGAGGACAGATTATGAAGCACTGGAGAAACAGAAG                         AATCACATTCAAAAGAAACCGAAAATGGCAAGGAAAGGTGTGCTGCACAAG
genomic: AGAGTAAGTGGAGGGAGAGGACAGATTATGAAGCACTGGAGAAACAGAAGgtagcaattt ... tacatggcagAATCACATTCAAAAGAAACCGAAAATGGCAAGGAAAGGTGTGCTGCACAAG
EST: gi|193355864|gb|FK323473.1|FK323473
EST:     AGAGTAAGTGGAGGGAGAGGACAGATTATGAAGCACTGGAGAAACAGAAG                         AATCACATTCAAAAGAAAACCGAAAAATGGCAAGGAAAGGT
genomic: AGAGTAAGTGGAGGGAGAGGACAGATTATGAAGCACTGGAGAAACAGAAGgtagcaattt ... tacatggcagAATCACATTCAAAAGAAA-CCGAAAA-TGGCAAGGAAAGGT
EST: gi|193457410|gb|FK423176.1|FK423176
EST:     AGAGGACAGATTATGAAGCACTGGAGAAACAGAAG                         AATCACATTCAAAAGAAACCGAAAATGGCAAGGAAAGGTGTGCTGCACAAG
genomic: AGAGGACAGATTATGAAGCACTGGAGAAACAGAAGgtagcaattt ... tacatggcagAATCACATTCAAAAGAAACCGAAAATGGCAAGGAAAGGTGTGCTGCACAAG
EST: gi|6341837|gb|AW164661.1|AW164661
EST:     AGAGTAAGTGGAGGGAGAGGACAGATTATGAAGCACTGGAGAAACAGAAG                         AATCACATTCAAAAGAAACCGAAAATGGCAAGGAAAGGTGTGCTGCACAAG
genomic: AGAGTAAGTGGAGGGAGAGGACAGATTATGAAGCACTGGAGAAACAGAAGgtagcaattt ... tacatggcagAATCACATTCAAAAGAAACCGAAAATGGCAAGGAAAGGTGTGCTGCACAAG
EST: gi|207793984|gb|GD763874.1|GD763874
EST:     AGAGTAAGTGGAGGGAGAGGACAGATTATGAAGCACTGGAGAAACAGAAG                         AATCACATTCAAAAGAAACCGAAAATGGCAAGGAAAGGTGTGCTGCACAAG
genomic: AGAGTAAGTGGAGGGAGAGGACAGATTATGAAGCACTGGAGAAACAGAAGgtagcaattt ... tacatggcagAATCACATTCAAAAGAAACCGAAAATGGCAAGGAAAGGTGTGCTGCACAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTAAGTATGTTGGAAACCGTCCTATAAAACTACGCAAGAGTAAGTGGAGGGAGAGGACAGATTATGAAGCACTGGAGAAACAGAAGgtagcaattttctttgtcaatgatttgaaattatgctgttaaatgtaaccttttgtatgaccaacttaattcttctattgtttacatggcag

- - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA