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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgatcaagatctgagtatgcctttacatcatgcgtgttctttgtttttcctctcataaaagcaaccagtaagatctgagaatgtcctgtttcatggtcatgctgatttttggagttgcttcatacttaacagTGCCTTGTCTTCGGAGAGCTGCATCTGTTGAAGAGGAATATGAAGCTGCTGGAGGGGAAGTTCTACTCGATGATGAAGATAATGATGGCTGGCTAGCAAC

Basic information

species Glycine max
transcript GLYMA12G00830.3
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G00830.3 (Glycine max), 3'ss of exon 2
lower sequence: AT5G61500.1 (Arabidopsis thaliana), 3'ss of exon 2
gtatgatcaagatctgagtatgcctttacatcatgcgtgttctttgtttttcctctcataaaagcaaccagtaagatctgagaatgtcctgtttcatggtcatgc-tgatttttggagttgcttcatacttaacagTGCCTTGTCTTCGGAGAGCTGCATCTGTTGAAGAGGAATATGAAGCTGCTGGAGGGGAAGTTCTACTCGATGATGAAGATAATGATGGCTGGCTAGCAAC
                                            |   |||    || | |||||      | |  ||||      |  |  ||| || |    | | || ||  |   |  ||     || ||||| |||||||| ||||||||||| ||||| | |||||| ||||||||||||||||| |||||  |  | |||||||||||||||||||| ||||| || ||
-------------------------------------------gtaaatttgaaatctttaaagc------ttatttctgttggctttgtagttc-tgattgcacattatgttgtggactttttacgggttgacagTACCTTGTCTACGGAGAGCTGCTTCTGTGGCAGAGGATTATGAAGCTGCTGGAGGTGAAGTGTTGGTTGATGATGAAGATAATGATGGTTGGCTGGCTAC

upper sequence: GLYMA12G00830.3 (Glycine max), 3'ss of exon 2
lower sequence: EFJ26505 (Selaginella moellendorffii), 3'ss of exon 2
gtatgatcaagatctgagtatgcctttacatcatgcgtgttctttgtttttcctctcataaaagcaaccagtaagatctgagaatgtcctgtttcatggtcatgctgatttttggagttgcttcatacttaacagTGCCTTGTCTTCGGAGAGCTGCATCTGTTGAAGAGGAATATGAAGCTGCTGGAGGGGAAGTTCTACTCGATGATGAAGATAATGATGGCTGGCTAGCAAC
                                                                                  |||| | |     |   |   | |    |||  | |   ||  | |||  |||| || ||  | ||  |||| ||  |  ||||||||||||| | ||||||||| ||||||||| | |||||||  |||||    || || |||||||| ||
--------------------------------------------------------------------------------gtaatgcctttgagaagcttttggatagagttttcattctttttttccttttcagTTCCATGCTTGCGACGAGCGGCCGCGTTTGAAGAGGAATACGCAGCTGCTGGTGGGGAAGTTTTGCTCGATGGAGAAGACGGGGAAGGGTGGCTAGCGAC

upper sequence: GLYMA12G00830.3 (Glycine max), 3'ss of exon 2
lower sequence: EFJ14759 (Selaginella moellendorffii), 3'ss of exon 2
gtatgatcaagatctgagtatgcctttacatcatgcgtgttctttgtttttcctctcataaaagcaaccagtaagatctgagaatgtcctgtttcatggtcatgctgatttttggagttgcttcatacttaacagTGCCTTGTCTTCGGAGAGCTGCATCTGTTGAAGAGGAATATGAAGCTGCTGGAGGGGAAGTTCTACTCGATGATGAAGATAATGATGGCTGGCTAGCAAC
                                                                                  |||| | |     |   |   | |    |||  | |   ||  | |||   ||| || || || ||  |||| ||  |  ||||||||||||| | ||||||||| ||||||||| | |||||||  |||||    || ||||||||||| ||
--------------------------------------------------------------------------------gtaatgcctttgagaagcttttggatagagttttcattctttttttcctttttagTTCCATGCCTGCGACGAGCGGCCGCGTTTGAAGAGGAATACGCAGCTGCTGGTGGGGAAGTTTTGCTCGATGGAGAAGACGGGGAAGGCTGGCTAGCGAC

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|298192494|gb|HO036576.1|HO036576
EST:     GAGGAAGCCATACTTGCCACCTGAGAAACAGTTCTTGATTACTAGAAATG                         TGCCTTGTCTTCGGAGAGCTGCATCTGTTGAAGAGGAATATGAAGCTGCTG
genomic: GAGGAAGCCATACTTGCCACCTGAGAAACAGTTCTTGATTACTAGAAATGgtatgatcaa ... tacttaacagTGCCTTGTCTTCGGAGAGCTGCATCTGTTGAAGAGGAATATGAAGCTGCTG
EST: gi|192330860|gb|FK021619.1|FK021619
EST:     GAGGAAGCCATACTTGCCACCTGAGAAACAGTTCTTGATTACTAGAAATG                         TGCCTTGTCTTCGGAGAGCTGCATCTGTTGAAGAGGAATATGAAGCTGCTG
genomic: GAGGAAGCCATACTTGCCACCTGAGAAACAGTTCTTGATTACTAGAAATGgtatgatcaa ... tacttaacagTGCCTTGTCTTCGGAGAGCTGCATCTGTTGAAGAGGAATATGAAGCTGCTG
EST: gi|192306687|gb|FG998085.1|FG998085
EST:     GAGGAAGCCATACTTGCCACCTGAGAAACAGTTCTTGATTACTAGAAATG                         TGCCTTGTCTTCGGAGAGCTGCATCTGTTGAAGAGGAATATGAAGCTGCTG
genomic: GAGGAAGCCATACTTGCCACCTGAGAAACAGTTCTTGATTACTAGAAATGgtatgatcaa ... tacttaacagTGCCTTGTCTTCGGAGAGCTGCATCTGTTGAAGAGGAATATGAAGCTGCTG
EST: gi|213591644|gb|DB969744.1|DB969744
EST:     GAGGAAGCCATACTTGCCGCCTGAGAAACAGTTCTTGATTACTAGAAATG                         TGCCTTGTCTTCGGAGAGCTGCATCTGTTGAAGAGGAATATGAAGCTGCTG
genomic: GAGGAAGCCATACTTGCCACCTGAGAAACAGTTCTTGATTACTAGAAATGgtatgatcaa ... tacttaacagTGCCTTGTCTTCGGAGAGCTGCATCTGTTGAAGAGGAATATGAAGCTGCTG
EST: gi|192324977|gb|FK016133.1|FK016133
EST:     GAGGAAGCCATACTTGCCACCTGAGAAACAGTTCTTGATTACTAGAAATG                         TGCCTTGTCTTCGGAGAGCTGCATCTGTTGAAGAGGAATATGAAGCTGCTG
genomic: GAGGAAGCCATACTTGCCACCTGAGAAACAGTTCTTGATTACTAGAAATGgtatgatcaa ... tacttaacagTGCCTTGTCTTCGGAGAGCTGCATCTGTTGAAGAGGAATATGAAGCTGCTG
EST: gi|7684723|gb|AW755371.1|AW755371
EST:     GAGGAAGCCATACTTGCCACCTGAGAAACAGTTCTTGATTACTAGAAATG                         TGCCTTGTCTTCGGAGAGCTGCATCTGTTGAAGAGGAATATGAAGCTGCTG
genomic: GAGGAAGCCATACTTGCCACCTGAGAAACAGTTCTTGATTACTAGAAATGgtatgatcaa ... tacttaacagTGCCTTGTCTTCGGAGAGCTGCATCTGTTGAAGAGGAATATGAAGCTGCTG
EST: gi|298169552|gb|HO020912.1|HO020912
EST:     GAGGAAGCCATACTTGCCACCTGAGAAACAGTTCTTGATTACTAGAAATG                         TGCCTTGTCTTCGGAGAGCTGCATCTGTTGAAGAGGAATATGAAGCTGCTG
genomic: GAGGAAGCCATACTTGCCACCTGAGAAACAGTTCTTGATTACTAGAAATGgtatgatcaa ... tacttaacagTGCCTTGTCTTCGGAGAGCTGCATCTGTTGAAGAGGAATATGAAGCTGCTG
EST: gi|298186631|gb|HO037264.1|HO037264
EST:     GAGGAAGCCATACTTGCCACCTGAGAAACAGTTCTTGATTACTAGAAATG                         TGCCTTGTCTTCGGAGAGCTGCATCTGTTGAAGAGGAATATGAAGCTGCTG
genomic: GAGGAAGCCATACTTGCCACCTGAGAAACAGTTCTTGATTACTAGAAATGgtatgatcaa ... tacttaacagTGCCTTGTCTTCGGAGAGCTGCATCTGTTGAAGAGGAATATGAAGCTGCTG
EST: gi|151404711|gb|EV274525.1|EV274525
EST:     GAGGAAGCCATACTTGCCACCTGAGAAACAGTTCTTGATTACTAGAAATG                         TGCCTTGTCTTCGGAGAGCTGCATCTGTTGAAGAGGAATATGAAGCTGCTG
genomic: GAGGAAGCCATACTTGCCACCTGAGAAACAGTTCTTGATTACTAGAAATGgtatgatcaa ... tacttaacagTGCCTTGTCTTCGGAGAGCTGCATCTGTTGAAGAGGAATATGAAGCTGCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agaatgtcctgtttcatggtcatgctgatttttggagttgcttcatacttaacagTGCCTTGTCTTCGGAGAGCTGCATCTGTTGAAGAGGAATATGAAGCTGCTGGAGGGGAAGTTCTACTCGATGATGAAGATAATGATGGCTGGCTAGCAAC
                      tgctgat  putative branch site (score: 3)
                         tgattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgatcaagatctgagtatgcctttacatcatgcgtgttctttgtttttcctctcataaaagcaaccagtaagatctgagaatgtcctgtttcatggtcatgctgatttttggagttgcttcatacttaacagTGCCTTGTCTTCGGAGAGCTGCATCTGTTGAAGAGGAATATGAAGCTGCTGGAGGGGAAGTTCTACTCGATGATGAAGATAATGATGGCTGGCTAGCAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA