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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaattgttatttatattttactgttatgtctttccttgtaaattgtctgtctcgcctaccatacatctctcttcattattctgatgctttttccgtgcagCTTCTTGGCAGGGTGTTTAACATTCTACGTGAGAATAATCCAGAACTAGCTGGAGATCGGCGAAGGACAGTTATGAGGCCTCCTCAAGTTCTTCGTGAGG

Basic information

species Glycine max
transcript GLYMA02G40310.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G40310.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv06s0004g08180.t01 (Vitis vinifera), 3'ss of exon 6
--gaattgttatttatattttactgttatgtctttccttgtaaattgtctgtctcgcctaccatacatctctcttcattattctgatgcttttt---ccgtgcagCTTCTTGGCAGGGTGTTTAACATTCTACGTGAGAATAATCCAGAACTAGCTGGAGATCGGCGAAGGACAGTTATGAGGCCTCCTCAAGTTCTTCGTGAGG
     |  | |||||| | ||  |   |  |  ||  |  |    | |  ||     | |  || ||  ||  |  |  ||  |||  ||||||   | |||||||||||||| ||||||||||||||||| || |||||||||||||| || ||||||||| || | || |||||||||||||| || ||||| |||||||| |
gcctttcttcatttatttatttttaccaaattattattcatgttgtattagta----ccatgatgcag-tccttgtaggatattgaccctttttgtactgtgcagCTTCTTGGTAGGGTGTTTAACATTCTTCGGGAGAATAATCCAGAGCTTGCTGGAGATAGGAGGAGAACAGTTATGAGGCCCCCACAAGTCCTTCGTGAAG
















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|151412916|gb|EV282728.1|EV282728
EST:     AGGCTCGCTATCCTTGGGAAGGGAGTGATCGTGATTATGAATATGAGGAG                         CTTCTTGGCAGGGTGTTTAACATTCTACGTGAGAATAATCCAGAACTAGCT
genomic: AGGCTCGCTATCCTTGGGAAGGGAGTGATCGTGATTATGAATATGAGGAGgtttgttgtt ... ttccgtgcagCTTCTTGGCAGGGTGTTTAACATTCTACGTGAGAATAATCCAGAACTAGCT
EST: gi|254337821|gb|GR849560.1|GR849560
EST:     AGGCTCGCTATCCTTGGGAAGGGAGTGATCGTGATTATGAATATGAGGAG                         CTTCTTGGCAGGGTGTTTAACATTCTACGTGAGAATAATCCAGAACTAGCT
genomic: AGGCTCGCTATCCTTGGGAAGGGAGTGATCGTGATTATGAATATGAGGAGgtttgttgtt ... ttccgtgcagCTTCTTGGCAGGGTGTTTAACATTCTACGTGAGAATAATCCAGAACTAGCT
EST: gi|208244387|gb|GE042572.1|GE042572
EST:     AGGCTCGCTATCCTTGGGAAGGGAGTGATCGTGATTATGAATATGAGGAG                         CTTCTTGGCAGGGTGTTTAACATTCTACGTGAGAATAATCCAGAACTAG
genomic: AGGCTCGCTATCCTTGGGAAGGGAGTGATCGTGATTATGAATATGAGGAGgtttgttgtt ... ttccgtgcagCTTCTTGGCAGGGTGTTTAACATTCTACGTGAGAATAATCCAGAACTAG
EST: gi|58022083|gb|CX708824.1|CX708824
EST:     AGGCTCGCTATCCTGGGGAAGGGAGTGATCGTGATTATGAATATGAGGAG                         CTTCTTGGCAGGGTGTTTAACATTCTACGTGAGAATAATCCAGAACTAGCT
genomic: AGGCTCGCTATCCTTGGGAAGGGAGTGATCGTGATTATGAATATGAGGAGgtttgttgtt ... ttccgtgcagCTTCTTGGCAGGGTGTTTAACATTCTACGTGAGAATAATCCAGAACTAGCT
EST: gi|8827357|gb|BE211087.1|BE211087
EST:     AGGCTCGCTATCCTTGGGAAGGGAGTGATCGTGATTATGAATATGAGGAG                         CTTCTTGGCAGGGTGTTTAACATTCTACGTGAGAATAATCCAGAACTAGCT
genomic: AGGCTCGCTATCCTTGGGAAGGGAGTGATCGTGATTATGAATATGAGGAGgtttgttgtt ... ttccgtgcagCTTCTTGGCAGGGTGTTTAACATTCTACGTGAGAATAATCCAGAACTAGCT
EST: gi|208314970|gb|GE112262.1|GE112262
EST:     AGGCTCGCTATCCTTGGGAAGGGAGTGATCGTGATTATGAATATGAGGAG                         CTTCTTGGCAGGGTGTTTAACATTCTACGTGAGAATAATCCAGAACTAG
genomic: AGGCTCGCTATCCTTGGGAAGGGAGTGATCGTGATTATGAATATGAGGAGgtttgttgtt ... ttccgtgcagCTTCTTGGCAGGGTGTTTAACATTCTACGTGAGAATAATCCAGAACTAG
EST: gi|58020605|gb|CX707347.1|CX707347
EST:     AGGCTCGCTATCCTTGGGAAGGGAGTGATCGTGATTATGAATATGAGGAG                         CTTCTTGGCAGGGTGTTTAACATTCTACGTGAGAATAATCCAGAACTAGCT
genomic: AGGCTCGCTATCCTTGGGAAGGGAGTGATCGTGATTATGAATATGAGGAGgtttgttgtt ... ttccgtgcagCTTCTTGGCAGGGTGTTTAACATTCTACGTGAGAATAATCCAGAACTAGCT
EST: gi|254337820|gb|GR849559.1|GR849559
EST:     AGGCTCGCTATCCTTGGGAAGGGAGTGATCGTGATTATGAATATGAGGAG                         CTTCTTGGCAGGGTGTTTAACATTCTACGTGAGAATAATCCAGAACTAGCT
genomic: AGGCTCGCTATCCTTGGGAAGGGAGTGATCGTGATTATGAATATGAGGAGgtttgttgtt ... ttccgtgcagCTTCTTGGCAGGGTGTTTAACATTCTACGTGAGAATAATCCAGAACTAGCT
EST: gi|16347705|gb|BI973300.1|BI973300
EST:     NNGCTCGCTATCCTTGGGAAGGGAGTGATCGTGATTATGAATATGAGGAG                         CTTCTTGGCAGGGTGTTTAACATTCTACGTGAGAATAATCCAGAACTAGCT
genomic: AGGCTCGCTATCCTTGGGAAGGGAGTGATCGTGATTATGAATATGAGGAGgtttgttgtt ... ttccgtgcagCTTCTTGGCAGGGTGTTTAACATTCTACGTGAGAATAATCCAGAACTAGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgtctcgcctaccatacatctctcttcattattctgatgctttttccgtgcagCTTCTTGGCAGGGTGTTTAACATTCTACGTGAGAATAATCCAGAACTAGCTGGAGATCGGCGAAGGACAGTTATGAGGCCTCCTCAAGTTCTTCGTGAGG
                                 ttctgat  putative branch site (score: 3)
                                       tgctttttcc  CT-rich tract
                          ttcattatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaattgttatttatattttactgttatgtctttccttgtaaattgtctgtctcgcctaccatacatctctcttcattattctgatgctttttccgtgcagCTTCTTGGCAGGGTGTTTAACATTCTACGTGAGAATAATCCAGAACTAGCTGGAGATCGGCGAAGGACAGTTATGAGGCCTCCTCAAGTTCTTCGTGAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC
- - - - - - - - - - -tgttatg
- - - - - - - - - - - - - - - - -ccttgta
- - - - - - - - - - - - - - - - - - - - - ttgtctg
- - - - - - - - - - - - - - - - - - - - - - - - - - cgcctac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gatgctt