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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgtatgtatatttatgtatttttcacttcctttcttggtttctggagaaggtaccatctgtttctacataaaatattctcattgttatcttttgattgcagAATCTGTGTGTCACAGCAGCTCACTGTCCAATACGAGAGATCTTGGAGAAGGAAAAGAAG

Basic information

species Glycine max
transcript GLYMA10G02400.1
intron # 24
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G02400.1 (Glycine max), 3'ss of exon 24
lower sequence: AT4G02480.1 (Arabidopsis thaliana), 3'ss of exon 24
gttgtatgtatatttatgtatttttcacttcctttcttggtttctggagaaggtaccatctgtttctacataaaatattctcattgttatcttttgattgcagAATCTGTGTGTCACAGCAGCTCACTGTCCAATACGAGAGATCTTGGAGAAGGAAAAGAAG
                     | |  |||| || |     |  ||    |   |  | |     | || | ||| |        | || | ||||| ||||||||||||||||| || ||||| || | |||||| ||||| ||  ||||||| |||||||||
--------------------gtctcgactttctataaccttccctctcaa---tctccttcccctgtaaaaaaactcacacacgtattcttttttggttgcagAATCTGTGTGTGACCGCAGCACATTTTCCAATCCGAGAAATACTGGAGAAAGAAAAGAAG
















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|24135420|gb|BU925930.1|BU925930
EST:     TTGAAGCAATAGCTAATATGACTGATGGATATTCTGGGAGTGACCTAAAG                         AATCTGTGTGTCACAGCAGCTCACTGTCCAATACGAGAGATCTTGGAGAAG
genomic: TTGAAGCAATAGCTAATATGACTGATGGATATTCTGGGAGTGACCTAAAGgttgtatgta ... ttgattgcagAATCTGTGTGTCACAGCAGCTCACTGTCCAATACGAGAGATCTTGGAGAAG
EST: gi|192316676|gb|FK009361.1|FK009361
EST:     GGGAGTGACCTAAAG                         AATCTGTGTGTCACAGCAGCTCACTGTCCAATACGAGAGATCTTGGAGAAG
genomic: GGGAGTGACCTAAAGgttgtatgta ... ttgattgcagAATCTGTGTGTCACAGCAGCTCACTGTCCAATACGAGAGATCTTGGAGAAG
EST: gi|58019392|gb|CX706134.1|CX706134
EST:     TTGAAGCAATAGCTAATATGACTGATGGATATTCTGGGAGTGACCTAAAG                         AATCTGTGTGTCACAGCAGCTCACTGTCCAATACGAGAGATCTTGGAGAAG
genomic: TTGAAGCAATAGCTAATATGACTGATGGATATTCTGGGAGTGACCTAAAGgttgtatgta ... ttgattgcagAATCTGTGTGTCACAGCAGCTCACTGTCCAATACGAGAGATCTTGGAGAAG
EST: gi|15814532|gb|BI786807.1|BI786807
EST:     TTGAAGCAATAGCTAATATGACTGATGGATATTCTGGGAGTGACCTAAAG                         AATCTGTGTGTCACAGCAGCTCACTGTCCAATACGAGAGATCTTGGAGAAG
genomic: TTGAAGCAATAGCTAATATGACTGATGGATATTCTGGGAGTGACCTAAAGgttgtatgta ... ttgattgcagAATCTGTGTGTCACAGCAGCTCACTGTCCAATACGAGAGATCTTGGAGAAG
EST: gi|26057754|gb|CA800668.1|CA800668
EST:     TTGAAGCAATAGCTAATATGACTGATGGATATTCTGGGAGTGACCTAAAG                         AATCTGTGTGTCACAGCAGCTCACTGTCCAATACGATAGATCTTGGAGAAG
genomic: TTGAAGCAATAGCTAATATGACTGATGGATATTCTGGGAGTGACCTAAAGgttgtatgta ... ttgattgcagAATCTGTGTGTCACAGCAGCTCACTGTCCAATACGAGAGATCTTGGAGAAG
EST: gi|192316471|gb|FK009296.1|FK009296
EST:     TTGAAGCAATAGCTAATATGACTGATGGATATTCTGGGAGTGACCTAAAG                         AATCTGTGTGTCACAGCAGCTCACTGTCCAATACGAGAGATCTTGGAGAAG
genomic: TTGAAGCAATAGCTAATATGACTGATGGATATTCTGGGAGTGACCTAAAGgttgtatgta ... ttgattgcagAATCTGTGTGTCACAGCAGCTCACTGTCCAATACGAGAGATCTTGGAGAAG
EST: gi|22933686|gb|BU550825.1|BU550825
EST:     TTGAAGCAATAGCTAATATGACTGATGGATATTCTGGGAGTGACCTAAAG                         AATCTGTGTGTCACAGCAGCTCACTGTCCAATACGAGAGATCTTGGAGAAG
genomic: TTGAAGCAATAGCTAATATGACTGATGGATATTCTGGGAGTGACCTAAAGgttgtatgta ... ttgattgcagAATCTGTGTGTCACAGCAGCTCACTGTCCAATACGAGAGATCTTGGAGAAG
EST: gi|192312529|gb|FK005001.1|FK005001
EST:     TTGAAGCAATAGCTAATATGACTGATGGATATTCTGGGAGTGACCTAAAG                         AATCTGTGTGTCACAGCAGCTCACTGTCCAATACGAGAGATCTTGGAGAAG
genomic: TTGAAGCAATAGCTAATATGACTGATGGATATTCTGGGAGTGACCTAAAGgttgtatgta ... ttgattgcagAATCTGTGTGTCACAGCAGCTCACTGTCCAATACGAGAGATCTTGGAGAAG
EST: gi|37997295|gb|CF808884.1|CF808884
EST:     AATAGCTAATATGACTGATGGATATTCTGGGAGTGACCTAAAG                         AATCTGTGTGTCACAGCAGCTCACTGTCCAATACGAGAGATCTTGGAGAAG
genomic: AATAGCTAATATGACTGATGGATATTCTGGGAGTGACCTAAAGgttgtatgta ... ttgattgcagAATCTGTGTGTCACAGCAGCTCACTGTCCAATACGAGAGATCTTGGAGAAG
EST: gi|20811998|gb|BQ296476.1|BQ296476
EST:     TTGAAGCAATAGCTAATATGACTGATGGATATTCTGGGAGTGACCTAAAG                         AATCTGTGTGTCACAGCAGCTCACTGTCCAATACGAGAGATCTTGGAGAAG
genomic: TTGAAGCAATAGCTAATATGACTGATGGATATTCTGGGAGTGACCTAAAGgttgtatgta ... ttgattgcagAATCTGTGTGTCACAGCAGCTCACTGTCCAATACGAGAGATCTTGGAGAAG
EST: gi|192312514|gb|FK005000.1|FK005000
EST:     TTGAAGCAATAGCTAATATGACTGATGGATATTCTGGGAGTGACCTAAAG                         AATCTGTGTGTCACAGCAGCTCACTGTCCAATACGAGAGATCTTGGAGAAG
genomic: TTGAAGCAATAGCTAATATGACTGATGGATATTCTGGGAGTGACCTAAAGgttgtatgta ... ttgattgcagAATCTGTGTGTCACAGCAGCTCACTGTCCAATACGAGAGATCTTGGAGAAG
EST: gi|22929414|gb|BU546553.1|BU546553
EST:     GAAGCAATAGCTAATATGACTGATGGATATTCTGGGAGTGACCTAAAG                         AATCTGTGTGTCACAGCAGCTCACTGTCCAATACGAGAGATCTTGGAGAAG
genomic: GAAGCAATAGCTAATATGACTGATGGATATTCTGGGAGTGACCTAAAGgttgtatgta ... ttgattgcagAATCTGTGTGTCACAGCAGCTCACTGTCCAATACGAGAGATCTTGGAGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaggtaccatctgtttctacataaaatattctcattgttatcttttgattgcagAATCTGTGTGTCACAGCAGCTCACTGTCCAATACGAGAGATCTTGGAGAAGGAAAAGAAG
                                           ttttgat  putative branch site (score: 4)
                                      ttatctttt  CT-rich tract
                     ataaaatattctcatt  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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgtatgtatatttatgtatttttcacttcctttcttggtttctggagaaggtaccatctgtttctacataaaatattctcattgttatcttttgattgcagAATCTGTGTGTCACAGCAGCTCACTGTCCAATACGAGAGATCTTGGAGAAGGAAAAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG