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 5'  3'   		2  
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 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgcctttgtccattactatcaactgggccagtcctggtagagtatttgcaccttgcttcatttgaatcttgattttgattatgatcttgtaacattccagGGTTATGTGATTTACCGTGTTCGTGTACGAAGGGGTGGCCGGAAGAGACCAGTTCCAAAAGGTATTGTTTATGGTAAGCCCACCAACCAAGGTGTTACTC

Basic information

species Glycine max
transcript GLYMA05G04870.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G04870.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os05g19370.1 (Oryza sativa), 3'ss of exon 2
tgcctttgtccattactat-caactgggccagtcctggtagagtatttgcaccttgcttcatttgaatcttgattttgattatgatcttgtaaca-ttccagGGTTATGTGATTTACCGTGTTCGTGTACGAAGGGGTGGCCGGAAGAGACCAGTTCCAAAAGGTATTGTTTATGGTAAGCCCACCAACCAAGGTGTTACTC
 |||    |  |||   || |  |||    | ||    | || | |||   || |   | ||   ||| |||    | | |||  | |        || ||||| |||||| ||||||||||||| ||  |  | |||||| ||||||| ||||| || || |||||||| ||||| |||||||   |||| ||| |||| |
agccaaaatgtattcacatgctgctgtctgattcacttttgaatgttttggcccta--taatccaaatattgtgcataactattttttgaccttgctttcagGGCTATGTGGTTTACCGTGTTCGCGTCAGGCGTGGTGGCAGGAAGAGGCCAGTGCCCAAGGGTATTGTCTATGGCAAGCCCAAGCACCAGGGTATTACCC

upper sequence: GLYMA05G04870.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os03g40180.1 (Oryza sativa), 3'ss of exon 2
---tgcctttgtccattactatcaactgggccagtcctggtagagtatttgcaccttgcttcatttgaatcttgattttgattatgatcttgtaacattcc--agGGTTATGTGATTTACCGTGTTCGTGTACGAAGGGGTGGCCGGAAGAGACCAGTTCCAAAAGGTATTGTTTATGGTAAGCCCACCAACCAAGGTGTTACTC
   |||     |  |||  || ||| |     | ||    | || |||||    | ||  | ||   ||| |||   || | |||       || | ||||  ||||||||||| |||||||||| |||||  |  | |||||| ||||||| ||||| || || |||||||| || || |||||||   |||| ||| | || |
gggtgctcccatttatt--taccaatttatataatcacatttgaatattt-tgtcctg--taatcaaaatattgtgcttaactatttgtcgttacctttcctcagGGTTATGTGGTTTACCGTGTCCGTGTGAGGCGTGGTGGCAGGAAGAGGCCAGTGCCCAAGGGTATTGTCTACGGCAAGCCCAAGCACCAGGGTATCACCC

upper sequence: GLYMA05G04870.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv16s0013g02020.t01 (Vitis vinifera), 3'ss of exon 2
----tgcctttgtccattactatcaactgggccagtcctggtagagtatttgcaccttgcttcatttgaatcttgattttgattatgatcttgtaa-cattccagGGTTATGTGATTTACCGTGTTCGTGTACGAAGGGGTGGCCGGAAGAGACCAGTTCCAAAAGGTATTGTTTATGGTAAGCCCACCAACCAAGGTGTTACTC
    |  || | | ||||  |  |  ||||     ||    |  |||   |||| |    || || |  || || || | |  ||     |   || | || |||||||||||||| || ||||| |||||| || | |||||  ||||||| ||||| ||||| |||||||| |||||||||||||| ||||||||||| ||||
tgattttctgtttacatttttccctgctgg--tgctctatatttagtcactgcagcg---ttaatattcatattaatatcgtgtacatgttaacaatcttttcagGGTTATGTGATCTATCGTGTACGTGTAAGACGCGGTGGAAGGAAGAGGCCAGTCCCAAAGGGTATTGTGTATGGTAAGCCCACAAACCAAGGTGTCACTC

upper sequence: GLYMA05G04870.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv15s0021g02480.t01 (Vitis vinifera), 3'ss of exon 2
tgcctttgtccattactatcaactgggccagt--cctggtagagtatttgcaccttgcttcatttgaatcttgattttgattatgatct---tgtaacattccagGGTTATGTGATTTACCGTGTTCGTGTACGAAGGGGTGGCCGGAAGAGACCAGTTCCAAAAGGTATTGTTTATGGTAAGCCCACCAACCAAGGTGTTACTC
     ||    ||||  |  |||||| ||| |    || || || ||    ||  || ||| |||  |  |||||| | ||    | |    | |   |||  |||| ||||| || || |||||||||||  || | ||||| |||||||| || ||||| || || ||||||||||| ||||| || ||||| ||||| || |
---tgtttaaaattatgacaaactggcccattaatttgata-agcatcaagacgatgattc-tttttactttgattataatgccaaacactattttctattttagGGGTATGTTATCTATCGTGTTCGTGTTAGACGTGGTGGTCGGAAGAGGCCTGTTCCCAAGGGCATTGTTTATGGAAAGCCTACAAACCAGGGTGTCACCC

upper sequence: GLYMA05G04870.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv00s0551g00020.t01 (Vitis vinifera), 3'ss of exon 2
tgcctttgtccattactatcaactgggccagtcctggtagagtatttgcaccttgcttcatttga-atcttgattttgattatgatct---tgtaacattc-cagGGTTATGTGATTTACCGTGTTCGTGTACGAAGGGGTGGCCGGAAGAGACCAGTTCCAAAAGGTATTGTTTATGGTAAGCCCACCAACCAAGGTGTTACTC
    | |   || | || || |    |     |    |  | | | |   ||| |  |   |||  || |  |     || |   |||   ||||   ||  ||||||||||||||||| |||||||||||  || | ||||| |||||||| || || || || || |||||||||||||||||||| |||||||||||||| |
----tctaatcact-ctctcgatccagttctgctgcttgtaatctataagcctggaattggttgctatatctacacaaatgacactctggatgtactgttttcagGGTTATGTGATTTATCGTGTTCGTGTTAGACGTGGTGGTCGGAAGAGGCCTGTGCCCAAGGGAATTGTTTATGGTAAGCCCACAAACCAAGGTGTTACCC

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|17022947|gb|BM093981.1|BM093981
EST:     GGTCTACTCGCCCAGACAAGGCTCGCCGCTTGGGTTTCAAGGCTAAGCAG                         GGTTATGTGATTTACCGTGTTCGTGTACGAAGGGGTGGCCGGAAGAGACCA
genomic: GGTCTACTCGCCCAGACAAGGCTCGCCGCTTGGGTTTCAAGGCTAAGCAGgtgaagaaat ... aacattccagGGTTATGTGATTTACCGTGTTCGTGTACGAAGGGGTGGCCGGAAGAGACCA
EST: gi|207816719|gb|GD787098.1|GD787098
EST:     ACAAGGCTCGCCGCTTGGGTTTCAAGGCTAAGCAG                         GGTTATGTGATTTACCGTGTTCGTGTACGAAGGGGTGGCCGGAAGAGACTA
genomic: ACAAGGCTCGCCGCTTGGGTTTCAAGGCTAAGCAGgtgaagaaat ... aacattccagGGTTATGTGATTTACCGTGTTCGTGTACGAAGGGGTGGCCGGAAGAGACCA
EST: gi|298192088|gb|HO036170.1|HO036170
EST:     GGTCTACTCGCCCAGACAAGGCTCGCCGCTTGGGTTTCAAGGCTAAGCAG                         GGTTATGTGATTTACCGTGTTCGTGTACGAAGGGGTGGCCGGAAGAGACCA
genomic: GGTCTACTCGCCCAGACAAGGCTCGCCGCTTGGGTTTCAAGGCTAAGCAGgtgaagaaat ... aacattccagGGTTATGTGATTTACCGTGTTCGTGTACGAAGGGGTGGCCGGAAGAGACCA
EST: gi|4396093|gb|AI495090.1|AI495090
EST:     GGTCTACTCGCCCAGACAAGGCTCGCCGCTTGGGTTTCAAGGCTAAGCAG                         GGTTATGTGATTTACCGTGTTCGTGTACGAAGGGGTGGCCGGAAGAGACCA
genomic: GGTCTACTCGCCCAGACAAGGCTCGCCGCTTGGGTTTCAAGGCTAAGCAGgtgaagaaat ... aacattccagGGTTATGTGATTTACCGTGTTCGTGTACGAAGGGGTGGCCGGAAGAGACCA
EST: gi|213603531|gb|DB970516.1|DB970516
EST:     GGTCTACTCGCCCAGACAAGGCTCGCCGCTTGGGTTTCAAGGCTAAGCAG                         GGTTATGTGATTTACCGTGTTCGTGTACGAAGGGGTGGCCGGAAGAGACCA
genomic: GGTCTACTCGCCCAGACAAGGCTCGCCGCTTGGGTTTCAAGGCTAAGCAGgtgaagaaat ... aacattccagGGTTATGTGATTTACCGTGTTCGTGTACGAAGGGGTGGCCGGAAGAGACCA
EST: gi|151396959|gb|EV266832.1|EV266832
EST:     GGTCTACTCGCCCAGACAAGGCTCGCCGCTTGGGTTTCAAGGCTAAGCAG                         GGTTATGTGATTTACCGTGTTCGTGTACGAAGGGGTGGCCGGAAGAGACCA
genomic: GGTCTACTCGCCCAGACAAGGCTCGCCGCTTGGGTTTCAAGGCTAAGCAGgtgaagaaat ... aacattccagGGTTATGTGATTTACCGTGTTCGTGTACGAAGGGGTGGCCGGAAGAGACCA
EST: gi|58023239|gb|CX709980.1|CX709980
EST:     GGTCTACTCGCCCAGACAAGGCTCGCCGCTTGGGTTTCAAGGCTAAGCAG                         GGTTATGTGATTTACCGTGTTCGTGTACGAAGGGGTGGCCGGAAGAGACCA
genomic: GGTCTACTCGCCCAGACAAGGCTCGCCGCTTGGGTTTCAAGGCTAAGCAGgtgaagaaat ... aacattccagGGTTATGTGATTTACCGTGTTCGTGTACGAAGGGGTGGCCGGAAGAGACCA
EST: gi|26045629|gb|CA783157.1|CA783157
EST:     GGTCTACTCGCCCAGACAAGGCTCGCCGCTTGGGTTTCAAGGCTAAGCAG                         GGTTATGTGATTTACCGTGTTCGTGTACGAAGGGGTGGCCGGAAGAGACCA
genomic: GGTCTACTCGCCCAGACAAGGCTCGCCGCTTGGGTTTCAAGGCTAAGCAGgtgaagaaat ... aacattccagGGTTATGTGATTTACCGTGTTCGTGTACGAAGGGGTGGCCGGAAGAGACCA
EST: gi|298181275|gb|HO022714.1|HO022714
EST:     GGTCTACTCGCCCAGACAAGGCTCGCCGCTTGGGTTTCAAGGCTAAGCAG                         GGTTATGTGATTTACCATGTTCGTGTACGAAGGGGTGGCCGGAAGAGACCA
genomic: GGTCTACTCGCCCAGACAAGGCTCGCCGCTTGGGTTTCAAGGCTAAGCAGgtgaagaaat ... aacattccagGGTTATGTGATTTACCGTGTTCGTGTACGAAGGGGTGGCCGGAAGAGACCA
EST: gi|17519400|gb|BM188442.1|BM188442
EST:     GGTCTACTCGCCCAGACAAGGCTCGCCGCTTGGGTTTCAAGGCTAAGCAG                         GGTTATGTGATTTACCGTGTTCGTGTACGAAGGGGTGGCCGGAAGAGACCA
genomic: GGTCTACTCGCCCAGACAAGGCTCGCCGCTTGGGTTTCAAGGCTAAGCAGgtgaagaaat ... aacattccagGGTTATGTGATTTACCGTGTTCGTGTACGAAGGGGTGGCCGGAAGAGACCA
EST: gi|254347217|gb|GR856887.1|GR856887
EST:     GGTCTACTCGCCCAGACAAGGCTCGCCGCTTGGGTTTCAAGGCTAAGCAG                         GGTTATGTGATTTACCGTGTTCGTGTACGAAGGGGTGGCCGGAAGAGACCA
genomic: GGTCTACTCGCCCAGACAAGGCTCGCCGCTTGGGTTTCAAGGCTAAGCAGgtgaagaaat ... aacattccagGGTTATGTGATTTACCGTGTTCGTGTACGAAGGGGTGGCCGGAAGAGACCA
EST: gi|192332651|gb|FK025308.1|FK025308
EST:     GGTCTACTCGCCCAGACAAGGCTCGCCGCTTGGGTTTCAAGGCTAAGCAG                         GGTTATGTGATTTACCGTGTTCGTGTACGAAGGGGTGGCCGGAA
genomic: GGTCTACTCGCCCAGACAAGGCTCGCCGCTTGGGTTTCAAGGCTAAGCAGgtgaagaaat ... aacattccagGGTTATGTGATTTACCGTGTTCGTGTACGAAGGGGTGGCCGGAA
EST: gi|209711012|gb|BW676409.1|BW676409
EST:     GGTCTACTCGCCCAGACAAGGCTCGCCGCTTGGGTTTCAAGGCTAAGCAG                         GGTTATGTGATTTACCGTGTTCGTGTACGAAGGGGTGGCCGGAAGAGACCA
genomic: GGTCTACTCGCCCAGACAAGGCTCGCCGCTTGGGTTTCAAGGCTAAGCAGgtgaagaaat ... aacattccagGGTTATGTGATTTACCGTGTTCGTGTACGAAGGGGTGGCCGGAAGAGACCA
EST: gi|298163888|gb|HO013533.1|HO013533
EST:     GGTCTACTCGCCCAGACAAGGCTCGCCGCTTGGGTTTCAAGGCTAAGCAG                         GGTTATGTGATTTACCGTATTCGTGTACGAAGGGGTGGCCGGAAGAGACCA
genomic: GGTCTACTCGCCCAGACAAGGCTCGCCGCTTGGGTTTCAAGGCTAAGCAGgtgaagaaat ... aacattccagGGTTATGTGATTTACCGTGTTCGTGTACGAAGGGGTGGCCGGAAGAGACCA
EST: gi|298173489|gb|HO016825.1|HO016825
EST:     GGTCTACTCGCCCAGACAAGGCTCGCCGCTTGGGTTTCAAGGCTAAGCAG                         GGTTATGTGATTTACCGTGTTCGTGTACGAAGGGGTGGCCGGAAGAGACCA
genomic: GGTCTACTCGCCCAGACAAGGCTCGCCGCTTGGGTTTCAAGGCTAAGCAGgtgaagaaat ... aacattccagGGTTATGTGATTTACCGTGTTCGTGTACGAAGGGGTGGCCGGAAGAGACCA
EST: gi|298190442|gb|HO032563.1|HO032563
EST:     GGTCTACTCGCCCAGACAAGGCTCGCCGCTTGGGTTTCAAGGCTAAGCAG                         GGTTATGTGATTTACCGTGTTCGTGTACGAAGGGGTGGCCGGAAGAGACCA
genomic: GGTCTACTCGCCCAGACAAGGCTCGCCGCTTGGGTTTCAAGGCTAAGCAGgtgaagaaat ... aacattccagGGTTATGTGATTTACCGTGTTCGTGTACGAAGGGGTGGCCGGAAGAGACCA
EST: gi|15204431|gb|BI427199.1|BI427199
EST:     GGTCTACTCGCCCAGACAAGGCTCGCCGCTTGGGTTTCAAGGCTAAGCAG                         GGTTATGTGATTTACCGTGTTCGTGTACGAAGGGGTGGCCGGAAGAGACCA
genomic: GGTCTACTCGCCCAGACAAGGCTCGCCGCTTGGGTTTCAAGGCTAAGCAGgtgaagaaat ... aacattccagGGTTATGTGATTTACCGTGTTCGTGTACGAAGGGGTGGCCGGAAGAGACCA
EST: gi|10843868|gb|BF067229.1|BF067229
EST:     GGTCTACTCACCCAGACAAGGCTCGCCGCTTGGGTTTCAAGGCTAAACAG                         GCTTATGTGATTTAC
genomic: GGTCTACTCGCCCAGACAAGGCTCGCCGCTTGGGTTTCAAGGCTAAGCAGgtgaagaaat ... aacattccagGGTTATGTGATTTAC
EST: gi|254327465|gb|GR837088.1|GR837088
EST:     GGTCTACTCGCCCAGACAAGGCTCGCCGCTTGGGTTTCAAGGCTAAGCAG                         GGTTATGTGATTTACCGTGTTCGTGTACGAAGGGGTGGCCGGAAGAGACCA
genomic: GGTCTACTCGCCCAGACAAGGCTCGCCGCTTGGGTTTCAAGGCTAAGCAGgtgaagaaat ... aacattccagGGTTATGTGATTTACCGTGTTCGTGTACGAAGGGGTGGCCGGAAGAGACCA
EST: gi|16996585|gb|BM085957.1|BM085957
EST:     GGTCTACTCGCCCAGACAAGGCTCGCCGCTTGGGTTTCAAGGCTAAGCAG                         GGTTATGTGATTTACCGTGTTCGTGTACGAAGGGGTGGCCGGAAGAGACCA
genomic: GGTCTACTCGCCCAGACAAGGCTCGCCGCTTGGGTTTCAAGGCTAAGCAGgtgaagaaat ... aacattccagGGTTATGTGATTTACCGTGTTCGTGTACGAAGGGGTGGCCGGAAGAGACCA
EST: gi|120531327|gb|EH259460.1|EH259460
EST:     GGTCTACTCGCCCAGACAAGGCTCGCCGCTTGGGTTTCAAGGCTAAGCAG                         GGTTATGTGATTTACCGTGTTCGTGTACGAAGGGGTGGCCGGAAGAGACCA
genomic: GGTCTACTCGCCCAGACAAGGCTCGCCGCTTGGGTTTCAAGGCTAAGCAGgtgaagaaat ... aacattccagGGTTATGTGATTTACCGTGTTCGTGTACGAAGGGGTGGCCGGAAGAGACCA
EST: gi|254347218|gb|GR856888.1|GR856888
EST:     GGTCTACTCGCCCAGACAAGGCTCGCCGCTTGGGTTTCAAGGCTAAGCAG                         GGTTATGTGATTTACCGTGTTCGTGTACGAAGGGGTGGCCGGAAGAGACCA
genomic: GGTCTACTCGCCCAGACAAGGCTCGCCGCTTGGGTTTCAAGGCTAAGCAGgtgaagaaat ... aacattccagGGTTATGTGATTTACCGTGTTCGTGTACGAAGGGGTGGCCGGAAGAGACCA
EST: gi|192323314|gb|FK017420.1|FK017420
EST:     GGTCTACTCGCCCAGACAAGGCTCGCCGCTTGGGTTTCAAGGCTAAGCAG                         GGTTATGTGATTTACCGTGTTCGTGTACGAAGGGGTGGCCGGAAGAGACCA
genomic: GGTCTACTCGCCCAGACAAGGCTCGCCGCTTGGGTTTCAAGGCTAAGCAGgtgaagaaat ... aacattccagGGTTATGTGATTTACCGTGTTCGTGTACGAAGGGGTGGCCGGAAGAGACCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgcaccttgcttcatttgaatcttgattttgattatgatcttgtaacattccagGGTTATGTGATTTACCGTGTTCGTGTACGAAGGGGTGGCCGGAAGAGACCAGTTCCAAAAGGTATTGTTTATGGTAAGCCCACCAACCAAGGTGTTACTC
                                         ttgtaac  putative branch site (score: 2)
                       ttgattttgattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgcctttgtccattactatcaactgggccagtcctggtagagtatttgcaccttgcttcatttgaatcttgattttgattatgatcttgtaacattccagGGTTATGTGATTTACCGTGTTCGTGTACGAAGGGGTGGCCGGAAGAGACCAGTTCCAAAAGGTATTGTTTATGGTAAGCCCACCAACCAAGGTGTTACTC

tgccttt
- - - - - - - - - - - - - -ccagtcc