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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCCAAGCAGCATGAAGATTAAGGTGGTTGCTCCACCTGAGAGAAAGTACAGTGTCTGGATTGGTGGCTCTATCTTGGCTTCTCTCAGCACTTTCCAACAGgtaaacactttgctatgattctaatgcatgaatttaatttctttaaattgatcaaatcaactgtagatacatccttactttctcactgtacactttagaa...

Basic information

species Glycine max
transcript GLYMA12G06820.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G06820.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv06s0004g04570.t01 (Vitis vinifera), 5'ss of exon 4
CCCAAGCAGCATGAAGATTAAGGTGGTTGCTCCACCTGAGAGAAAGTACAGTGTCTGGATTGGTGGCTCTATCTTGGCTTCTCTCAGCACTTTCCAACAGgtaaacactttgctatgattctaatgcatgaatttaatttctttaaattgatcaaatcaactgtagatacatccttactttctcactgtacactttagaa---
|||||||||||||||||| |||||||| ||||| |||||||| ||||| || || |||||||| ||||| ||||| || || |||||||||||||| ||||||    | ||      ||  | |||  |    |||   |   |    ||  |   | ||  | ||   |||  ||| |  ||     ||| |   | |    
CCCAAGCAGCATGAAGATCAAGGTGGTGGCTCCTCCTGAGAGGAAGTATAGCGTATGGATTGGAGGCTCCATCTTAGCATCACTCAGCACTTTCCAGCAGgtatgttccttatacatataatgatgattatgattatgatacctgccctg--cgttttaatggcaggcccatattta-taccttgtcatactcaacaaataca

upper sequence: GLYMA12G06820.1 (Glycine max), 5'ss of exon 4
lower sequence: PP1S337_26V6.1 (Physcomitrella patens), 5'ss of exon 4
CCCAAGCAGCATGAAGATTAAGGTGGTTGCTCCACCTGAGAGAAAGTACAGTGTCTGGATTGGTGGCTCTATCTTGGCTTCTCTCAGCACTTTCCAACAGgtaaacactttgc--tatgatt--ctaat-gcatg---aatttaatttctttaaattgatcaaatcaactgtagatacatccttactttctcactgtacactttagaa
 |||   ||||||||||| |||||||| || || || ||||| ||||||||||| ||||| || || ||||| ||||| |||||||| || ||||||||||||     |||    ||   ||   || | |||||   ||| | ||||  ||| |||  |    |  | | ||  | |||  | || |      ||     |||  | 
ACCATCGAGCATGAAGATAAAGGTGGTGGCGCCGCCAGAGAGGAAGTACAGTGTATGGATAGGAGGGTCTATTTTGGCATCTCTCAGTACCTTCCAACAGgtatttcttttatattacagttgcttagttgcatgcataatctgattt--ttatattacttttttgcattttatctgcattttgacgt----gttggggtttttgcag

upper sequence: GLYMA12G06820.1 (Glycine max), 5'ss of exon 4
lower sequence: PP1S337_21V6.2 (Physcomitrella patens), 5'ss of exon 5
CCCAAGCAGCATGAAGATTAAGGTGGTTGCTCCACCTGAGAGAAAGTACAGTGTCTGGATTGGTGGCTCTATCTTGGCTTCTCTCAGCACTTTCCAACAGgtaaacactttgctatgattctaatgcatgaatttaatttctttaaat-tgatcaaatcaa-----ctgtagatacatccttactttctcactgtacacttt--agaa----------------------------
 |||   ||||||||||| |||||||| || || || ||||| ||||||||||| ||||| || || ||||| ||||| |||||||| || |||||||||||||    ||||    |  ||| |        |    ||| |||  || |  |||  ||       ||  | || |   | |   |     |||||  ||||   |||                            
ACCATCGAGCATGAAGATAAAGGTGGTGGCGCCGCCAGAGAGGAAGTACAGTGTATGGATAGGAGGGTCTATTTTGGCATCTCTCAGTACCTTCCAACAGgtaatgtatttgactcgtgtctgagttgcatttcgtgtttttttttatgtcttcatgtctttgtttcttcaaatgctcgcgtttgtcgaggctgtaatctttctggaatttaatccgtttacttgttgtggtgcag

upper sequence: GLYMA12G06820.1 (Glycine max), 5'ss of exon 4
lower sequence: PP1S372_48V6.1 (Physcomitrella patens), 5'ss of exon 3
CCCAAGCAGCATGAAGATTAAGGTGGTTGCTCCACCTGAGAGAAAGTACAGTGTCTGGATTGGTGGCTCTATCTTGGCTTCTCTCAGCACTTTCCAACAGgtaaac--actttgct--atgattctaatgcatga----------atttaatttctttaaattgatcaaatcaactgtagatacatccttac---tttctcactgtacactttagaa-----------------------
 ||    ||||||||||| |||||||| || || || ||||| |||||||| || ||||| || ||||| |||||||| || |||||||| ||||| |||||||||  | |||||   ||  ||   | |   ||          ||| || ||||||  | | | ||     | | |   ||  |    |    ||  | | |      |||  |                        
GCCGTCAAGCATGAAGATCAAGGTGGTGGCGCCTCCGGAGAGGAAGTACAGCGTGTGGATCGGAGGCTCCATCTTGGCATCCCTCAGCACCTTCCAGCAGgtaaactgagtttgcatgatattttctacgttggacgtggtaaatattgaacttcttttcagttagcagtcggaatttgagtatgtttcgagaggttggttaattcggtgtttgcacatattgttctttctgtggtgcag

upper sequence: GLYMA12G06820.1 (Glycine max), 5'ss of exon 4
lower sequence: EFJ17401 (Selaginella moellendorffii), 5'ss of exon 3
CCCAAGCAGCATGAAGATTAAGGTGGTTGCTCCACCTGAGAGAAAGTACAGTGTCTGGATTGGTGGCTCTATCTTGGCTTCTCTCAGCACTTTCCAACAGgta----aacactttgctatgattctaatgcatgaatttaatttctttaaattgatcaaatcaactgtagatacatccttactttctcactgtacactttagaa
 || |||||||||||||| |||||||||||||| || ||||| |||||||| ||||||||||| || |||||| ||||||| |||||||| ||||||||||||    |||| | |  |     | |     || |   |  ||| | |   | | |     ||                                         
TCCCAGCAGCATGAAGATCAAGGTGGTTGCTCCTCCGGAGAGGAAGTACAGCGTCTGGATTGGAGGTTCTATCCTGGCTTCGCTCAGCACCTTCCAACAGgtaccacaacattcttttgctcgtttttcttatcagccttgtttttctttttcgtttctcgcag----------------------------------------

upper sequence: GLYMA12G06820.1 (Glycine max), 5'ss of exon 4
lower sequence: EFJ35077 (Selaginella moellendorffii), 5'ss of exon 3
CCCAAGCAGCATGAAGATTAAGGTGGTTGCTCCACCTGAGAGAAAGTACAGTGTCTGGATTGGTGGCTCTATCTTGGCTTCTCTCAGCACTTTCCAACAGgta----aacactttgctatgattctaatgcatgaatttaatttctttaaattgatcaaatcaactgtagatacatccttactttctcactgtacactttagaa
 || |||||||||||||| |||||||||||||| || ||||| |||||||| |||||||| || || |||||| ||||||| |||||||| ||||||||||||    |||| | |  |     | |     || |   |  ||| | |   |   |     ||                                         
TCCCAGCAGCATGAAGATCAAGGTGGTTGCTCCTCCGGAGAGGAAGTACAGCGTCTGGATCGGAGGTTCTATCCTGGCTTCGCTCAGCACCTTCCAACAGgtaccacaacattcttttgctcgtttttcttatcagccttgtttttctttttcttttttcgcag----------------------------------------

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|26268492|gb|CA819555.1|CA819555
EST:     GCTTCTCTCAGCACTCTCCAACAG                         ATGTGGATTGCAAAGGCTGAGTATGATGAGGCTGGTCCTTCAATTGTACAC
genomic: GCTTCTCTCAGCACTTTCCAACAGgtaaacactt ... tgaaatgcagATGTGGATTGCAAAGGCTGAGTATGATGAGGCTGGTCCTTCAATTGTACAC
EST: gi|31463583|gb|CD405611.1|CD405611
EST:     GTGTCTGGATTGGTGGCTCTATCTTGGCTTCTCTCAGCACTTTCCAACAG                         ATGTGGATTGCAAAGGCTGAGTATGATGAGGCTGGTCCTTCAATTGTACAC
genomic: GTGTCTGGATTGGTGGCTCTATCTTGGCTTCTCTCAGCACTTTCCAACAGgtaaacactt ... tgaaatgcagATGTGGATTGCAAAGGCTGAGTATGATGAGGCTGGTCCTTCAATTGTACAC
EST: gi|31458829|gb|CD400857.1|CD400857
EST:     GTGTCTGGATTGGTGGCTCTATCTTGGCTTCTCTCAGCACTTTCCAACAG                         ATGTGGATTGCAAAGGCTGAGTATGATGAGGCTGGTCCTTCAATTGTACAC
genomic: GTGTCTGGATTGGTGGCTCTATCTTGGCTTCTCTCAGCACTTTCCAACAGgtaaacactt ... tgaaatgcagATGTGGATTGCAAAGGCTGAGTATGATGAGGCTGGTCCTTCAATTGTACAC
EST: gi|31465176|gb|CD407204.1|CD407204
EST:     GTGTCTGGATTGGTGGCTCTATCTTGGCTTCTCTCAGCACTTTCCAACAG                         ATGTGGATTGCAAAGGCTGAGTATGATGAGGCTGGTCCTTCAATTGTACAC
genomic: GTGTCTGGATTGGTGGCTCTATCTTGGCTTCTCTCAGCACTTTCCAACAGgtaaacactt ... tgaaatgcagATGTGGATTGCAAAGGCTGAGTATGATGAGGCTGGTCCTTCAATTGTACAC
EST: gi|151411582|gb|EV281393.1|EV281393
EST:     GTGTCTGGATTGGTGGCTCTATCTTGGCTTCTCTCAGCACTTTCCAACAG                         ATGTGGATTGCAAAGGCTGAGTATGATGAGGTTGGTCCTTCAATTGTACAC
genomic: GTGTCTGGATTGGTGGCTCTATCTTGGCTTCTCTCAGCACTTTCCAACAGgtaaacactt ... tgaaatgcagATGTGGATTGCAAAGGCTGAGTATGATGAGGCTGGTCCTTCAATTGTACAC
EST: gi|209705759|gb|BW661427.1|BW661427
EST:     GTGTCTGGATTGGTGGCTCTATCTTGGCTTCTCTCAGCACTTTCCAACAG                         ATGTGGATTGCAAAGGCTGAGTATGATGAGGCTGGCCCTTCAATTGTACAC
genomic: GTGTCTGGATTGGTGGCTCTATCTTGGCTTCTCTCAGCACTTTCCAACAGgtaaacactt ... tgaaatgcagATGTGGATTGCAAAGGCTGAGTATGATGAGGCTGGTCCTTCAATTGTACAC
EST: gi|209699902|gb|BW652542.1|BW652542
EST:     GTGTCTGGATTGGTGGCTCTATCTTGGCTTCTCTCAGCACTTTCCAACAG                         ATGTGGATTGCAAAGGCTGAGTATGATGAGGCTGGCCCTTCAATTGTACAC
genomic: GTGTCTGGATTGGTGGCTCTATCTTGGCTTCTCTCAGCACTTTCCAACAGgtaaacactt ... tgaaatgcagATGTGGATTGCAAAGGCTGAGTATGATGAGGCTGGTCCTTCAATTGTACAC
EST: gi|192319555|gb|FK009537.1|FK009537
EST:     GTGTCTGGATTGGTGGCTCTATCTTGGCTTCTCTCAGCACTTTCCAACAG                         ATGTGGATTGCAAAGGCTGAGTATGATGAGGCTGGTCCTTCAATTGTACAC
genomic: GTGTCTGGATTGGTGGCTCTATCTTGGCTTCTCTCAGCACTTTCCAACAGgtaaacactt ... tgaaatgcagATGTGGATTGCAAAGGCTGAGTATGATGAGGCTGGTCCTTCAATTGTACAC
EST: gi|192319554|gb|FK009536.1|FK009536
EST:     GTGTCTGGATTGGTGGCTCTATCTTGGCTTCTCTCAGCACTTTCCAACAG                         ATGTGGATTGCAAAGGCTGAGTATGATGAGGCTGGTCCTTCAATTGTACAC
genomic: GTGTCTGGATTGGTGGCTCTATCTTGGCTTCTCTCAGCACTTTCCAACAGgtaaacactt ... tgaaatgcagATGTGGATTGCAAAGGCTGAGTATGATGAGGCTGGTCCTTCAATTGTACAC
EST: gi|26059387|gb|CA802301.1|CA802301
EST:     GTGTCTGGATTGGTGGCTCTATCTTGGCTTCTCTCAGCACTTTCCAACAA                         ATGTGGATTGCAAAGGCTGAGTATGATGAGGCTGGTCCTTTCA-TTGTACA
genomic: GTGTCTGGATTGGTGGCTCTATCTTGGCTTCTCTCAGCACTTTCCAACAGgtaaacactt ... tgaaatgcagATGTGGATTGCAAAGGCTGAGTATGATGAGGCTGGTCCTT-CAATTGTACA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCCAAGCAGCATGAAGATTAAGGTGGTTGCTCCACCTGAGAGAAAGTACAGTGTCTGGATTGGTGGCTCTATCTTGGCTTCTCTCAGCACTTTCCAACAGgtaaacactttgctatgattctaatgcatgaatttaatttctttaaattgatcaaatcaactgtagatacatccttactttctcactgtacactttagaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG