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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...accaaacataaaattttggcatctttaatggccatgttcagttttatgtttcactgtctactgttcaccaaccattattgatctttgtttgttattgcagATGCTATGATGCAAATCTCATAGACATTCCTGTCGAAATAGAGAGTCCTGATCATCATTATTATCAT

Basic information

species Glycine max
transcript GLYMA03G41020.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G41020.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ20940 (Selaginella moellendorffii), 3'ss of exon 2
accaaacataaaattttggcatctttaatggccatgttcagttttatgtttcactgtctactgttcaccaaccattattgatctttgtttgttattgcagATGCTATGATGCAAATCTCATAGACATTCCTGTCGAAATAGAGAGTCCTGATCATCATTATTATCAT
                                       | | |  | | ||  |   | |       | | | ||  | |||   |||  ||  | ||| ||    ||||| |||||||| ||||||||||||||||| ||| |||| ||||  || |  || || 
-------------------------------------gtactgtcgtctctcgtttctttccagcgctcgatctttcgt-atcaacgttgtttcctccagGTGTGGAGATGCCAATCTCATCGACATTCCTGTCGAAATCGAGTGTCCCGATCGACACTTCTACCAC
















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|58024869|gb|CX711610.1|CX711610
EST:     TGTTTAGATGCAACAAAGAATGGAAATGTCGGAAGGTTCATCAATCATAG                         ATGCTATGATGCAAATCTCATAGACATTCCTGTCGAAATAGAGAGTCCTGA
genomic: TGTTTAGATGCAACAAAGAATGGAAATGTCGGAAGGTTCATCAATCATAGgtaaccatat ... gttattgcagATGCTATGATGCAAATCTCATAGACATTCCTGTCGAAATAGAGAGTCCTGA
EST: gi|193508516|gb|FK465379.1|FK465379
EST:     AAGGTTCATCAATCATAG                         ATGCTATGATGCAAATCTCATAGACATTCCTGTCGAAATAGAGAGTCCTGA
genomic: AAGGTTCATCAATCATAGgtaaccatat ... gttattgcagATGCTATGATGCAAATCTCATAGACATTCCTGTCGAAATAGAGAGTCCTGA
EST: gi|193640173|gb|FK589296.1|FK589296
EST:     TGTTTAGATGCAACAAAGAATGGAAATGTCGGAAGGTTCATCAATCATAG                         ATGCTATGATGCAAATCTCATAGACATTCCTGTCGAAA
genomic: TGTTTAGATGCAACAAAGAATGGAAATGTCGGAAGGTTCATCAATCATAGgtaaccatat ... gttattgcagATGCTATGATGCAAATCTCATAGACATTCCTGTCGAAA
EST: gi|298176786|gb|HO023259.1|HO023259
EST:     TGTTTAGATGCAACAAAGAATGGAAATGTCGGAAGGTTCATCAATCATAG                         ATGCTATGATGCAAATCTCATAGACATTCCTGTCGAAATAGAGAGTCCTGA
genomic: TGTTTAGATGCAACAAAGAATGGAAATGTCGGAAGGTTCATCAATCATAGgtaaccatat ... gttattgcagATGCTATGATGCAAATCTCATAGACATTCCTGTCGAAATAGAGAGTCCTGA
EST: gi|193464117|gb|FK426123.1|FK426123
EST:     AGATGCAACAAAGAATGGAAATGTCGGAAGGTTCATCAATCATAG                         ATGCTATGATGCAAATCTCATAGACATTCCTGTCGAAATAGAGAGTCCTGA
genomic: AGATGCAACAAAGAATGGAAATGTCGGAAGGTTCATCAATCATAGgtaaccatat ... gttattgcagATGCTATGATGCAAATCTCATAGACATTCCTGTCGAAATAGAGAGTCCTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgtttcactgtctactgttcaccaaccattattgatctttgtttgttattgcagATGCTATGATGCAAATCTCATAGACATTCCTGTCGAAATAGAGAGTCCTGATCATCATTATTATCAT
                              tattgat  putative branch site (score: 3)
                            attattgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
accaaacataaaattttggcatctttaatggccatgttcagttttatgtttcactgtctactgttcaccaaccattattgatctttgtttgttattgcagATGCTATGATGCAAATCTCATAGACATTCCTGTCGAAATAGAGAGTCCTGATCATCATTATTATCAT

-ccaaaca
- - - - - - - - - - - - - - - - catgttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - tctactg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccaacca