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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agatggattggtggatgttgttattaagcttcatacacctcctttttgagtcttgtatataatatggtcctaaacaatgccatttatctattgccaacagGTATGCAAGTTCTTTTTATGGTCCATTTAGAGAGGCACTAGACTCAAACCCCCGGTTTGGAGACAAGAAAAC

Basic information

species Glycine max
transcript GLYMA04G42670.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G42670.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv18s0001g02550.t01 (Vitis vinifera), 3'ss of exon 8
agatggattggtggatgttgttattaagcttcatacac-ctcctttttg--agtcttgtatataatatggtcctaa-acaatgccatttatct-attgccaacagGTATGCAAGTTCTTTTTATGGTCCATTTAGAGAGGCACTAGACTCAAACCCCCGGTTTGGAGACAAGAAAAC
     | |   ||||| |||||  ||| |||  | | | ||| |||  |  | || | ||   |  ||  |  ||| |   |    | ||  | ||||| ||||||||||||||| | ||||||||||||||  |||| ||| | |||||||| || || ||||||||||| |||||
-----gctgtttggatattgttggtaaactttgttctcactcatttccggcaatcatatagtcatcatttttttaacatgttaatctctacttcattgcaaacagGTATGCAAGTGCATTTTATGGTCCATTCCGAGAAGCATTGGACTCAAATCCACGCTTTGGAGACAAAAAAAC

upper sequence: GLYMA04G42670.1 (Glycine max), 3'ss of exon 9
lower sequence: EFJ10919 (Selaginella moellendorffii), 3'ss of exon 8
agatggattggtggatgttgttattaagcttcatacacctcctttttgagtcttgtatataatatggtcctaaacaatgccatttatctattgccaacagGTATGCAAGTTCTTTTTATGGTCCATTTAGAGAGGCACTAGACTCAAACCCCCGGTTTGGAGACAAGAAAAC
                                        |  ||| |   ||| | | |  | |||  || |       |     |    ||    ||||||||||||  | || ||||||||||| ||||| || || |||||||| ||||| |||||||| ||||||||
------------------------------------gtaactctttcgtcccttctctcttttttggatctga-------cgcgccttcgctgttctcagGTATGCAAGCGCGTTCTATGGTCCATTCAGAGAAGCTCTGGACTCAAATCCCCGTTTTGGAGATAAGAAAAC

upper sequence: GLYMA04G42670.1 (Glycine max), 3'ss of exon 9
lower sequence: EFJ25898 (Selaginella moellendorffii), 3'ss of exon 8
agatggattggtggatgttgttattaagcttcatacacctcctttttgagtcttgtatataatatggtcctaaacaatgccatttatctattgccaacagGTATGCAAGTTCTTTTTATGGTCCATTTAGAGAGGCACTAGACTCAAACCCCCGGTTTGGAGACAAGAAAAC
                                        |  ||| |   ||| | | |  | |||  || |       |     |    ||    ||||||||||||  | || ||||||||||| ||||| ||  | |||||||| ||||| |||||||| ||||||||
------------------------------------gtaactctttcgtcccttctctcttttttggatctga-------cgcgccttcgctgttctcagGTATGCAAGCGCGTTCTATGGTCCATTCAGAGAAGCTTTGGACTCAAATCCCCGTTTTGGAGATAAGAAAAC

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|7028233|gb|AW458016.1|AW458016
EST:     CTGGATGCTGAAGGCTTTCAGCATGTTTCTATAATGTCCTATACAGCAAA                         GTATGCAAGTTCTTTTTATGGTCCATTTAGAGAGGCACTAGACTCAAACCC
genomic: CTGGATGCTGAAGGCTTTCAGCATGTTTCTATAATGTCCTATACAGCAAAgtaagttttt ... ttgccaacagGTATGCAAGTTCTTTTTATGGTCCATTTAGAGAGGCACTAGACTCAAACCC
EST: gi|7691223|gb|AW759354.1|AW759354
EST:     CTGGATGCTGAAGGCTTTCAGCATGTTTCTATAATGTCCTATACAGCAAA                         GTATGCAAGTTCTTTTTATGGTCCATTTAGAGAGGCACTAGACTCAAACCC
genomic: CTGGATGCTGAAGGCTTTCAGCATGTTTCTATAATGTCCTATACAGCAAAgtaagttttt ... ttgccaacagGTATGCAAGTTCTTTTTATGGTCCATTTAGAGAGGCACTAGACTCAAACCC
EST: gi|208060750|gb|GD856686.1|GD856686
EST:     CTGGATGCTGAAGGCTTTCAGCATGTTTCTATAATGTCCTATACAGCAAA                         GTATGCAAGTTCTTTTTATGGTCCATTTAGAGAGGCACTAGACTCAAACCC
genomic: CTGGATGCTGAAGGCTTTCAGCATGTTTCTATAATGTCCTATACAGCAAAgtaagttttt ... ttgccaacagGTATGCAAGTTCTTTTTATGGTCCATTTAGAGAGGCACTAGACTCAAACCC
EST: gi|23057473|gb|BU578156.1|BU578156
EST:     CTGGATGCTGAAGGCTTTCAGCATGTTTCTATAATGTCCTATACAGCAAA                         GTATGCAAGTTCTTTTTATGGTCCATTTAGAGAGGCACTAGACTCAAACCC
genomic: CTGGATGCTGAAGGCTTTCAGCATGTTTCTATAATGTCCTATACAGCAAAgtaagttttt ... ttgccaacagGTATGCAAGTTCTTTTTATGGTCCATTTAGAGAGGCACTAGACTCAAACCC
EST: gi|208339448|gb|GE138566.1|GE138566
EST:     CTGGATGCTGAAGGCTTTCNGCATGTTTCTATAATGTCCTATACAGCAAA                         GTATGCAAGTTCTTTTTATGGTCCATTTAGAGAGGCACTAGACTCAAACCC
genomic: CTGGATGCTGAAGGCTTTCAGCATGTTTCTATAATGTCCTATACAGCAAAgtaagttttt ... ttgccaacagGTATGCAAGTTCTTTTTATGGTCCATTTAGAGAGGCACTAGACTCAAACCC
EST: gi|17022525|gb|BM093559.1|BM093559
EST:     CTGGATGCTGAAGGCTTTCAGCATGTTTCTATAATGTCCTATACAGCAAA                         GTATGCAAGTTCTTTTTATGGTCCATTTAGAGAGGCACTAGACTCAAACCC
genomic: CTGGATGCTGAAGGCTTTCAGCATGTTTCTATAATGTCCTATACAGCAAAgtaagttttt ... ttgccaacagGTATGCAAGTTCTTTTTATGGTCCATTTAGAGAGGCACTAGACTCAAACCC
EST: gi|7693203|gb|AW761299.1|AW761299
EST:     CTGGATGCTGAAGGCTNTCAGCATGTTTCTATAATGTCCTATACAGCAAA                         GTATGCAAGTTCTTTTTATGGTCCATTTAGAGAGGCACTAGACTCAGACCC
genomic: CTGGATGCTGAAGGCTTTCAGCATGTTTCTATAATGTCCTATACAGCAAAgtaagttttt ... ttgccaacagGTATGCAAGTTCTTTTTATGGTCCATTTAGAGAGGCACTAGACTCAAACCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgagtcttgtatataatatggtcctaaacaatgccatttatctattgccaacagGTATGCAAGTTCTTTTTATGGTCCATTTAGAGAGGCACTAGACTCAAACCCCCGGTTTGGAGACAAGAAAAC
                      tcctaaa  putative branch site (score: 2)
     tcttgtatataatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agatggattggtggatgttgttattaagcttcatacacctcctttttgagtcttgtatataatatggtcctaaacaatgccatttatctattgccaacagGTATGCAAGTTCTTTTTATGGTCCATTTAGAGAGGCACTAGACTCAAACCCCCGGTTTGGAGACAAGAAAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - tggtgga
- - - - - - - -tgttgtt
- - - - - - - - - - - - - - - -catacac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caatgcc