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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACTAGGTGGGAGGGCTGCAGAAGAAATTATTTTCGGTGAGCCTGAAGTTACAACTGGAGCAGCTGGTGATTTGCAGCAAATCACCAGTTTGGCAAAACAGgtactggttaattatgtgcttgtgttaaattatatctcctttttctttacttttttttttgttgttgttgtgcaaaatgctaatactttatgaatttaat...

Basic information

species Glycine max
transcript GLYMA08G09160.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G09160.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv12s0028g01600.t01 (Vitis vinifera), 5'ss of exon 4
ACTAGGTGGGAGGGCTGCAGAAGAAATTATTTTCGGTGAGCCTGAAGTTACAACTGGAGCAGCTGGTGATTTGCAGCAAATCACCAGTTTGGCAAAACAGgtactggttaattatgtgcttgtgttaaattatatctcctttttctttacttttttttttgtt-gttgttgtgcaaaatgctaatactttatgaatttaat
||| ||||| || ||||| |||||| | || || ||||||||||| || ||||| || || ||||||||||||||||| |||||  ||||||| ||||||||| |    | ||   | | | || |      |     | |||    | |   | |  ||||  |||  | | |  ||     | |    |       |  
ACTCGGTGGCAGAGCTGCTGAAGAAGTGATCTTTGGTGAGCCTGAGGTGACAACAGGTGCTGCTGGTGATTTGCAGCAGATCACTGGTTTGGCCAAACAGgtaataaacagttcc-tccatctgcttccagctggtaacatttaaactgcaaatgtcattgtcagtttctattctcaacatatacaaaacacagtaccacc

upper sequence: GLYMA08G09160.1 (Glycine max), 5'ss of exon 4
lower sequence: PP1S9_115V6.1 (Physcomitrella patens), 5'ss of exon 5
ACTAGGTGGGAGGGCTGCAGAAGAAATTATTTTCGGTGAGCCTGAAGTTACAACTGGAGCAGCTGGTGATTTGCAGCAAATCACCAGTTTGGCAAAACAGgta----------ctggtta-attatgtgcttgtgttaaattatatctcctttttctttacttttttttttgttgttgttgtgcaaaatgctaatacttta-tgaatttaat-------------------------------
 || |||||| | |||||||||||| |||||||||||||  ||||||| || ||||| ||  |  |||||||||||||| || |     |||| || ||||||           || ||  |||  |    | ||| || || || |     ||   |  |      ||  |   |            || | ||| || | | || | ||                                
TCTGGGTGGGCGCGCTGCAGAAGAAGTTATTTTCGGTGACGCTGAAGTGACCACTGGCGCTTCCAGTGATTTGCAGCAAGTCTCTTCCATGGCGAAGCAGgtaagtgaatgcattgattgcatttgggagctttgtcaacttgtagcgataattgtctcgcaaacgattcgggcttccacaatttccttgttgataattgaatcaagtcaactgcttctgaagcaaacaaccccttggaacag
















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|105634352|gb|DW247501.1|DW247501
EST:     CAACTGGAGCAGCTGGTGATTTGCAGCAAATCACCAGTTTGGCAAAACAG                         ATGGTGACCACATTTGGAATGTCTGATATTGGTCCTTGGTCACTTATGGAA
genomic: CAACTGGAGCAGCTGGTGATTTGCAGCAAATCACCAGTTTGGCAAAACAGgtactggtta ... tttcttgcagATGGTGACCACATTTGGAATGTCTGATATTGGTCCTTGGTCACTTATGGAA
EST: gi|58020465|gb|CX707207.1|CX707207
EST:     CAACTGGAGCAGCTGGTGATTTGCAGCAAATCACCAGTTTGGCAAAACAG                         ATGGTGACCACATTTGGAATGTCTGATATTGGTCCTTGGTCACTTATGGAA
genomic: CAACTGGAGCAGCTGGTGATTTGCAGCAAATCACCAGTTTGGCAAAACAGgtactggtta ... tttcttgcagATGGTGACCACATTTGGAATGTCTGATATTGGTCCTTGGTCACTTATGGAA
EST: gi|192319073|gb|FK006885.1|FK006885
EST:     CAACTGGAGCAGCTGGTGATTTGCAGCAAATCACCAGTTTGGCAAAACAG                         ATGGTGACCACATTTGGAATGTCTGATATTGGTCCTTGGTCACTTATGGAA
genomic: CAACTGGAGCAGCTGGTGATTTGCAGCAAATCACCAGTTTGGCAAAACAGgtactggtta ... tttcttgcagATGGTGACCACATTTGGAATGTCTGATATTGGTCCTTGGTCACTTATGGAA
EST: gi|120491707|gb|EH219874.1|EH219874
EST:     CAACTGGAGCAGCTGGTGATTTGCAGCAAATCACCAGTTTGGCAAAACAG                         ATGGTGACCACATTTGGAATGTCTGATATTGGTCCTTGGTCACTTATGGAA
genomic: CAACTGGAGCAGCTGGTGATTTGCAGCAAATCACCAGTTTGGCAAAACAGgtactggtta ... tttcttgcagATGGTGACCACATTTGGAATGTCTGATATTGGTCCTTGGTCACTTATGGAA
EST: gi|26043767|gb|CA782158.1|CA782158
EST:     CAACTGGAGCAGCTGGTGATTTGCAGCAAATCACCAGTTTGGCAAAACAG                         ATGGTGACCACATTTGGAATGTCTGATATTGGTCCTTGGTCACTTATGGAA
genomic: CAACTGGAGCAGCTGGTGATTTGCAGCAAATCACCAGTTTGGCAAAACAGgtactggtta ... tttcttgcagATGGTGACCACATTTGGAATGTCTGATATTGGTCCTTGGTCACTTATGGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACTAGGTGGGAGGGCTGCAGAAGAAATTATTTTCGGTGAGCCTGAAGTTACAACTGGAGCAGCTGGTGATTTGCAGCAAATCACCAGTTTGGCAAAACAGgtactggttaattatgtgcttgtgttaaattatatctcctttttctttacttttttttttgttgttgttgtgcaaaatgctaatactttatgaatttaat

- - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG