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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgttgtaaataaataaaataaagttagagtttttaaatgttaatttttgtttttttggggttgtggcagTTGATTGTGCTGTACGTGGATTTCAAGCTTGATGAGAGTTACACGCCGAGCAAAGTTTCCATCCGTGCCGGTGATGGTTTTCACAACTTGAAG

Basic information

species Glycine max
transcript GLYMA02G06190.3
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G06190.3 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G054247_T04 (Zea mays), 3'ss of exon 2
-------gtacgttgtaaataa-ataaaataaagttagagtttttaaatgttaatttttgtttttttggggttgtg--gcagTTGATTGTGCTGTACGTGGATTTCAAGCTTGATGAGAGTTACACGCCGAGCAAAGTTTCCATCCGTGCCGGTGATGGTTTTCACAACTTGAAG-------
        | |  |  | ||   |     |    ||    ||      | || |   |  ||  ||    ||||||  | || |  ||||||| ||||||||||||||||| || ||||||||||||||||||||  | |||||||| ||||| ||||| || |||||| | |||       
gtgcctgcttcagtagagatgctactcctttgccttgtgattcgatggttttgagactaattggttctatgttgtgcggtagCTCGTTGTGCTCTACGTGGATTTCAAGCTCGACGAGAGTTACACGCCGAGCAAGATCTCCATCCGGGCCGGGGATGGCTTCCACAACCTAAAGGTACGCT

upper sequence: GLYMA02G06190.3 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G054247_T03 (Zea mays), 3'ss of exon 2
-------gtacgttgtaaataa-ataaaataaagttagagtttttaaatgttaatttttgtttttttggggttgtg--gcagTTGATTGTGCTGTACGTGGATTTCAAGCTTGATGAGAGTTACACGCCGAGCAAAGTTTCCATCCGTGCCGGTGATGGTTTTCACAACTTGAAG
        | |  |  | ||   |     |    ||    ||      | || |   |  ||  ||    ||||||  | || |  ||||||| ||||||||||||||||| || ||||||||||||||||||||  | |||||||| ||||| ||||| || |||||| | |||
gtgcctgcttcagtagagatgctactcctttgccttgtgattcgatggttttgagactaattggttctatgttgtgcggtagCTCGTTGTGCTCTACGTGGATTTCAAGCTCGACGAGAGTTACACGCCGAGCAAGATCTCCATCCGGGCCGGGGATGGCTTCCACAACCTAAAG

upper sequence: GLYMA02G06190.3 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G174971_T01 (Zea mays), 3'ss of exon 2
----------------gtacgttgtaaataaataaaataaagttagagtttttaaatgttaatttttgtttttttggggttgtggcagTTGATTGTGCTGTACGTGGATTTCAAGCTTGATGAGAGTTACACGCCGAGCAAAGTTTCCATCCGTGCCGGTGATGGTTTTCACAACTTGAAG
                  | | | |       |    |    || ||   |||  |  |||||   |  | | |||     ||||||| |  |||  || ||||||||||||||||| || ||||| |||||||| |||||  | |||||||| ||||| ||||| || |||||| | |||
gtgcctgcttcagtagagatgctattctctcttggcttgtgattcgatggttttgagattaatcggttctatgttg----cgtggcagCTTGTTGCTCTCTACGTGGATTTCAAGCTCGACGAGAGCTACACGCCCAGCAAGATCTCCATCCGGGCCGGGGATGGCTTCCACAACCTCAAG

upper sequence: GLYMA02G06190.3 (Glycine max), 3'ss of exon 3
lower sequence: Vv04s0023g01940.t01 (Vitis vinifera), 3'ss of exon 2
----gtacg---ttgtaaataaataaaataaagttagagtttttaaatgttaatttttgtttttttggggt-----------tgtggcagTTGATTGTGCTGTACGTGGATTTCAAGCTTGATGAGAGTTACACGCCGAGCAAAGTTTCCATCCGTGCCGGTGATGGTTTTCACAACTTGAAG
    ||| |   || |   |   | |  |     |       |||    ||  |||| ||   |    |||           | |   || || ||||  | || |||||||||||||| || ||||| ||||||||||| ||  | || || || ||||| ||||| || ||||||||||||
gtgtgtatgcaattttgggtttctgatttttttctttcccccttatcgtttggttttggtgactgaatggtgaatagatttctcttaaagCTGGTTGTAATTTATGTGGATTTCAAGCTGGACGAGAGCTACACGCCGAGTAAGATCTCTATTCGAGCCGGAGATGGCTTCCACAACTTGAAG

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|298182568|gb|HO031303.1|HO031303
EST:     GGCAACCCCATTTGGTCAACATTCAGTTTCAAAAGAAAGTTAGACTTCAG                         TTGATTGTGCTGTACGTGGATTTCAAGCTTGATGAGAGTTACACGCTGAGC
genomic: GGCAACCCCATTTGGTCAACATTCAGTTTCAAAAGAAAGTTAGACTTCAGgtacgttgta ... gttgtggcagTTGATTGTGCTGTACGTGGATTTCAAGCTTGATGAGAGTTACACGCCGAGC
EST: gi|4397247|gb|AI496244.1|AI496244
EST:     GGCAACCCCATTTGGTCAACATTCAGTTTCAAAAGAAAGTTAGACCTCAG                         TTGATTGTGCTTGT-CGTG-ATTTCAAGCTTGATGAGA-TTACACGC
genomic: GGCAACCCCATTTGGTCAACATTCAGTTTCAAAAGAAAGTTAGACTTCAGgtacgttgta ... gttgtggcagTTGATTGTGCT-GTACGTGGATTTCAAGCTTGATGAGAGTTACACGC
EST: gi|192310829|gb|FK000315.1|FK000315
EST:     GGCAACCCCATTTGGTCAACATTCAGTTTCAAAAGAAAGTTAGACTTCAG                         TTGATTGTGCTGTACGTGGATTTCAAGCTTGATGAGAGTTACACGCCGAGC
genomic: GGCAACCCCATTTGGTCAACATTCAGTTTCAAAAGAAAGTTAGACTTCAGgtacgttgta ... gttgtggcagTTGATTGTGCTGTACGTGGATTTCAAGCTTGATGAGAGTTACACGCCGAGC
EST: gi|6567209|gb|AW234820.1|AW234820
EST:     GGCAACCCCATTTGGTCAACATTCAGTTTCAAAAGAAAGTTAGACTTCAG                         TTGATTGTGCTGTACGTGGATTTCAAGCTTGATGAGAGTTACACGCCGAGC
genomic: GGCAACCCCATTTGGTCAACATTCAGTTTCAAAAGAAAGTTAGACTTCAGgtacgttgta ... gttgtggcagTTGATTGTGCTGTACGTGGATTTCAAGCTTGATGAGAGTTACACGCCGAGC
EST: gi|58024926|gb|CX711667.1|CX711667
EST:     GTTTCAAAAGAAAGTTAGACTTCAG                         TTGATTGTGCTGTACGTGGATTTCAAGCTTGATGAGAGTTACACGCCGAGC
genomic: GTTTCAAAAGAAAGTTAGACTTCAGgtacgttgta ... gttgtggcagTTGATTGTGCTGTACGTGGATTTCAAGCTTGATGAGAGTTACACGCCGAGC
EST: gi|151407570|gb|EV277385.1|EV277385
EST:     GGCAACCCCATTTGGTCAACATTCAGTTTCAAAAGAAAGTTAGACTTCAG                         TTGATTGTGCTGTACGTGGATTTCAAGCTTGATGAGAGTTACACGCCGAGC
genomic: GGCAACCCCATTTGGTCAACATTCAGTTTCAAAAGAAAGTTAGACTTCAGgtacgttgta ... gttgtggcagTTGATTGTGCTGTACGTGGATTTCAAGCTTGATGAGAGTTACACGCCGAGC
EST: gi|193723936|gb|FK656314.1|FK656314
EST:     GGCAA-CCCATTTGGTCAACATTCAGTTTC-AAAGAAAGTTAGACTTCAG                         TTGATTGTGCTGTACGTGGATTTCAAGCTTGATGAGAGTTACACGCCGAGC
genomic: GGCAACCCCATTTGGTCAACATTCAGTTTCAAAAGAAAGTTAGACTTCAGgtacgttgta ... gttgtggcagTTGATTGTGCTGTACGTGGATTTCAAGCTTGATGAGAGTTACACGCCGAGC
EST: gi|209711476|gb|BW665228.1|BW665228
EST:     GGCAACCCCATTTGGTCAACATTCAGTTTCAAAAGAAAGTTAGACTTCAG                         TTGATTGTGCTGTACGTGGATTTCAAGCTTGATGAGAGTTACACGCCGAGC
genomic: GGCAACCCCATTTGGTCAACATTCAGTTTCAAAAGAAAGTTAGACTTCAGgtacgttgta ... gttgtggcagTTGATTGTGCTGTACGTGGATTTCAAGCTTGATGAGAGTTACACGCCGAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaataaagttagagtttttaaatgttaatttttgtttttttggggttgtggcagTTGATTGTGCTGTACGTGGATTTCAAGCTTGATGAGAGTTACACGCCGAGCAAAGTTTCCATCCGTGCCGGTGATGGTTTTCACAACTTGAAG
                       tgttaat  putative branch site (score: 3)
     aaagttagagttttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgttgtaaataaataaaataaagttagagtttttaaatgttaatttttgtttttttggggttgtggcagTTGATTGTGCTGTACGTGGATTTCAAGCTTGATGAGAGTTACACGCCGAGCAAAGTTTCCATCCGTGCCGGTGATGGTTTTCACAACTTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG