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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acagatatttgattagtgttatttcatttctgctgaaatgaatctcagtgcattgcacttattatttcctatcttaactaaattctgttgggtattctagTCAGGTTGATCCCATAGTGGCATCATTCTCTGGAGGAGCAGTTGGAGTAATCTCGGCATTAATGGTGGTTGAGATAAACAATGTAAAACAGCAGGAGCAG

Basic information

species Glycine max
transcript GLYMA09G36770.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G36770.2 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os02g43500.1 (Oryza sativa), 3'ss of exon 5
------------acagatatttgattagtgttatt----tcatttctgctgaaatgaatctcagtgcattgc--acttattatttcct-atcttaactaaattctgttgggtattctagTCAGGTTGATCCCATAGTGGCATCATTCTCTGGAGGAGCAGTTGGAGTAATCTCGGCATTAATGGTGGTTGAGATAAACAATGTAAAACAGCAGGAGCAG
                || ||  ||| ||||  |     || |||   | |   |  ||  ||| | | | |  |  ||   | | || ||| |    |   | | |       |  |||||||| ||||| || |||||||| ||||| || |||||||||||||| ||||| ||  ||||||| |||||||| |||||||| |||||||||||||| 
gtattacaactattccatgttctattggtgtagtgaacatcttttaaccagttcttgataccagggaagttctgagataccgtgtgctgatccttttcatgatttttctatctgtacagTCAGGTAGATCCTATTGTGGCATCGTTCTCAGGTGGAGCAGTTGGAGTTATCTCCGCTCTAATGGTTGTTGAGATCAACAATGTCAAACAGCAGGAGCAT

upper sequence: GLYMA09G36770.2 (Glycine max), 3'ss of exon 5
lower sequence: Vv16s0013g00290.t01 (Vitis vinifera), 3'ss of exon 5
acagatatttgattagtgttatttcatttct-gctgaaatgaatctcagtgcattgcacttattatttcctatcttaactaaattctgttgggtat--tctagTCAGGTTGATCCCATAGTGGCATCATTCTCTGGAGGAGCAGTTGGAGTAATCTCGGCATTAATGGTGGTTGAGATAAACAATGTAAAACAGCAGGAGCAG
     ||| ||| |  | |      |    |   |||  | ||  | | |  ||||    | ||||    || ||| | |   |  || | |  |   |  |||||||| ||||| ||||||||||| || |||||||||||||||||||| ||||| || || ||||| ||||| |||||||| ||||||||||||||| | 
ggctgtatgtgacttctctagggggacagatcattgatgtcaaatttact--attgtttgtgttatccttta-cttcattgtttggtggttgtcaaaatgcagTCAGGTAGATCCTATAGTGGCATCTTTTTCTGGAGGAGCAGTTGGAGTGATCTCAGCCTTGATGGTCGTTGAAATAAACAACGTAAAACAGCAGGAGAAT

upper sequence: GLYMA09G36770.2 (Glycine max), 3'ss of exon 5
lower sequence: Vv16s0013g00350.t01 (Vitis vinifera), 3'ss of exon 4
-acagatatttgattagtgttatttcatttctgctgaaatgaatctcagtgcattgcacttattatttcctatcttaactaaattct--gttgg-gtattctagTCAGGTTGATCCCATAGTGGCATCATTCTCTGGAGGAGCAGTTGGAGTAATCTCGGCATTAATGGTGGTTGAGATAAACAATGTAAAACAGCAGGAGCAG
      ||| ||| |  | |      |       ||| || ||    | |||       || |   ||||  |  | | ||  || |  ||||    | |  |||||||| ||||| ||||||||||| ||||||||||| ||||||||||| |||||  | || ||| | ||||| |||||||| ||||||||||||||| | 
gggctgtatgtgacttttctagggggaaaatcattgatatcaaatatactgc----tgtttgtagcttccagtagttaatagtttgtcagttgccaaaatgcagTCAGGTAGATCCTATAGTGGCATCTTTCTCTGGAGGGGCAGTTGGAGTGATCTCATCCTTGATGATTGTTGAAATAAACAACGTAAAACAGCAGGAGAAA

upper sequence: GLYMA09G36770.2 (Glycine max), 3'ss of exon 5
lower sequence: PP1S380_25V6.1 (Physcomitrella patens), 3'ss of exon 5
-----------------------------acagatatttgat-tagtgttatttcatttctgc--tgaaatgaatctcagtgcattgcactt-------attatttcctatcttaactaaattctgttg-ggtattctagTCAGGTTGATCCCATAGTGGCATCATTCTCTGGAGGAGCAGTTGGAGTAATCTCGGCATTAATGGTGGTTGAGATAAACAATGTAAAACAGCAGGAGCAG
                              | ||| || ||  | |||  | | |||    ||  || |||      || |   || |           ||  |     ||      | | || || || |||  |  ||| | || ||||| || ||||| ||||||||||||||||| || ||||| || ||  |  | ||||| || ||||| ||||||||||||||||| || || 
gtacatcctcggcattcattcaagctgactccgatcttcgaagttgtgccaatgcatacaagcagtgtaatctccgccaatttgttccgggatgagaagatagtcaaaaattcatttttagttttgatgtggttgtgcagTGAAGTGGATCCAATTGTGGCTTCATTCTCTGGAGGAGCTGTAGGAGTGATTTCATCGCTCATGGTTGTGGAGATCAACAATGTAAAACAGCAAGAACAT

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|15813355|gb|BI785630.1|BI785630
EST:     ACATCTTATGCAGATTTTATTGAAAGTGTGCATCTGCCTATGCAGCTGAG                         TCAGGTTGATCCCATAGTGGCATCATTCTCTGGAGGAGCAGTTGGAGTAAT
genomic: ACATCTTATGCAGATTTTATTGAAAGTGTGCATCTGCCTATGCAGCTGAGgtagtgcctt ... ggtattctagTCAGGTTGATCCCATAGTGGCATCATTCTCTGGAGGAGCAGTTGGAGTAAT
EST: gi|13791409|gb|BG654000.1|BG654000
EST:     ACATCTTATGCAGACTTTATTGAAAGTGTGCATCTGCCTATGCAGCTGAG                         TCAGGTTGATCCCATAGTGGCATCATTCTCTGGAGGAGCAGTTGGAGTAAT
genomic: ACATCTTATGCAGATTTTATTGAAAGTGTGCATCTGCCTATGCAGCTGAGgtagtgcctt ... ggtattctagTCAGGTTGATCCCATAGTGGCATCATTCTCTGGAGGAGCAGTTGGAGTAAT
EST: gi|5753292|gb|AI960579.1|AI960579
EST:     ACATCTTATGCAGATTTTATTGAAAGTGTGCATCTGCCTATGCAGCTGAG                         TCAGGTTGATCCCATAGTGGCATCATTCTCTGGAGGAGCAGTTGGAGTAAT
genomic: ACATCTTATGCAGATTTTATTGAAAGTGTGCATCTGCCTATGCAGCTGAGgtagtgcctt ... ggtattctagTCAGGTTGATCCCATAGTGGCATCATTCTCTGGAGGAGCAGTTGGAGTAAT
EST: gi|254342695|gb|GR858857.1|GR858857
EST:     ACATCTTATGCAGATTTTATTGAAAGTGTGCATCTGCCTATGCAGCTGAG                         TCAGGTTGATCCCATAGTGGCATCATTCTCTGGAGGAGCAGTTGGAGTAAT
genomic: ACATCTTATGCAGATTTTATTGAAAGTGTGCATCTGCCTATGCAGCTGAGgtagtgcctt ... ggtattctagTCAGGTTGATCCCATAGTGGCATCATTCTCTGGAGGAGCAGTTGGAGTAAT
EST: gi|193684207|gb|FK623471.1|FK623471
EST:     ACATCTTATGCAGATTTTATTGAAAGTGTGCATCTGCCTATGCAGCTGAG                         TCAGGTTGATCCCATAGTGGCATCATTCTC
genomic: ACATCTTATGCAGATTTTATTGAAAGTGTGCATCTGCCTATGCAGCTGAGgtagtgcctt ... ggtattctagTCAGGTTGATCCCATAGTGGCATCATTCTC
EST: gi|21285677|gb|BQ473548.1|BQ473548
EST:     ACATCTTATGCAGACTTTATTGAAAGTGTGCATCTGCCTATGCAGCTGAG                         TCAGGTTGATCCCATAGTGGCATCATTCTCTGGAGGAGCAGTTGGAGTAAT
genomic: ACATCTTATGCAGATTTTATTGAAAGTGTGCATCTGCCTATGCAGCTGAGgtagtgcctt ... ggtattctagTCAGGTTGATCCCATAGTGGCATCATTCTCTGGAGGAGCAGTTGGAGTAAT
EST: gi|31310538|gb|CD395741.1|CD395741
EST:     GAAAGTGTGCATCTGCCTATGCAGCTGAG                         TCAGGTTGATCCCATAGTGGCATCATTCTCTGGAGGAGCAGTTGGAGTAAT
genomic: GAAAGTGTGCATCTGCCTATGCAGCTGAGgtagtgcctt ... ggtattctagTCAGGTTGATCCCATAGTGGCATCATTCTCTGGAGGAGCAGTTGGAGTAAT
EST: gi|15336929|gb|BI497585.1|BI497585
EST:     ACATCTTATGCAGATTTTATTGAAAGTGTGCATCTGCCTATGCAGCTGAG                         TCAGGTTGATCCCATAGTGGCATCATTCTCTGGAGGAGCAGTTGGAGTAAT
genomic: ACATCTTATGCAGATTTTATTGAAAGTGTGCATCTGCCTATGCAGCTGAGgtagtgcctt ... ggtattctagTCAGGTTGATCCCATAGTGGCATCATTCTCTGGAGGAGCAGTTGGAGTAAT
EST: gi|151400607|gb|EV270421.1|EV270421
EST:     ACATCTTATGCAGATTTTATTGAAAGTGTGCATCTGCCTATGCAGCTGAG                         TCAG-TTGATCCCATAGTGGCATCATTCTCTGGAGGAGCAGTTGGAGTA
genomic: ACATCTTATGCAGATTTTATTGAAAGTGTGCATCTGCCTATGCAGCTGAGgtagtgcctt ... ggtattctagTCAGGTTGATCCCATAGTGGCATCATTCTCTGGAGGAGCAGTTGGAGTA
EST: gi|193727963|gb|FK666693.1|FK666693
EST:     ACATCTTATGCAGATTTTATTGAAAGTGTGCATCTGCCTATGCAGCTGAG                         TCAGGTTGATCCCATAGTGGACATCATTCTC
genomic: ACATCTTATGCAGATTTTATTGAAAGTGTGCATCTGCCTATGCAGCTGAGgtagtgcctt ... ggtattctagTCAGGTTGATCCCATAGTGG-CATCATTCTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagtgcattgcacttattatttcctatcttaactaaattctgttgggtattctagTCAGGTTGATCCCATAGTGGCATCATTCTCTGGAGGAGCAGTTGGAGTAATCTCGGCATTAATGGTGGTTGAGATAAACAATGTAAAACAGCAGGAGCAG
                              aactaaa  putative branch site (score: 2)
                        tatcttaactaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acagatatttgattagtgttatttcatttctgctgaaatgaatctcagtgcattgcacttattatttcctatcttaactaaattctgttgggtattctagTCAGGTTGATCCCATAGTGGCATCATTCTCTGGAGGAGCAGTTGGAGTAATCTCGGCATTAATGGTGGTTGAGATAAACAATGTAAAACAGCAGGAGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG