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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaagcaaattcagaaatcatttctacagtagctttgctgctttgctagagaatatgattaatatatttgcaagagatgatgcaaaatatttaagatcttacttgaatattgtcaactccagTTTATAGGGAAGAAAGCTGCCTATGCTTTGAGCCAAGGTCTTGGGGTGATTGCATGCATTGGAGAATTGTTAGAAGAAAGGGAGGCTGGAAAAACTTTTG

Basic information

species Glycine max
transcript GLYMA03G34300.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G34300.1 (Glycine max), 3'ss of exon 5
lower sequence: AT2G21170.2 (Arabidopsis thaliana), 3'ss of exon 4
gtaaagcaaattcagaaatcatttctacagtagctttgctgctttgctagagaatatgattaatatatttgcaagagatgatgcaaaatatttaagatcttacttgaatattgtcaactccagTTTATAGGGAAGAAAGCTGCCTATGCTTTGAGCCAAGGTCTTGGGGTGATTGCATGCATTGGAGAATTGTTAGAAGAAAGGGAGGCTGGAAAAACTTTTG
                     |   || | ||         ||||   ||     |    | |  || |   ||  | |  || |||| || |  | |||    | || |     |||   ||||||| |||||||||||||| ||||| |||||  | |||||||| ||||| || || ||||| |||  | ||||||| ||||| || || || || ||||
--------------------gtcagtaaaataa----aacactttataag----cactggtgagttactaagaaagggttgtg-aaaacatatttgctctgttctcaacaa----aaccatagTTTATCGGGAAGAAAGCTGCATATGCATTGAGTGAGGGTCTTGGAGTGATAGCTTGTATTGGGGAAAAGCTAGAAGAGAGGGAAGCAGGCAAGACGTTTG

upper sequence: GLYMA03G34300.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv03s0038g01780.t01 (Vitis vinifera), 3'ss of exon 5
gtaaagcaaattcagaaatcatttctacagtagctttgctgctttgctagagaatatgattaatatatttgcaagagatgatgcaaa--atatttaagatcttacttgaatattgtcaactccagTTTATAGGGAAGAAAGCTGCCTATGCTTTGAGCCAAGGTCTTGGGGTGATTGCATGCATTGGAGAATTGTTAGAAGAAAGGGAGGCTGGAAAAACTTTTG
|| ||  ||| ||  | || |  |    | ||  | || ||    |  |    ||||    ||  | |||      ||| |   ||   ||||| |  |  | |||       ||  |  | ||||| ||||| ||||||||||| ||||| |||||||| ||||||   || || || || ||||||||| ||||| |||||||||| || |||||||||||||
gtgaa--aaactctaatattagattgttactatttatg-tgaaacgtgaagctatattcagaactttttttttttggataagtgaagctatattcagaacttgactgtgggtctgaaattttcagTTCATAGGAAAGAAAGCTGCTTATGCCTTGAGCCAGGGTCTTAAAGTAATAGCTTGTATTGGAGAACTGTTACAAGAAAGGGAAGCAGGAAAAACTTTTG
















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|16281659|gb|BI944602.1|BI944602
EST:     TTGTTCTTGGACATTCTGAGCGAAGACATGTTATTGGAGAAAATGATGAG                         TTTATAGGGAAGAAAGCTGCCTATGCTTTGAGCCAAGGTCTTGGGGTGATT
genomic: TTGTTCTTGGACATTCTGAGCGAAGACATGTTATTGGAGAAAATGATGAGgtaaagcaaa ... tcaactccagTTTATAGGGAAGAAAGCTGCCTATGCTTTGAGCCAAGGTCTTGGGGTGATT
EST: gi|298193423|gb|HO033857.1|HO033857
EST:     TTGTTCTTGGACATTCTGAGCGAAGACATGTTATTGGAGAAAATGATGAG                         TTTATAGGGAAGAAAGCTGCCTATGCTTTGAGCCAAGGTCTTGGGGTGATT
genomic: TTGTTCTTGGACATTCTGAGCGAAGACATGTTATTGGAGAAAATGATGAGgtaaagcaaa ... tcaactccagTTTATAGGGAAGAAAGCTGCCTATGCTTTGAGCCAAGGTCTTGGGGTGATT
EST: gi|151395984|gb|EV265861.1|EV265861
EST:     TTGTTCTTGGACATTCTGAGCGAAGACATGTTATTGGAGAAAATGATGAG                         TTTATAGGGAAGAAAGCTGCCTATGCTTTGAGCCAAGGTCTTGGGGTGATT
genomic: TTGTTCTTGGACATTCTGAGCGAAGACATGTTATTGGAGAAAATGATGAGgtaaagcaaa ... tcaactccagTTTATAGGGAAGAAAGCTGCCTATGCTTTGAGCCAAGGTCTTGGGGTGATT
EST: gi|209724178|gb|BW659712.1|BW659712
EST:     TTGTTCTTGGACATTCTGAGCGAAGACATGTTATTGGAGAAAATGATGAG                         TTTATAGGGAAGAAAGCTGCCTATGCTTTGAGCCAAGGTCTTGGGGTGATT
genomic: TTGTTCTTGGACATTCTGAGCGAAGACATGTTATTGGAGAAAATGATGAGgtaaagcaaa ... tcaactccagTTTATAGGGAAGAAAGCTGCCTATGCTTTGAGCCAAGGTCTTGGGGTGATT
EST: gi|31308297|gb|CD393500.1|CD393500
EST:     ATTGGAGAAAATGATGAG                         TTTATAGGGAAGAAAGCTGCCTATGCTTTGAGCCAAGGTCTTGGGGTGATT
genomic: ATTGGAGAAAATGATGAGgtaaagcaaa ... tcaactccagTTTATAGGGAAGAAAGCTGCCTATGCTTTGAGCCAAGGTCTTGGGGTGATT
EST: gi|16279304|gb|BI943365.1|BI943365
EST:     TTGTTCTTGGACATTCTGAGCGAAGACATGTTATTGGAGAAAATGATGAG                         TTTATAGGGAAGAAAGCTGCCTATGCTTTGAGCCAAGGTCTTGGGGTGATT
genomic: TTGTTCTTGGACATTCTGAGCGAAGACATGTTATTGGAGAAAATGATGAGgtaaagcaaa ... tcaactccagTTTATAGGGAAGAAAGCTGCCTATGCTTTGAGCCAAGGTCTTGGGGTGATT
EST: gi|4314103|gb|AI461222.1|AI461222
EST:     TTGTTCTTGGACATTCTGAGCGAAGACATGTTATTGGAGAAAATGATGAG                         TTTATAGGGAAGAAAGCTGCCTATGCTTTGAGCCAAGGTCNTTGGG-TGAT
genomic: TTGTTCTTGGACATTCTGAGCGAAGACATGTTATTGGAGAAAATGATGAGgtaaagcaaa ... tcaactccagTTTATAGGGAAGAAAGCTGCCTATGCTTTGAGCCAAGGTC-TTGGGGTGAT
EST: gi|15204096|gb|BI426864.1|BI426864
EST:     TTGTTCTTGGACATTCTGAGCGAAGACATGTTATTGGAGAAAATGATGAG                         TTTATAGGGAAGAAAGCTGCCTATGCTTTGAGCCAAGGTCTTGGGGTGATT
genomic: TTGTTCTTGGACATTCTGAGCGAAGACATGTTATTGGAGAAAATGATGAGgtaaagcaaa ... tcaactccagTTTATAGGGAAGAAAGCTGCCTATGCTTTGAGCCAAGGTCTTGGGGTGATT
EST: gi|10233567|gb|BE802455.1|BE802455
EST:     TTGTTCTTGGACATTCTGAGCGAAGACATGTTATTGGAGAAAATGATGAG                         TTTATAGGGAAGAATGCTGCCTATGCTATGAGCCAAGGTCT-GGTGGTGAA
genomic: TTGTTCTTGGACATTCTGAGCGAAGACATGTTATTGGAGAAAATGATGAGgtaaagcaaa ... tcaactccagTTTATAGGGAAGAAAGCTGCCTATGCTTTGAGCCAAGGTCTTGG-GGTGAT
EST: gi|20449080|gb|BQ253204.1|BQ253204
EST:     TTGTTCTTGGACATTCTGAGCGAAGACATGTTATTGGAGAAAATGATGAG                         TTTATAGGGAAGAAAGCTGCCTATGCTTTGAGCCAAGGTCTTGGGGTGATT
genomic: TTGTTCTTGGACATTCTGAGCGAAGACATGTTATTGGAGAAAATGATGAGgtaaagcaaa ... tcaactccagTTTATAGGGAAGAAAGCTGCCTATGCTTTGAGCCAAGGTCTTGGGGTGATT
EST: gi|9204176|gb|BE330400.1|BE330400
EST:     TTGGTCTGGG-CATTCTGAGCGAAGACATGTTATTGGAGAAAATGATGAG                         TTTATAGGGGAAGAAAGCTGCCTATGCTTTGAGCCAAGGTCTTGGGGTGAT
genomic: TTGTTCTTGGACATTCTGAGCGAAGACATGTTATTGGAGAAAATGATGAGgtaaagcaaa ... tcaactccagTTTATAGGG-AAGAAAGCTGCCTATGCTTTGAGCCAAGGTCTTGGGGTGAT
EST: gi|120530487|gb|EH258620.1|EH258620
EST:     TTGTTCTTGGACATTCTGAGCGAATACATGTTATTGGAGAAAATGATGAG                         TTTATAGGGAAGAAAGCTGCCTATGCTTTGAGCCAAGGTCTTGGGGTGATT
genomic: TTGTTCTTGGACATTCTGAGCGAAGACATGTTATTGGAGAAAATGATGAGgtaaagcaaa ... tcaactccagTTTATAGGGAAGAAAGCTGCCTATGCTTTGAGCCAAGGTCTTGGGGTGATT
EST: gi|9563997|gb|BE473506.1|BE473506
EST:     TTGTTCTTGGACATTCTGAGCGAAGACATGTTATTGGAGAAAATGATGAG                         TTTATTAGG-AAGAAAGCTGCCTATGCTTTGAGCCAAGGTCCTGGGGTGAT
genomic: TTGTTCTTGGACATTCTGAGCGAAGACATGTTATTGGAGAAAATGATGAGgtaaagcaaa ... tcaactccagTTTAT-AGGGAAGAAAGCTGCCTATGCTTTGAGCCAAGGTCTTGGGGTGAT
EST: gi|209715618|gb|BW657385.1|BW657385
EST:     TTGTTCTTGGACATTCTGAGCGAAGACATGTTATTGGAGAAAATGATGAG                         TTTATAGGGAAGAAAGCTGCCTATGCTTTGAGCCAAGGTCTTGGGGTGATT
genomic: TTGTTCTTGGACATTCTGAGCGAAGACATGTTATTGGAGAAAATGATGAGgtaaagcaaa ... tcaactccagTTTATAGGGAAGAAAGCTGCCTATGCTTTGAGCCAAGGTCTTGGGGTGATT
EST: gi|17964485|gb|BM271219.1|BM271219
EST:     TTGTTCTTGGACATTCTGAGCGAAGACATGTTATTGGAGAAAATGATGAG                         TTTATAGGGAAGAAAGCTGCCTATGCTTTGAGCCAAGGTCTTGGGGTGATT
genomic: TTGTTCTTGGACATTCTGAGCGAAGACATGTTATTGGAGAAAATGATGAGgtaaagcaaa ... tcaactccagTTTATAGGGAAGAAAGCTGCCTATGCTTTGAGCCAAGGTCTTGGGGTGATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgcaagagatgatgcaaaatatttaagatcttacttgaatattgtcaactccagTTTATAGGGAAGAAAGCTGCCTATGCTTTGAGCCAAGGTCTTGGGGTGATTGCATGCATTGGAGAATTGTTAGAAGAAAGGGAGGCTGGAAAAACTTTTG
                            atcttac  putative branch site (score: 3)
                aaaatatttaagatct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaagcaaattcagaaatcatttctacagtagctttgctgctttgctagagaatatgattaatatatttgcaagagatgatgcaaaatatttaagatcttacttgaatattgtcaactccagTTTATAGGGAAGAAAGCTGCCTATGCTTTGAGCCAAGGTCTTGGGGTGATTGCATGCATTGGAGAATTGTTAGAAGAAAGGGAGGCTGGAAAAACTTTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA