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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtcctgttaaagttatatttcctctcttcctcctttttccttggtgttgctcttgacttgtagattgcctgctcagaggagaatttgatgcaccatcccagataatagtcactagtttggactatgttgataactaagtctgccaactacgtattttttggttttggtcttgattctttcttttccagGGAAGAAGTGCAGACTCTTTGTCCCAGTACTTTGGGGAGGATCCAGCTAGATGCCCTTTTGAACAAG

Basic information

species Glycine max
transcript GLYMA04G14770.1
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G14770.1 (Glycine max), 3'ss of exon 16
lower sequence: AT1G31810.1 (Arabidopsis thaliana), 3'ss of exon 16
gtgagtcctgttaaagttatatttcctctcttcctcctttttccttggtgttgctcttgacttgtagattgcctgctcagaggagaatttgatgcaccatcccagataatagtcactagtttggactatgttgataactaagtctgccaactacgtattttttggttttggtcttgattctttcttttccagGGAAGAAGTGCAGACTCTTTGTCCCAGTACTTTGGGGAGGATCCAGCTAGATGCCCTTTTGAACAAG
                                                                                  | || ||  ||  | || | ||        ||| |   ||  ||  | ||    || |    | | ||||    || ||    |  |    || |||      ||  |||||||||| |||||| ||||| || || ||||| || |||||||||||| |||| |||||||| ||||
----------------------------------------------------------------------------------gtgagttatatttaacagctca--------tcagttacttaaacactttttgggacaagcagttcaaact---catgttccaatcctaaaattaattgcaa--ttcacagGGAAGAAATGCAGATTCTTTATCTCACTACTTCGGTGAGGATCCAGCTCGATGTCCTTTTGAGCAAG

upper sequence: GLYMA04G14770.1 (Glycine max), 3'ss of exon 16
lower sequence: Vv02s0033g01360.t01 (Vitis vinifera), 3'ss of exon 16
gtgagtcctgttaaagttatatttcctctcttcctcctttttccttggtgttgctcttgacttgtagattgcctgctcagaggagaatttgatgcaccatcccagataatagtcactagtttggactatgttgataactaagtctgccaactacgtattttttggttttggtcttgattctttcttttccagGGAAGAAGTGCAGACTCTTTGTCCCAGTACTTTGGGGAGGATCCAGCTAGATGCCCTTTTGAACAAG
                                                                                                              ||||       ||| ||  |||| | || |        |  ||  |   |  || |||||||  || | | || | || |||||||||| ||||||||| ||||||||||||||||| || ||||||||| | || || ||||| ||||
-----------------------------------------------------------------------------------------------------------gtgagtcttctccatggtcttagttgctgacaactgtgagtatgtagttcggtactgattttggtactgctacattgtcttgcagGGAAGAAATGCAGACTCCTTGTCCCAGTACTTTGGAGAAGATCCAGCTCGGTGTCCATTTGAGCAAG
















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|7590237|gb|AW705994.1|AW705994
EST:     ATATTGCTGAAGCTGATGTGAGGTCTCTTATATCATTGTATTCTGAAGTG                         GGAAGAAGTGCAGACTCTTTGTCCCAGTACTTTGGGGAGGATCCAGCTAGA
genomic: ATATTGCTGAAGCTGATGTGAGGTCTCTTATATCATTGTATTCTGAAGTGgtgagtcctg ... tcttttccagGGAAGAAGTGCAGACTCTTTGTCCCAGTACTTTGGGGAGGATCCAGCTAGA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctaagtctgccaactacgtattttttggttttggtcttgattctttcttttccagGGAAGAAGTGCAGACTCTTTGTCCCAGTACTTTGGGGAGGATCCAGCTAGATGCCCTTTTGAACAAG
                                  tcttgat  putative branch site (score: 4)
                                  tcttgattctttcttt  CT-rich tract
                  tattttttggtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtcctgttaaagttatatttcctctcttcctcctttttccttggtgttgctcttgacttgtagattgcctgctcagaggagaatttgatgcaccatcccagataatagtcactagtttggactatgttgataactaagtctgccaactacgtattttttggttttggtcttgattctttcttttccagGGAAGAAGTGCAGACTCTTTGTCCCAGTACTTTGGGGAGGATCCAGCTAGATGCCCTTTTGAACAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT