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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agcactccttgtgctacaaaaatcacattggagatagatagactctgatcttcgtacttgtgtgctcattcattacctattttgtttgattatttttcagACTCAGAAGAAAAAGAAGAGCAGTGATCTGAAGTATGACATATTTGGATGGATAATTCTGGCAGTCGGCATTGTTGCATGGGTGGGATTTGCAAAATCAA

Basic information

species Glycine max
transcript GLYMA19G17930.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G17930.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv14s0068g02030.t01 (Vitis vinifera), 3'ss of exon 5
agcactccttgtgctacaaaaatcacattggagatagatagactctgatcttcgtacttgtgtgctcattcattacctattttgtttgatta---tttttcagACTCAGAAGAAAAAGAAGAGCAGTGATCTGAAGTATGACATATTTGGATGGATAATTCTGGCAGTCGGCATTGTTGCATGGGTGGGATTTGCAAAATCAA
   |  | |      ||     ||||  | ||  |   || | |    | ||   |  ||  |    ||   |||  |    | |||||||    | |||||||||  ||||||||||||||| || ||||| |||||||||||||||||||||||||| || || || ||||||||||||||||| || ||||| |||||  
-ttatgcttgacagcacggtc-tcactcttgaattgcttatatttattttttatcagctg-ataagtatatcttaagttggatttttgattcatctctttcagACTTCGAAGAAAAAGAAGAGTAGCGATCTCAAGTATGACATATTTGGATGGATAATCCTTGCTGTTGGCATTGTTGCATGGGTAGGCTTTGCTAAATCCC
















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|27425559|gb|CA937079.1|CA937079
EST:     AGCAGGCGGCAGCAACAGCTGGATCTTCTACTTCTGCTTCGG-TACAAAG                         ACTCAGAAGAAAAAGAAGAGCAGTGATCTGAAGTATGACATATTTGGATGG
genomic: AGCAGGCGGCAGCAACAGCTGGATCTTCTACTTCTGCTTCGGGTACAAAGgtaatacttc ... tatttttcagACTCAGAAGAAAAAGAAGAGCAGTGATCTGAAGTATGACATATTTGGATGG
EST: gi|8284555|gb|BE022123.1|BE022123
EST:     GCAAGCGGCAGCAACAGCTGGATCTTCTACTTTCTGCT-CGGGTACAAAG                         ACTCAGAAGAAAAAGAAGAGCAGT
genomic: GCAGGCGGCAGCAACAGCTGGATCTTCTACTT-CTGCTTCGGGTACAAAGgtaatacttc ... tatttttcagACTCAGAAGAAAAAGAAGAGCAGT
EST: gi|15664573|gb|BI701944.1|BI701944
EST:     AGCAGGCGGCAGCAACAGCTGGATCTTCTACTTCTGCTTCGGGTACAAAG                         ACTCAGAAGAAAAAGAAGAGCAGTGATCTGAAGTATGACATATTTGGATGG
genomic: AGCAGGCGGCAGCAACAGCTGGATCTTCTACTTCTGCTTCGGGTACAAAGgtaatacttc ... tatttttcagACTCAGAAGAAAAAGAAGAGCAGTGATCTGAAGTATGACATATTTGGATGG
EST: gi|20498591|gb|BQ273521.1|BQ273521
EST:     AGCAGGCGGCAGCAACAGCTGGATCTTCTACTTCTGCTTCGGGTACAAAG                         ACTCAGAAGAAAAAGAAGAGCAGTGATCTGAAGTATGACATA
genomic: AGCAGGCGGCAGCAACAGCTGGATCTTCTACTTCTGCTTCGGGTACAAAGgtaatacttc ... tatttttcagACTCAGAAGAAAAAGAAGAGCAGTGATCTGAAGTATGACATA
EST: gi|31458839|gb|CD400867.1|CD400867
EST:     AGCAGGCGGCAGCAACAGCTGGATCTTCTACTTCTGCTTTGGGTACAAAG                         ACTCAGAAGAAAAAGAAGAGCAGTGATCTGAAGTATGACATATTTGGATGG
genomic: AGCAGGCGGCAGCAACAGCTGGATCTTCTACTTCTGCTTCGGGTACAAAGgtaatacttc ... tatttttcagACTCAGAAGAAAAAGAAGAGCAGTGATCTGAAGTATGACATATTTGGATGG
EST: gi|19269795|gb|BM886051.1|BM886051
EST:     AGCAGGCGGCAGCAACAGCTGGATCTTCTACTTCTGCTTCGGGTACAAAG                         ACTCAGAAGAAAAAGAAGAGCAGTGATCTGAAGTATGACATATTTGGATGG
genomic: AGCAGGCGGCAGCAACAGCTGGATCTTCTACTTCTGCTTCGGGTACAAAGgtaatacttc ... tatttttcagACTCAGAAGAAAAAGAAGAGCAGTGATCTGAAGTATGACATATTTGGATGG
EST: gi|13252576|gb|BG363479.1|BG363479
EST:     AGCAGGCGGCAGCAACAGCTGGATCTTCTACTTCTGCTTCGGGTACAAAG                         ACTCAGAAGAAAAAGAAGAGCAGTGATCTGAAGTATGACATATTTGGATGG
genomic: AGCAGGCGGCAGCAACAGCTGGATCTTCTACTTCTGCTTCGGGTACAAAGgtaatacttc ... tatttttcagACTCAGAAGAAAAAGAAGAGCAGTGATCTGAAGTATGACATATTTGGATGG
EST: gi|151401792|gb|EV271605.1|EV271605
EST:     AGCAGGCGGCAGCAACAGCTGGATCTTCTACTTCTGCTTCGGGTACAAAG                         ACTCAGAAGAAAAAGAAGAGCAGTGATCTGAAGTATGACATATTTGGATGG
genomic: AGCAGGCGGCAGCAACAGCTGGATCTTCTACTTCTGCTTCGGGTACAAAGgtaatacttc ... tatttttcagACTCAGAAGAAAAAGAAGAGCAGTGATCTGAAGTATGACATATTTGGATGG
EST: gi|192312150|gb|FK005649.1|FK005649
EST:     AGCAGGCGGCAGCAACAGCTGGATCTTCTACTTCTGCTTCGGGTACAAAG                         ACTCAGAGGAAAAAGAAGAGCAGTGATCTGAAGTATGACATATTTGGATGG
genomic: AGCAGGCGGCAGCAACAGCTGGATCTTCTACTTCTGCTTCGGGTACAAAGgtaatacttc ... tatttttcagACTCAGAAGAAAAAGAAGAGCAGTGATCTGAAGTATGACATATTTGGATGG
EST: gi|21602124|gb|BQ612455.1|BQ612455
EST:     AGCAGGCGGCAGCAACAGCTGGATCTTCTACTTCTGCTTCGGGTACAAAG                         ACTCAGAAGAAAAAGAAGAGCAGTGATCTGAAGTATGACATATTTGGATGG
genomic: AGCAGGCGGCAGCAACAGCTGGATCTTCTACTTCTGCTTCGGGTACAAAGgtaatacttc ... tatttttcagACTCAGAAGAAAAAGAAGAGCAGTGATCTGAAGTATGACATATTTGGATGG
EST: gi|151394370|gb|EV264241.1|EV264241
EST:     AGCAGGCGGCAGCAACAGCTGGGTCTTCTACTTCTGCTTCGGGTACAAAG                         ACTCAGAAGAAAAAGAAGAGCAGTGATCTGAAGTATGACATATTTGGATGG
genomic: AGCAGGCGGCAGCAACAGCTGGATCTTCTACTTCTGCTTCGGGTACAAAGgtaatacttc ... tatttttcagACTCAGAAGAAAAAGAAGAGCAGTGATCTGAAGTATGACATATTTGGATGG
EST: gi|10237666|gb|BE806554.1|BE806554
EST:     AGCAGGCGGCAGCAACAGCTGGATCTTCTACTTCTGCTTCGGGTACAAAG                         ACTCAGAAGAAAAAGAAGAGCAGTGATCTGAAGTATGACATATTTGGATGG
genomic: AGCAGGCGGCAGCAACAGCTGGATCTTCTACTTCTGCTTCGGGTACAAAGgtaatacttc ... tatttttcagACTCAGAAGAAAAAGAAGAGCAGTGATCTGAAGTATGACATATTTGGATGG
EST: gi|58024209|gb|CX710950.1|CX710950
EST:     AGCAGGCGGCAGCAACAGCTGGATCTTCTACTTCTGCTTCGGGTACAAAG                         ACTCAGAAGAAAAAGAAGAGCAGTGATCTGAAGTATGACATATTTGGATGG
genomic: AGCAGGCGGCAGCAACAGCTGGATCTTCTACTTCTGCTTCGGGTACAAAGgtaatacttc ... tatttttcagACTCAGAAGAAAAAGAAGAGCAGTGATCTGAAGTATGACATATTTGGATGG
EST: gi|120496919|gb|EH225086.1|EH225086
EST:     AGCAGGCGGCAGCAACAGCTGGATCTTCTACTTCTGCTTCGGGTACAAAG                         ACTCAGAAGAAAAAGAAGAGCAGTGATCTGAAGTATGACATATTTGGATGG
genomic: AGCAGGCGGCAGCAACAGCTGGATCTTCTACTTCTGCTTCGGGTACAAAGgtaatacttc ... tatttttcagACTCAGAAGAAAAAGAAGAGCAGTGATCTGAAGTATGACATATTTGGATGG
EST: gi|10253915|gb|BE821730.1|BE821730
EST:     AGNANGCGGCNGNNNCAGCTGGATCTTCTACTTCTGCTTCGGGTACAAAG                         ACTCAGAAGAAAAAGAAGAGCAGTGANCTGAAGTATGACATATTTGGATGG
genomic: AGCAGGCGGCAGCAACAGCTGGATCTTCTACTTCTGCTTCGGGTACAAAGgtaatacttc ... tatttttcagACTCAGAAGAAAAAGAAGAGCAGTGATCTGAAGTATGACATATTTGGATGG
EST: gi|192312151|gb|FK005650.1|FK005650
EST:     AGCAGGCGGCAGCAACAGCTGGATCTTCTACTTCTGCTTCGGGTACAAAG                         ACTCAGAGGAAAAAGAAGAGCAGTGATCTGAAGTATGACATATTTGGATGG
genomic: AGCAGGCGGCAGCAACAGCTGGATCTTCTACTTCTGCTTCGGGTACAAAGgtaatacttc ... tatttttcagACTCAGAAGAAAAAGAAGAGCAGTGATCTGAAGTATGACATATTTGGATGG
EST: gi|14991587|gb|BI317260.1|BI317260
EST:     AGCAGGCGGCAGCAACAGCTGGATCTTCTACTTCTGCTTCGGGTACAAAG                         ACTCAGAAGAAAAAGAAGAGCAGTGATCTGAAGTATGACATATTTGGATGG
genomic: AGCAGGCGGCAGCAACAGCTGGATCTTCTACTTCTGCTTCGGGTACAAAGgtaatacttc ... tatttttcagACTCAGAAGAAAAAGAAGAGCAGTGATCTGAAGTATGACATATTTGGATGG
EST: gi|58016306|gb|CX703048.1|CX703048
EST:     AGCAGGCGGCAGCAACAGCTGGATCTTCTACTTCTGCTTCGGGTACAAAG                         ACTCAGAAGAAAAAGAAGAGCAGTGATCTGAAGTATGACATATTTGGATGG
genomic: AGCAGGCGGCAGCAACAGCTGGATCTTCTACTTCTGCTTCGGGTACAAAGgtaatacttc ... tatttttcagACTCAGAAGAAAAAGAAGAGCAGTGATCTGAAGTATGACATATTTGGATGG
EST: gi|8282903|gb|BE020464.1|BE020464
EST:     AGCAGGCGGCAGCAACAGCTGGATCTTCTACTTCTGCTTCGGGTACAAAG                         ACTCAGAAGAAAAAGAAGAGCAGTGATCTGAAGTATGACATA
genomic: AGCAGGCGGCAGCAACAGCTGGATCTTCTACTTCTGCTTCGGGTACAAAGgtaatacttc ... tatttttcagACTCAGAAGAAAAAGAAGAGCAGTGATCTGAAGTATGACATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatcttcgtacttgtgtgctcattcattacctattttgtttgattatttttcagACTCAGAAGAAAAAGAAGAGCAGTGATCTGAAGTATGACATATTTGGATGGATAATTCTGGCAGTCGGCATTGTTGCATGGGTGGGATTTGCAAAATCAA
                                            ttatttttc  CT-rich tract
                                tattttgtttgattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agcactccttgtgctacaaaaatcacattggagatagatagactctgatcttcgtacttgtgtgctcattcattacctattttgtttgattatttttcagACTCAGAAGAAAAAGAAGAGCAGTGATCTGAAGTATGACATATTTGGATGGATAATTCTGGCAGTCGGCATTGTTGCATGGGTGGGATTTGCAAAATCAA

- - ctccttg
- - - - - -tgctaca
- - - - - - - - - - aatcaca
- - - - - - - - - - - - - - - - - - - - gactctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtgtgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cattcat