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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCTGGCACATCCAAATGCTCCCCTTGGATATGGGTTGTGTTTCCTGAACCTTGCTTTTGATGGATTTACCAATGCAACCCAGGATTCTTTAAAAGCAAGgtaataatagagaagctcctctctcttttgttctggcatacagaaattcctgtctgtctgatgtcatgcaaactaccaaatttgcacatgcaattccttg...

Basic information

species Glycine max
transcript GLYMA02G02330.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G02330.1 (Glycine max), 5'ss of exon 6
lower sequence: AT1G14360.1 (Arabidopsis thaliana), 5'ss of exon 6
AGCTGGCACATCCAAATGCTCCCCTTGGATATGGGTTGTGTTTCCTGAACCTTGCTTTTGATGGATTTACCAATGCAACCCAGGATTCTTTAAAAGCAAGgtaataatagagaagctcc------tctctcttttgttctggcatacagaaatt--cctgtctgtctgatgtcatgcaaactaccaaatttgcacatgcaattccttg
|||| |||||||| ||||| |||||||| || ||| | || ||| | |||||||| ||||||||||| || || ||||||||||||||  | |  ||||||||  | |   ||   ||       |   |       |||| |||  | ||  |   ||   |||  ||  | |  |  |   ||| |  || | |            
AGCTAGCACATCCCAATGCACCCCTTGGTTACGGGCTTTGCTTCTTAAACCTTGCCTTTGATGGATTCACAAACGCAACCCAGGATTCCATTACCGCAAGgtatgactcttgacattctgtcagatacttaacccagtctgacatctacaacatggtctagatgttggacattaatc--atcgccatacatggatacag---------

upper sequence: GLYMA02G02330.1 (Glycine max), 5'ss of exon 6
lower sequence: Vv01s0026g01890.t01 (Vitis vinifera), 5'ss of exon 6
AGCTGGCACATCCAAATGCTCCCCTTGGATATGGGTTGTGTTTCCTGAACCTTGCTTTTGATGGATTTACCAATGCAACCCAGGATTCTTTAAAAGCAAGgtaataa--tagagaagctcctctctcttttgttctggca--tacagaaattcctgtctgtctgatgtcatgcaaactaccaaatttgcacatgcaattccttg
|| ||||||  |||||||| || |||||||||||| | |||||| |||||||||| ||||||||||| || ||||| || ||||||||  ||| ||||||||| |    ||  |||| |  | ||| |  ||   || |   ||  || |   ||  ||   || |   |||    | |  | ||| | |  |||  | | || 
AGTTGGCACGCCCAAATGCACCACTTGGATATGGGCTCTGTTTCTTGAACCTTGCATTTGATGGATTCACAAATGCCACACAGGATTCAATAACAGCAAGgtattctcctactgaagttt-tttctgtactgcaatgactattattgagaaaactaactcgttgtta--atgggtccaaagacattagta-gtgctttcctttt
















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|254343296|gb|GR857000.1|GR857000
EST:     CTTGCTTTTGATGGATTTACCAATGCAACCCAGGATTCTTTAAAAGCAAG                         GTATCCAAAAACAAGTGCTTGGGATATTATGCTGGGCATGAATTTATGGGG
genomic: CTTGCTTTTGATGGATTTACCAATGCAACCCAGGATTCTTTAAAAGCAAGgtaataatag ... gccttaccagGTATCCAAAAACAAGTGCTTGGGATATTATGCTGGGCATGAATTTATGGGG
EST: gi|192298869|gb|FG987614.1|FG987614
EST:     CTTGCTTTTGATGGATTTACCAATGCAACCCAGGATTCTTTAAAAGCAAA                         GTATCCAAAAACAAGTGCTTGGGATATTATGCTGGGCATGAATTTATGGGG
genomic: CTTGCTTTTGATGGATTTACCAATGCAACCCAGGATTCTTTAAAAGCAAGgtaataatag ... gccttaccagGTATCCAAAAACAAGTGCTTGGGATATTATGCTGGGCATGAATTTATGGGG
EST: gi|209721388|gb|BW654584.1|BW654584
EST:     CTTGCTTTTGATGGATTTACCAATGCAACCCAGGATTCTTTAAAAGCAAG                         GTATCCAAAAACAAGTGCTTGGGATATTATGCTGGGCATGAATTTATGGGG
genomic: CTTGCTTTTGATGGATTTACCAATGCAACCCAGGATTCTTTAAAAGCAAGgtaataatag ... gccttaccagGTATCCAAAAACAAGTGCTTGGGATATTATGCTGGGCATGAATTTATGGGG
EST: gi|192304303|gb|FG996443.1|FG996443
EST:     CTTGCTTTTGATGGATTTACCAATGCAACCCAGGATTCTTTAAAAGCAAG                         GTATCCAAAAACAAGTGCTTGGGGATATTATGCTGGGCATGAATTTATGGG
genomic: CTTGCTTTTGATGGATTTACCAATGCAACCCAGGATTCTTTAAAAGCAAGgtaataatag ... gccttaccagGTATCCAAAAACAAGTGCTTGGG-ATATTATGCTGGGCATGAATTTATGGG
EST: gi|151411658|gb|EV281469.1|EV281469
EST:     CTTGCTTTTGATGGATTTACCAATGCAACCCAGGATTCTTTAAAAGCAAA                         GTATCCAAAAACAAGTGCTTGGGATATTATGCTGGGCATGAATTTATGGGG
genomic: CTTGCTTTTGATGGATTTACCAATGCAACCCAGGATTCTTTAAAAGCAAGgtaataatag ... gccttaccagGTATCCAAAAACAAGTGCTTGGGATATTATGCTGGGCATGAATTTATGGGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCTGGCACATCCAAATGCTCCCCTTGGATATGGGTTGTGTTTCCTGAACCTTGCTTTTGATGGATTTACCAATGCAACCCAGGATTCTTTAAAAGCAAGgtaataatagagaagctcctctctcttttgttctggcatacagaaattcctgtctgtctgatgtcatgcaaactaccaaatttgcacatgcaattccttg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctctctc