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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAAGTATGTTGGAAATCGGCCGATAAAACTACGCAAGAGTAAGTGGAAGGAGAGGACAGATTATGAAGCACTGGAAAAACAGAAGgtcgcaactttctttgtaaatgatttgaaattgtttttaatgtatgtctaacttaattcttctattgtttaaatgacag

Basic information

species Glycine max
transcript GLYMA11G01300.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G01300.1 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G016106_T01 (Zea mays), 5'ss of exon 4
GAAAGTATGTTGGAAATCGGCCGATAAAACTACGCAAGAGTAAGTGGAAGGAGAGGACAGATTATGAAGCACTGGAAAAACAGAAGgtcgcaactttctttgtaaatgatttgaaattgtttttaatgtatg-tctaacttaattcttctattgtttaaatgacag
||||||||||||| ||||| || || ||| | || |||||||| ||||||||||||||||||  ||| || ||| ||| ||| ||||| || |      |  |   | || ||   ||| | |  |||| |  ||||| ||  | | |   || |  |     |||
GAAAGTATGTTGGGAATCGCCCTATTAAATTGCGTAAGAGTAACTGGAAGGAGAGGACAGATGTTGAGGCTCTGCAAAGACAAAAGgtagctatccatctccttcgttatgtgtt-ttgctctccatgtctcctctaatttcgtccatgcttt-tccatccttcag

upper sequence: GLYMA11G01300.1 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G068255_T01 (Zea mays), 5'ss of exon 4
GAAAGTATGTTGGAAATCGGCCGATAAAACTACGCAAGAGTAAGTGGAAGGAGAGGACAGATTATGAAGCACTGGAAAAACAGAAGgt-----cgcaactttctttgtaaatgatttgaaattgtttttaatgtatgtctaacttaattcttctattgtttaaatgacag
||||||||||||| || || || || ||| | || |||||||| ||||||||||||||||||  ||| || ||||||| ||| |||||        |  |   | | |||||| |||     ||| |    | ||  |    ||    | ||| || ||| |        
GAAAGTATGTTGGGAACCGCCCTATTAAATTGCGTAAGAGTAACTGGAAGGAGAGGACAGATGTTGAGGCTCTGGAAAGACAAAAGgtacttgtctatttccttctttaaatgttttctctctgtgtcc--tttaatttcgtctatgcttttccatcgttcag-------

upper sequence: GLYMA11G01300.1 (Glycine max), 5'ss of exon 5
lower sequence: AT3G04500.1 (Arabidopsis thaliana), 5'ss of exon 5
GAAAGTATGTTGGAAATCGGCCGATAAAACTACGCAAGAGTAAGTGGAAGGAGAGGACAGATTATGAAGCACTGGAAAAACAGAAGg------tcgcaactt-----tctttgtaaatg-atttgaaattgttttta-----atgtatgtctaa--cttaattctt-ctattgtttaaatgacag-------------
| ||||||||||||||||| |||||||||||||| |||||||  ||||| ||||| |||||| | || ||    |||| ||| ||||      ||   |||      | ||  || ||  ||||| ||  | |||||     |||  | |||||  ||| ||| |  ||  || ||   ||   |             
GTAAGTATGTTGGAAATCGTCCGATAAAACTACGAAAGAGTAGCTGGAAAGAGAGAACAGATCAGGAGGCTGCTGAAAGACAAAAGgcaagtatcttgactcgaacgttttgatagatacatttgcaaaggattttatttttatgagtatctaattcttgattataactgatggttctctgtttgattgtaaatgcag

upper sequence: GLYMA11G01300.1 (Glycine max), 5'ss of exon 5
lower sequence: Vv09s0018g01710.t01 (Vitis vinifera), 5'ss of exon 5
GAAAGTATGTTGGAAATCGGCCGATAAAACTACGCAAGAGTAAGTGGAAGGAGAGGACAGATTATGAAGCACTGGAAAAACAGAAGgt-----cgcaacttt-------------ctttgtaaatgatttgaaattgtttttaatgtatgt-ctaacttaattcttctattg-tttaaatgacag
| ||||||||||||||| |||| || |||||||| ||||| || ||||||||||||||||||| ||||||  |||||| ||| |||||     | ||  |||             |  |||  ||| ||||   ||  |||   ||  | | || |||| || | |||  ||  | |  || |||
GCAAGTATGTTGGAAATAGGCCAATCAAACTACGGAAGAGCAATTGGAAGGAGAGGACAGATTCTGAAGCCTTGGAAAGACAAAAGgtatattcacacttttgtgtttacggcttccatgtttatgctttgcc-ttcctttgggtgggtatacttactttatccatctcctgactcacttggcag

upper sequence: GLYMA11G01300.1 (Glycine max), 5'ss of exon 5
lower sequence: Vv14s0036g00630.t01 (Vitis vinifera), 5'ss of exon 5
GAAAGTATGTTGGAAATCGGCCGATAAAACTACGCAAGAGTAAGTGGAAGGAGAGGACAGATTATGAAGCACTGGAAAAACAGAAGgtcgcaactttctttgtaaatgatttgaaattgtttttaatgtatgtctaacttaattcttctattgtttaaatgacag----------------
|||| |||||||||||| |||| || |||||||| ||||| || |||| |||||||||||||| ||||||  |||||| ||| |||||       |||||||    ||  | |      | ||||   | || || ||||      |   |  |||   || |                  
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|208153822|gb|GD954791.1|GD954791
EST:     AGAGTAAGTAGAAGGAGAGGACAGATTATGAAGCACTGGAAAAACAGAAG                         AATCACATTCAAAAGAAACCGAAATTGCCAAGGAAAGGCGTGCTGCACAAG
genomic: AGAGTAAGTGGAAGGAGAGGACAGATTATGAAGCACTGGAAAAACAGAAGgtcgcaactt ... taaatgacagAATCACATTCAAAAGAAACCGAAATTGCCAAGGAAAGGCGTGCTGCACAAG
EST: gi|208290546|gb|GE087608.1|GE087608
EST:     AGAGTAAGTGGAAGGAGAGGACAGATTATGAAGCACTGGAAAAACAGAAG                         AATCACATTCAAAAGAAACCGAAATTGCCAAGGAAAGGCGTG
genomic: AGAGTAAGTGGAAGGAGAGGACAGATTATGAAGCACTGGAAAAACAGAAGgtcgcaactt ... taaatgacagAATCACATTCAAAAGAAACCGAAATTGCCAAGGAAAGGCGTG
EST: gi|6725839|gb|AW310238.1|AW310238
EST:     AGAGTAAGTGGAAGGAGAGGACAGATTATGAAGCACTGGAAAAACAGAAG                         AATCACATTCAAAAGAAACCGAAATTGCCAAGGAAAGGCGTGCTGCACAAG
genomic: AGAGTAAGTGGAAGGAGAGGACAGATTATGAAGCACTGGAAAAACAGAAGgtcgcaactt ... taaatgacagAATCACATTCAAAAGAAACCGAAATTGCCAAGGAAAGGCGTGCTGCACAAG
EST: gi|207740117|gb|GD714727.1|GD714727
EST:     AGAGTAAGTGGAAGGAGAGGACAGATTATGAAGCACTGGAAAAACAGAAG                         AATCACATTCAAAAGAAACCGAAATTGCCAAG
genomic: AGAGTAAGTGGAAGGAGAGGACAGATTATGAAGCACTGGAAAAACAGAAGgtcgcaactt ... taaatgacagAATCACATTCAAAAGAAACCGAAATTGCCAAG
EST: gi|6566353|gb|AW234022.1|AW234022
EST:     AGAGTAAGTGGAAGGAGAGGACAGATTATGAAGCACTGGAAAAACAGAAG                         AATCACATTCAAAAGAAACCGAAATTGCCAAGGAAAGGCGTGCTGCACAAG
genomic: AGAGTAAGTGGAAGGAGAGGACAGATTATGAAGCACTGGAAAAACAGAAGgtcgcaactt ... taaatgacagAATCACATTCAAAAGAAACCGAAATTGCCAAGGAAAGGCGTGCTGCACAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAAGTATGTTGGAAATCGGCCGATAAAACTACGCAAGAGTAAGTGGAAGGAGAGGACAGATTATGAAGCACTGGAAAAACAGAAGgtcgcaactttctttgtaaatgatttgaaattgtttttaatgtatgtctaacttaattcttctattgtttaaatgacag

- - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC