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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctgtttcagatatttacatttttgtcttttatatttcattaataatatgcgagctccttgttttgaaacgtaaaatctgccttggtcttctttgttacagTTATGAAATGCTTCCATTGGAGGAACAGCTTGAAATTGCTAACCAGATTGGAACAACTCGATCACAAATTCTGTCAAATCTAAGCGATCTGTCTCTTGGA

Basic information

species Glycine max
transcript GLYMA09G28030.1
intron # 25
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G28030.1 (Glycine max), 3'ss of exon 25
lower sequence: AT5G51660.1 (Arabidopsis thaliana), 3'ss of exon 25
-----------------------------------ctgtttcagatattt-acatttttgtcttttatat--------ttcat----taataatatgcgagctccttgttttgaaacgtaaaatctgcct-------tggtcttc----tttgttacagTTATGAAATGCTTCCATTGGAGGAACAGCTTGAAATTGCTAACCAGATTGGAACAACTCGATCACAAATTCTGTCAAATCTAAGCGATCTGTCTCTTGGA
                                     ||  |||| || | |||   | | | |  |  |          |||    ||||||  |   |  ||      | |||   | | |  ||| |       |||| ||       | || |||||| || ||||||||||||||||||||||||||| ||||| |||||||||| ||||| ||||     |||||     || ||   ||||| ||| | |||
gtaagttttcttccgcattctatatgttcaaacggtagtaacagacatatgacaaaatggacctcaaagtagagagagcacataggataataaactcgaaaatcacacgatagaaggatcatagatgcatatcctcatggttttgaaaacattttgcagTTACGAGATGCTTCCATTGGAGGAACAGCTTGAACTTGCTCACCAGATTGGGACAACCCGATATTCGATTCTCAAGGATTTAGTTGATCTCTCTGTCGGA
















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|51338498|gb|CO982364.1|CO982364
EST:     GCCCATCGGCCAGGCCCTGACAGTATAGTTGATTGCGAGCTGCTATGCCA                         TTATGAAATGCTTCCATTGGAGGAACAGCTTGAAATTGCTAACCAGATTGG
genomic: GCCCATCGGCCAGGCCCTGACAGTATAGTTGATTGCGAGCTGCTATGCCAgtaagtttta ... tttgttacagTTATGAAATGCTTCCATTGGAGGAACAGCTTGAAATTGCTAACCAGATTGG
EST: gi|208334527|gb|GE131562.1|GE131562
EST:     CGGCCGGGCCCTGACAGTATAGTTGATTGCGAGCTGCTATGCCA                         TTATGAAATGCTTCCATTGGAGGAACAGCTTGAAATTGCTAACCAGATTGG
genomic: CGGCCAGGCCCTGACAGTATAGTTGATTGCGAGCTGCTATGCCAgtaagtttta ... tttgttacagTTATGAAATGCTTCCATTGGAGGAACAGCTTGAAATTGCTAACCAGATTGG
EST: gi|21676594|gb|BQ628945.1|BQ628945
EST:     GCCCTGACAGTATAGTTGATTGCGAGCTGCTATGCCA                         TTATGAAATGCTTCCATTGGAGGAACAGCTTGAAATTGCTAACCAGATTGG
genomic: GCCCTGACAGTATAGTTGATTGCGAGCTGCTATGCCAgtaagtttta ... tttgttacagTTATGAAATGCTTCCATTGGAGGAACAGCTTGAAATTGCTAACCAGATTGG
EST: gi|208265648|gb|GE063176.1|GE063176
EST:     ACAGTATAGTTGATTGCGAGCTGCTATGCCA                         TTATGAAATGCTTCCATTGGAGGAACAGCTTGAAATTGCTAACCAGATTGG
genomic: ACAGTATAGTTGATTGCGAGCTGCTATGCCAgtaagtttta ... tttgttacagTTATGAAATGCTTCCATTGGAGGAACAGCTTGAAATTGCTAACCAGATTGG
EST: gi|208089297|gb|GD888630.1|GD888630
EST:     CGGCCGGGCCCTGACTAGTATAGTTGATTGTCGAGCTGCTATGCCA                         TTATGAAATGCTTCCATTGGAGGAACAGCTTGAAATTGCTAACCAGATTGG
genomic: CGGCCAGGCCCTGAC-AGTATAGTTGATTG-CGAGCTGCTATGCCAgtaagtttta ... tttgttacagTTATGAAATGCTTCCATTGGAGGAACAGCTTGAAATTGCTAACCAGATTGG
EST: gi|193582250|gb|FK535621.1|FK535621
EST:     CCCTGACAGTATAGTTGATTGCGAGCTGCTATGCCA                         TTATGAAATGCTTCCATTGGAGGAACAGCTTGAAATTGCTAACCAGATTGG
genomic: CCCTGACAGTATAGTTGATTGCGAGCTGCTATGCCAgtaagtttta ... tttgttacagTTATGAAATGCTTCCATTGGAGGAACAGCTTGAAATTGCTAACCAGATTGG
EST: gi|193400147|gb|FK365716.1|FK365716
EST:     CGGCCGGGCCCTGACAGTATAGTTGATTGCGAGCTGCTATGCCA                         TTATGAAATGCTTCCATTGGAGGAACAGCTTGAAATTGCTAACCAGATTGG
genomic: CGGCCAGGCCCTGACAGTATAGTTGATTGCGAGCTGCTATGCCAgtaagtttta ... tttgttacagTTATGAAATGCTTCCATTGGAGGAACAGCTTGAAATTGCTAACCAGATTGG
EST: gi|151406196|gb|EV276011.1|EV276011
EST:     GCCCATCGGCCAGGCCCTGACAGTATAGTTGATTGCGAGCTGCTATGCCA                         TTATGAAATGCTTCCATTGGAGGAACAGCTTGAAATTGCTAACCAGATTGG
genomic: GCCCATCGGCCAGGCCCTGACAGTATAGTTGATTGCGAGCTGCTATGCCAgtaagtttta ... tttgttacagTTATGAAATGCTTCCATTGGAGGAACAGCTTGAAATTGCTAACCAGATTGG
EST: gi|208275540|gb|GE078202.1|GE078202
EST:     CCCTGACAGTATAGTTGATTGCGAGCTGCTATGCCA                         TTATGAAATGCTTCCATTGGAGGAACAGCTTGAAATTGCTAACCAGATTGG
genomic: CCCTGACAGTATAGTTGATTGCGAGCTGCTATGCCAgtaagtttta ... tttgttacagTTATGAAATGCTTCCATTGGAGGAACAGCTTGAAATTGCTAACCAGATTGG
EST: gi|13311388|gb|BG405039.1|BG405039
EST:     GCCCATCGGCCAGGCCCTGACAGTATAGTTGATTGCGAGCTGCTATGCCA                         TTATGAAATGCTTCCATTGGAGGAACAGCTTGAAATTGCTAACCAGATTGG
genomic: GCCCATCGGCCAGGCCCTGACAGTATAGTTGATTGCGAGCTGCTATGCCAgtaagtttta ... tttgttacagTTATGAAATGCTTCCATTGGAGGAACAGCTTGAAATTGCTAACCAGATTGG
EST: gi|208127573|gb|GD923499.1|GD923499
EST:     CGGCCGGGCCCTGACAGTATAGTTGATTGCGAGCTGCTATGCCA                         TTATGAAATGCTTCCATTGGAGGAACAGCTTGAAATTGCTAACCAGATTGG
genomic: CGGCCAGGCCCTGACAGTATAGTTGATTGCGAGCTGCTATGCCAgtaagtttta ... tttgttacagTTATGAAATGCTTCCATTGGAGGAACAGCTTGAAATTGCTAACCAGATTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgcgagctccttgttttgaaacgtaaaatctgccttggtcttctttgttacagTTATGAAATGCTTCCATTGGAGGAACAGCTTGAAATTGCTAACCAGATTGGAACAACTCGATCACAAATTCTGTCAAATCTAAGCGATCTGTCTCTTGGA
                                  ccttggtcttcttt  CT-rich tract
               ttttgaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctgtttcagatatttacatttttgtcttttatatttcattaataatatgcgagctccttgttttgaaacgtaaaatctgccttggtcttctttgttacagTTATGAAATGCTTCCATTGGAGGAACAGCTTGAAATTGCTAACCAGATTGGAACAACTCGATCACAAATTCTGTCAAATCTAAGCGATCTGTCTCTTGGA

ctgtttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgcctt