Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctactttttcatggtgtcaccatgattctgtggagtaaaatttattcttgtgtgttatccaaactcactatgaatgtgctttgttgtgtgtggatgcagCAAAGTGGTTCGGCTTTCGATAGCGCGGGTGCTGACAGTGATTTCCCAGAAGCAAAAGGCAGCGTTGAGGGAAGCTTACAAGAAGAAGAAATACCTTCCT

Basic information

species Glycine max
transcript GLYMA15G04730.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G04730.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os04g30730.1 (Oryza sativa), 3'ss of exon 2
-----tctactttttcatggtgtcaccatgattctgtggagtaaaatttattcttgtgtgttatccaaactcactatgaatgtgctttgttgtgtgtggatgcagCAAAGTGGTTCGGCTTTCGATAGCGCGGGTGCTGACAGTGATTTCCCAGAAGCAAAAGGCAGCGTTGAGGGAAGCTTACAAGAAGAAGAAATACCTTCCT
      || |||  || |  | || |  |  ||   ||| ||            ||  | |    ||  |    | |    ||| |   || | | |    ||||||| ||||| ||    ||||| ||||| |||||||| ||||| || |||||||| ||||| ||| ||||||| || |||||||||||||     || || 
gtgcgcctccttcctccttctctctcgctcgtttgttggtgtgg---------ctggatctcgctca--cgggttcttggggtggtgaatttttttt---cgcagCAAGGTGGTGCGCACCTCGATCGCGCGCGTGCTGACGGTGATCTCGCAGAAGCAGAAGGCGGCGCTGAGGGAGGCGTACAAGAAGAAGAGCCTGCTCCCG

upper sequence: GLYMA15G04730.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os02g30050.1 (Oryza sativa), 3'ss of exon 2
tctactttttcatggtgtcaccatgattctgtggagtaaaatttattcttgtgtgttatccaaactcactatgaatgtgctttgttgtgtgtggatgcagCAAAGTGGTTCGGCTTTCGATAGCGCGGGTGCTGACAGTGATTTCCCAGAAGCAAAAGGCAGCGTTGAGGGAAGCTTACAAGAAGAAGAAATACCTTCCT
      |   |     |    |  | |   |   | |      | ||  ||||||   |    | | | |  ||||   || ||| || |     |||||||| ||||| ||    ||||| |||||||||||||| ||||| || |||||||| | ||| ||| || | || || |||||||||||||    ||| || 
-----gtacgcgcttcgcgctcgcgctcgcgctcattctctcctctttctgtgtgcccttgtgattgatt--gaat---ctctgtggttt-----tgcagCAAGGTGGTGCGCACGTCGATCGCGCGGGTGCTGACGGTGATCTCGCAGAAGCAGAGGGCGGCGCTGCGTGAGGCGTACAAGAAGAAGAGCCTCCTCCCC

upper sequence: GLYMA15G04730.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G043279_T03 (Zea mays), 3'ss of exon 2
tctactttttcatggtgtcaccatgattctgtggagtaaaatttattcttgtgtgttatccaaactcactatgaatgtgctttgttgtgtgtggatgcagCAAAGTGGTTCGGCTTTCGATAGCGCGGGTGCTGACAGTGATTTCCCAGAAGCAAAAGGCAGCGTTGAGGGAAGCTTACAAGAAGAAGAAATACCTTCCT
  | | |        | ||    |  | ||||    ||   | |  || ||    |   |  ||   | |   | |||     |   |   |     |||||| ||||| ||    ||||| ||||| ||||| |||||||| || |||||||| ||| | |||||| |||| || ||||||||||||||    || || 
-gtgcgtacctgcaatctctattttctcctgt----tattctctgctcctgaac-tcgactgaatcgattcgaattgtatccggcccttctt-----cagCAAGGTGGTGCGCACCTCGATCGCGCGCGTGCTCACAGTGATCTCGCAGAAGCAGAAGTCGGCGTTGCGGGAGGCGTACAAGAAGAAGAACCTGCTCCCC

upper sequence: GLYMA15G04730.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G043279_T02 (Zea mays), 3'ss of exon 2
tctactttttcatggtgtcaccatgattctgtggagtaaaatttattcttgtgtgttatccaaactcactatgaatgtgctttgttgtgtgtggatgcagCAAAGTGGTTCGGCTTTCGATAGCGCGGGTGCTGACAGTGATTTCCCAGAAGCAAAAGGCAGCGTTGAGGGAAGCTTACAAGAAGAAGAAATACCTTCCT----
  | | |        | ||    |  | ||||    ||   | |  || ||    |   |  ||   | |   | |||     |   |   |     |||||| ||||| ||    ||||| ||||| ||||| |||||||| || |||||||| ||| | |||||| |||| || ||||||||||||||    || ||     
-gtgcgtacctgcaatctctattttctcctgt----tattctctgctcctgaac-tcgactgaatcgattcgaattgtatccggcccttctt-----cagcaagGTGGTGCGCACCTCGATCGCGCGCGTGCTCACAGTGATCTCGCAGAAGCAGAAGTCGGCGTTGCGGGAGGCGTACAAGAAGAAGAACCTGCTCCCCCTCG

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|14258928|gb|BG881827.1|BG881827
EST:     CTCCGCGTCGCTAAGGTCACCGGCGGAGCCCCAAACAAGCTTTCCAAAAT                         CAAAGTGGTTCGGCTTTCGATAGCGCGGGTGCTGACAGTGATTTCCCAGAA
genomic: CTCCGCGTCGCTAAGGTCACCGGCGGAGCCCCAAACAAGCTTTCCAAAATgtaccttcct ... gtggatgcagCAAAGTGGTTCGGCTTTCGATAGCGCGGGTGCTGACAGTGATTTCCCAGAA
EST: gi|298193744|gb|HO040392.1|HO040392
EST:     CTCCGCGTCGCTAAGGTCACCGGCGGAGCCCCAAACAAGCTTTCCAAAAT                         CAAAGTGGTTCGGCTTTCGATAGCGCGGGTGCTGACAGTGATTTCCCAGAA
genomic: CTCCGCGTCGCTAAGGTCACCGGCGGAGCCCCAAACAAGCTTTCCAAAATgtaccttcct ... gtggatgcagCAAAGTGGTTCGGCTTTCGATAGCGCGGGTGCTGACAGTGATTTCCCAGAA
EST: gi|26269460|gb|CA820523.1|CA820523
EST:     CTCCGCGTCGCTAAGGTCACCGGCGGAGCCCCAAACAAGCTTTCCAAAAT                         CAAAGTGGTTCGGCTTTCGATAGCGCGGGTGCTGACAGTGATTTCCCAGAA
genomic: CTCCGCGTCGCTAAGGTCACCGGCGGAGCCCCAAACAAGCTTTCCAAAATgtaccttcct ... gtggatgcagCAAAGTGGTTCGGCTTTCGATAGCGCGGGTGCTGACAGTGATTTCCCAGAA
EST: gi|298199272|gb|HO042635.1|HO042635
EST:     CTCCGCGTCGCTAAGGTCACCGGCGGAGCCCCAAACAAGCTTTCCAAAAT                         CAAAGTGGTTCGGCTTTCGATAGCGCGGGTGCTGACAGTGATTTCCCAGAA
genomic: CTCCGCGTCGCTAAGGTCACCGGCGGAGCCCCAAACAAGCTTTCCAAAATgtaccttcct ... gtggatgcagCAAAGTGGTTCGGCTTTCGATAGCGCGGGTGCTGACAGTGATTTCCCAGAA
EST: gi|22539768|gb|BU089611.1|BU089611
EST:     CTCCGCGTCGCTAAGGTCACCGGCGGAGCCCCAAACAAGCTTTCCAAAAT                         CAAAGTGGTTCGGCTTTCGATAGCGCGGGTGCTGACAGTGATTTCCCAGAA
genomic: CTCCGCGTCGCTAAGGTCACCGGCGGAGCCCCAAACAAGCTTTCCAAAATgtaccttcct ... gtggatgcagCAAAGTGGTTCGGCTTTCGATAGCGCGGGTGCTGACAGTGATTTCCCAGAA
EST: gi|14259744|gb|BG882652.1|BG882652
EST:     CTCCGCGTCGCTAAGGTCACCGGCGGAGCCCCAAACAAGCTTTCCAAAAT                         CAAAGTGGTTCGGCTTTCGATAGCGCGGGTGCTGACAGTGATTTCCCAGAA
genomic: CTCCGCGTCGCTAAGGTCACCGGCGGAGCCCCAAACAAGCTTTCCAAAATgtaccttcct ... gtggatgcagCAAAGTGGTTCGGCTTTCGATAGCGCGGGTGCTGACAGTGATTTCCCAGAA
EST: gi|7028584|gb|AW458367.1|AW458367
EST:     CTCCGCGTCGCTAAGGTCACCGGCGGAGCCCCAAACAAGCTTTCCAAAAT                         CAAAGTGGTTCGGCTTTCGATAGCGCGGGTGCTGACAGTGATTTCCCAGAA
genomic: CTCCGCGTCGCTAAGGTCACCGGCGGAGCCCCAAACAAGCTTTCCAAAATgtaccttcct ... gtggatgcagCAAAGTGGTTCGGCTTTCGATAGCGCGGGTGCTGACAGTGATTTCCCAGAA
EST: gi|208165258|gb|GD964422.1|GD964422
EST:     CTCCGCGTCGCTAAGGTCACCGGCGGAGCCCCAAACAAGCTTTCCAAAAT                         CAAAGTGGTTCGG
genomic: CTCCGCGTCGCTAAGGTCACCGGCGGAGCCCCAAACAAGCTTTCCAAAATgtaccttcct ... gtggatgcagCAAAGTGGTTCGG
EST: gi|7233279|gb|AW568627.1|AW568627
EST:     CTCCGCGTCGCTAAGGTCACCGGCGGAGCCCCAAACAAGCTTTCCAAAAT                         CAAAGTGGTTCGGCTTTCGATAGCGCGGGTGCTGACAGTGATTTCCCAGAA
genomic: CTCCGCGTCGCTAAGGTCACCGGCGGAGCCCCAAACAAGCTTTCCAAAATgtaccttcct ... gtggatgcagCAAAGTGGTTCGGCTTTCGATAGCGCGGGTGCTGACAGTGATTTCCCAGAA
EST: gi|298185885|gb|HO031046.1|HO031046
EST:     CTCCGCGTCGCTAAGGTCACCGGCGGAGCCCCAAACAAGCTTTCCAAAAT                         CAAAGCGGTTCGGCTTTCGATAGCGCGGGTGCTGACAGTGATTTCCCAGAA
genomic: CTCCGCGTCGCTAAGGTCACCGGCGGAGCCCCAAACAAGCTTTCCAAAATgtaccttcct ... gtggatgcagCAAAGTGGTTCGGCTTTCGATAGCGCGGGTGCTGACAGTGATTTCCCAGAA
EST: gi|193541875|gb|FK496645.1|FK496645
EST:     CTCCGCGTCGCTAAGGTCACCGGCGGAGCCCCAAACAAGCTTTCCAAAAT                         CAAAGTGGTTCGGCTTTCGATAGCGCGGGTG
genomic: CTCCGCGTCGCTAAGGTCACCGGCGGAGCCCCAAACAAGCTTTCCAAAATgtaccttcct ... gtggatgcagCAAAGTGGTTCGGCTTTCGATAGCGCGGGTG
EST: gi|4313402|gb|AI460521.1|AI460521
EST:     CTCCGCGTCGTTAAGGTCACCGGCGGAGCCCCAAACAAGCTTTCCAAAAT                         CAAAGTGGTTCGGCTTTCGATAGCGCGGGTGCTGACAGTGATTTCCCAGAA
genomic: CTCCGCGTCGCTAAGGTCACCGGCGGAGCCCCAAACAAGCTTTCCAAAATgtaccttcct ... gtggatgcagCAAAGTGGTTCGGCTTTCGATAGCGCGGGTGCTGACAGTGATTTCCCAGAA
EST: gi|298173583|gb|HO016919.1|HO016919
EST:     CTCCGCGTCGCTAAGGTCACCGGCGGAGCCCCAAACAAGCTTTCCAAAAT                         CAAAGTGGTTCAGCTTTCGATAGCGCGGGTGCTGACAGTGATTTCCCAGAA
genomic: CTCCGCGTCGCTAAGGTCACCGGCGGAGCCCCAAACAAGCTTTCCAAAATgtaccttcct ... gtggatgcagCAAAGTGGTTCGGCTTTCGATAGCGCGGGTGCTGACAGTGATTTCCCAGAA
EST: gi|207840821|gb|GD811014.1|GD811014
EST:     AAGCTTTCCAAAAT                         CAAAGTGGTTCGGCTTTCGATAGCGCGGGTGCTGACAGTGATTTCCCAGAA
genomic: AAGCTTTCCAAAATgtaccttcct ... gtggatgcagCAAAGTGGTTCGGCTTTCGATAGCGCGGGTGCTGACAGTGATTTCCCAGAA
EST: gi|193343178|gb|FK305772.1|FK305772
EST:     TCCGCGTCGCTAAGGTCACCGGCGGAGCCCCAAACAAGCTTTACCAAAAT                         CAAGGTGGTTCGGCTTTCG
genomic: TCCGCGTCGCTAAGGTCACCGGCGGAGCCCCAAACAAGCTTT-CCAAAATgtaccttcct ... gtggatgcagCAAAGTGGTTCGGCTTTCG
EST: gi|6341759|gb|AW164645.1|AW164645
EST:     CTCCGCGTCGCTAAGGTCACCGGCGGAGCCCCAAACAAGCTTTCCAAAAT                         CAAAGTGGTTCGGCTTTCGATAGCGCGGGTGCTGACAGTGATTTCCCAGAA
genomic: CTCCGCGTCGCTAAGGTCACCGGCGGAGCCCCAAACAAGCTTTCCAAAATgtaccttcct ... gtggatgcagCAAAGTGGTTCGGCTTTCGATAGCGCGGGTGCTGACAGTGATTTCCCAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcttgtgtgttatccaaactcactatgaatgtgctttgttgtgtgtggatgcagCAAAGTGGTTCGGCTTTCGATAGCGCGGGTGCTGACAGTGATTTCCCAGAAGCAAAAGGCAGCGTTGAGGGAAGCTTACAAGAAGAAGAAATACCTTCCT
                 aactcac  putative branch site (score: 2)
                        tatgaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctactttttcatggtgtcaccatgattctgtggagtaaaatttattcttgtgtgttatccaaactcactatgaatgtgctttgttgtgtgtggatgcagCAAAGTGGTTCGGCTTTCGATAGCGCGGGTGCTGACAGTGATTTCCCAGAAGCAAAAGGCAGCGTTGAGGGAAGCTTACAAGAAGAAGAAATACCTTCCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - ttcatgg
- - - - - - - -tgtcacc
- - - - - - - - - - - - - -tctgtgg
- - - - - - - - - - - - - - - - - - - - - - - - - gtgtgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccaaact
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaatgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttgtg