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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctagggaactatgctagtatgcttaattcaaaaccttttcaaatacagcttaaaaaatttcttcctgtgatgattgttgcactatttttgtttttacagTTCCAGATTTTCGAGGAGATGCTGACTGTGTAGAGAAGGTTGCCAAATCAGGATTAGATGTCTTTGCACACAACATTGAGACAGTTGAAGAGCTTCAGAG

Basic information

species Glycine max
transcript GLYMA12G32890.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G32890.1 (Glycine max), 3'ss of exon 2
lower sequence: AT2G20860.1 (Arabidopsis thaliana), 3'ss of exon 2
tctagggaactatgctagtatgcttaattcaa-aaccttttcaaatacagcttaaaaaatttcttcctgtgatgattgttgcactatttttgtttttacagTTCCAGATTTTCGAGGAGATGCTGACTGTGTAGAGAAGGTTGCCAAATCAGGATTAGATGTCTTTGCACACAACATTGAGACAGTTGAAGAGCTTCAGAG
                        ||||  ||  | ||  |   ||  | | | |  | |||     | | ||  |||||    | |||  | |  |  |||||| ||||| || ||||||| ||  ||||| ||||||||| |||| |||||  | |||||||| || ||||||||||||||||||||||||||||||||
-----------------------gtaatataatgatctggtgggattgatcatcatgagttttggtttttaat--ttgttttgttgttt--gatgatgtagTTCCTGATTTCCGCGGAGATGGTGGATGTGTTGAGAAGGTTTCCAAGTCAGGGCTTGATGTCTTAGCTCACAACATTGAGACAGTTGAAGAGCTTCAGAG

upper sequence: GLYMA12G32890.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv00s0445g00020.t01 (Vitis vinifera), 3'ss of exon 3
------------------------------------------------------------------------------------------------tctagggaactatgctagtatgcttaattcaaaaccttttcaaatacagct-taaaaaatttcttcctgtgatgattgttgcactatttttgtttttacagTTCCAGATTTTCGAGGAGATGCTGACTGTGTAGAGAAGGTTGCCAAATCAGGATTAGATGTCTTTGCACACAACATTGAGACAGTTGAAGAGCTTCAGAG
                                                                                                |  | ||||  ||  |  ||| || |  || | |  |   ||  | |     |     |||  |||      || || ||  | | ||     || |  |||||| || || ||||||||  ||| |||||| || || ||| | ||||| ||||||||||| ||||| ||||| |||||||| |||||||||||||| ||
gtagtaatctgctttattgctttttgtataaaataccagattgcactccatgacaatgcagactgaacgttggttgatatttcatggaaaccaaccttcaaggaatcatttt--tattctcacctctagaattccccagttgctctcatggttcattctttctaaacctggttttt--attgttgggaattgtgtagTTCCTGACTTCCGAGGAGACCCTGGCTGTGTGGAAAAAGTTTCTAAATCTGGATTAGATGTTTTTGCTCACAATATTGAGACGGTTGAAGAGCTTCAAAG
















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|51337329|gb|CO981195.1|CO981195
EST:     AGTGCAGAAGCTGAAGGCACTGAAGCCTAATATGCTGATAGAAGCCTTAG                         TTCCAGATTTTCGAGGAGATGCTGACTGTGTAGAGAAGGTTGCCAAATCAG
genomic: AGTGCAGAAGCTGAAGGCACTGAAGCCTAATATGCTGATAGAAGCCTTAGgtatgcattt ... gtttttacagTTCCAGATTTTCGAGGAGATGCTGACTGTGTAGAGAAGGTTGCCAAATCAG
EST: gi|6133855|gb|AW132248.1|AW132248
EST:     GTGCAGAAGCTGAAGGCACTGAAGCCCTA-TATGCTGATAGAAGCCTTAG                         TTCCAGATTTTCGAGGAGATGCTGACTGTGTAGAGAAGGTTGCCAAATCAG
genomic: GTGCAGAAGCTGAAGGCACTGAAGCC-TAATATGCTGATAGAAGCCTTAGgtatgcattt ... gtttttacagTTCCAGATTTTCGAGGAGATGCTGACTGTGTAGAGAAGGTTGCCAAATCAG
EST: gi|15199935|gb|BI424084.1|BI424084
EST:     AGTGCAGAAGCTGAAGGCACTGAAGCCTAATATGCTGATAGAAGCCTTAG                         TTCCAGATTTTCGAGGAGATGCTGACTGTGTAGAGAACGTTGCCAAATCAG
genomic: AGTGCAGAAGCTGAAGGCACTGAAGCCTAATATGCTGATAGAAGCCTTAGgtatgcattt ... gtttttacagTTCCAGATTTTCGAGGAGATGCTGACTGTGTAGAGAAGGTTGCCAAATCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acagcttaaaaaatttcttcctgtgatgattgttgcactatttttgtttttacagTTCCAGATTTTCGAGGAGATGCTGACTGTGTAGAGAAGGTTGCCAAATCAGGATTAGATGTCTTTGCACACAACATTGAGACAGTTGAAGAGCTTCAGAG
                                     ctatttttgttttt  CT-rich tract
                                    actatttttgttttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctagggaactatgctagtatgcttaattcaaaaccttttcaaatacagcttaaaaaatttcttcctgtgatgattgttgcactatttttgtttttacagTTCCAGATTTTCGAGGAGATGCTGACTGTGTAGAGAAGGTTGCCAAATCAGGATTAGATGTCTTTGCACACAACATTGAGACAGTTGAAGAGCTTCAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - -ctatgct
- - - - - - - - -gtatgct
- - - - - - - - - - - - - - -caaaacc
- - - - - - - - - - - - - - - - - - - - - - - - - -taaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcacta