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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATATTAACCCCTACACATTTGGCTATTGTGATGGAGTACGCTTCTGGGGGAGAGTTATTTGAGCGGATATGCAATGCAGGACGGTTTAGTGAAGATGAGgttcttttctattcctttcatgcatttttgttgcagttctgttgcagttactgcttaccattaatgcctattatgttttgttgcag

Basic information

species Glycine max
transcript GLYMA07G29500.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G29500.1 (Glycine max), 5'ss of exon 3
lower sequence: Vv03s0063g01080.t01 (Vitis vinifera), 5'ss of exon 3
CATATTAACCCCTACACATTTGGCTATTGTGATGGAGTACGCTTCTGGGGGAGAGTTATTTGAGCGGATATGCAATGCAGGACGGTTTAGTGAAGATGAGgttcttttctattcctttcatgcatttttgttgcagttctgttgcagttactgcttaccattaatgcctattatgttttgttgcag
 ||||| || || || ||  | |||||||||||||| || || ||||| |||||| | |||||||||||||||||||| || ||||| ||||| |||||||||||| |  |      ||||    |||| |   | |    | ||| |    | |||    | |       ||  || |  |||||
TATATTGACACCAACCCACCTTGCTATTGTGATGGAATATGCCTCTGGAGGAGAGCTCTTTGAGCGGATATGCAATGCCGGCCGGTTCAGTGAGGATGAGgttcttatgcaacttgctcatttggttttctgttactctcctcgcactc---gtttatggcttaccttctctagcttgtactgcag

upper sequence: GLYMA07G29500.1 (Glycine max), 5'ss of exon 3
lower sequence: PP1S116_98V6.1 (Physcomitrella patens), 5'ss of exon 3
CATATTAACCCCTACACATTTGGCTATTGTGATGGAGTACGCTTCTGGGGGAGAGTTATTTGAGCGGATATGCAATGCAGGACGGTTTAGTGAAGATGAGgttcttttctattcctttcatgcatttttgttgcagttctgttgcagttactgcttaccattaatgccta-ttatgttttgt--tgcag
||| || || || || || ||||| ||||||||||| || ||| |||| |||||| | |||||||| || || || ||||  ||||| ||||||||||||||  |    |  || |||  |  | | |   || | |  || | |  ||  |||     || ||  | |  |||  ||||||  |||||
CATGTTGACTCCAACCCACTTGGCCATTGTGATGGAATATGCTGCTGGTGGAGAGCTGTTTGAGCGAATTTGTAAAGCAGTCCGGTTCAGTGAAGATGAGgtattggaatcatcattttgttgactctgcctgaattcttggttctctttgtgcaaggtat-aacacttgcttaccttttgtgttgcag

upper sequence: GLYMA07G29500.1 (Glycine max), 5'ss of exon 3
lower sequence: PP1S218_59V6.1 (Physcomitrella patens), 5'ss of exon 3
CATATTAACCCCTACACATTTGGCTATTGTGATGGAGTACGCTTCTGGGGGAGAGTTATTTGAGCGGATATGCAATGCAGGACGGTTTAGTGAAGATGAGgttcttttctattcctttcatgcatttttgttgcagttctgttgcagtt--actgcttaccattaatgcctattatgttttgttgcag-----------------------------------------
|||  | || || || |||||||||||||| ||||| || ||| |||| |||||  | |||||||| || || || ||||| || || |||||||||||||| || || ||||  | |  ||  ||| | ||    || ||||    ||  | || ||    | ||||| || | |||   | |  |                                          
CATGCTGACTCCAACCCATTTGGCTATTGTTATGGAATATGCTGCTGGTGGAGAACTTTTTGAGCGAATCTGTAACGCAGGCCGCTTCAGTGAAGATGAGgt-ctgttttatttttgttttgtttttattttttgtttttgtttttatttgattgtttgt-gtcaatgcgtagtttgtgaagattgatcaaatgtttttcttacagagatatgatatgttgtgttgcag

upper sequence: GLYMA07G29500.1 (Glycine max), 5'ss of exon 3
lower sequence: PP1S240_91V6.1 (Physcomitrella patens), 5'ss of exon 3
CATATTAACCCCTACACATTTGGCTATTGTGATGGAGTACGCTTCTGGGGGAGAGTTATTTGAGCGGATATGCAATGCAGGACGGTTTAGTGAAGATGAGgttcttttcta--ttcctttcatgca--tttttgtt----gcagttctgtt-gcagttactgcttaccattaatgcctattatgttttgttgcag----------------------------------------
  | || || || || ||||| || || ||||||||||| ||| |||| |||||  | || ||||| || || |||||||| ||||| ||||||||||||||   |   ||  | |  | | || |  ||| || |    ||| || | ||   | ||| |  ||    ||     |  |||  ||||||| |                                          
TCTGTTGACACCAACTCATTTAGCCATCGTGATGGAGTATGCTGCTGGTGGAGAACTGTTCGAGCGAATTTGTAATGCAGGTCGGTTCAGTGAAGATGAGgtgagtacttaagtgctgtgcgtgtaagtttctgctctgcgcatttttttttatatttatttatttatcttctcatc-gttaacttttgtttctattcttaatgaaaggtttatcttctttttcctctgttatag

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|207843753|gb|GD813924.1|GD813924
EST:     GAGAGTTATTTGAGCGGATATGCAATGCAGGACGGTTTAGTGAAGATGAG                         GCACGCTTCTTCTTCCAACAACTTATATCAGGGGTTAGCTACTGTCATGCA
genomic: GAGAGTTATTTGAGCGGATATGCAATGCAGGACGGTTTAGTGAAGATGAGgttcttttct ... tttgttgcagGCACGCTTCTTCTTCCAACAACTTATATCAGGGGTTAGCTACTGTCATGCA
EST: gi|18038723|gb|BM307017.1|BM307017
EST:     GAGAGTTATTTGAGCGGATATGCAATGCAGGACGGTTTAGTGAAGATGAG                         GCACGCTTCTTCTTCCAACAACTTATATCAGGGGTTAGCTACTGTCATGCA
genomic: GAGAGTTATTTGAGCGGATATGCAATGCAGGACGGTTTAGTGAAGATGAGgttcttttct ... tttgttgcagGCACGCTTCTTCTTCCAACAACTTATATCAGGGGTTAGCTACTGTCATGCA
EST: gi|26059786|gb|CA802700.1|CA802700
EST:     GAGAGTTATTTGAGCGGATATGCAATGCAGGACGGTTTAGTGAAGATGAG                         GCACGCTTCTTCTTCCAACAACTTATATCAGGGGTTAGCTACTGTCATGCA
genomic: GAGAGTTATTTGAGCGGATATGCAATGCAGGACGGTTTAGTGAAGATGAGgttcttttct ... tttgttgcagGCACGCTTCTTCTTCCAACAACTTATATCAGGGGTTAGCTACTGTCATGCA
EST: gi|24205189|gb|BU964442.1|BU964442
EST:     GAGAGTTATTTGAGCGGATATGCAATGCAGGACGGTTTAGTGAAGATGAG                         GCACGCTTCTTCTTCCAACAACTTATATCAGGGGTTAGCTACTGTCATGCA
genomic: GAGAGTTATTTGAGCGGATATGCAATGCAGGACGGTTTAGTGAAGATGAGgttcttttct ... tttgttgcagGCACGCTTCTTCTTCCAACAACTTATATCAGGGGTTAGCTACTGTCATGCA
EST: gi|254328432|gb|GR835397.1|GR835397
EST:     GAGAGTTATTTGAGCGGATATGCAATGCAGGACGGTTTAGTGAAGATGAG                         GCACGCTTCTTCTTCCAACAACTTATATCAGGGGTTAGCTACTGTCATGCA
genomic: GAGAGTTATTTGAGCGGATATGCAATGCAGGACGGTTTAGTGAAGATGAGgttcttttct ... tttgttgcagGCACGCTTCTTCTTCCAACAACTTATATCAGGGGTTAGCTACTGTCATGCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CATATTAACCCCTACACATTTGGCTATTGTGATGGAGTACGCTTCTGGGGGAGAGTTATTTGAGCGGATATGCAATGCAGGACGGTTTAGTGAAGATGAGgttcttttctattcctttcatgcatttttgttgcagttctgttgcagttactgcttaccattaatgcctattatgttttgttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG