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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttttgttttcccgtcgaaagaattatcaaatgaataatggaagtatattgctcttacagttgaagttgatgcagATAACAGAGTTGAAGTTGTCGATTGATAGCCTTGAGAAGGAACGGGATTTCTACTTTGCAAAGCTGAGAGATATTGAGATACTGTGCCAGACTCCTGAGA

Basic information

species Glycine max
transcript GLYMA01G39720.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G39720.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv07s0129g01080.t01 (Vitis vinifera), 3'ss of exon 4
gta-tttttgttttcccgtcgaaagaattatcaaatga-ataatggaagtatattgct--cttac------agttgaagttgatgcagATAACAGAGTTGAAGTTGTCGATTGATAGCCTTGAGAAGGAACGGGATTTCTACTTTGCAAAGCTGAGAGATATTGAGATACTGTGCCAGACTCCTGAGA
||  ||||||       |  ||||  |  ||   || | | |||   ||| | || ||   |||       | ||     | |||||||| |||||||||||| |||| || |||||||||||||||||  |||| ||||||||||||||  |||| |||||||| ||  ||||||||  ||| ||||
gtgctttttgggccaatgcagaaattacaattttattatagaatttgagtctcttactggtttatttatttatttttttctaatgcagATCACAGAGTTGAAGCTGTCAATAGATAGCCTTGAGAAGGAGAGGGACTTCTACTTTGCAAAATTGAGGGATATTGAAATTTTGTGCCAGTGTCCAGAGA
















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|193552516|gb|FK510351.1|FK510351
EST:     GCCGGGAACCCTGCCTATGAAGAAAAG                         ATAACAGAGTTGAAGTTGTCGATTGATAGCCTTGAGAAGGAACGGGATTTC
genomic: GCCGGAAACCCTGCCTATGAAGAAAAGgtatttttgt ... gttgatgcagATAACAGAGTTGAAGTTGTCGATTGATAGCCTTGAGAAGGAACGGGATTTC
EST: gi|193430384|gb|FK393302.1|FK393302
EST:     GCCGGGAACCCTGCCTATGAAGAAAAG                         ATAACAGAGTTGAAGTTGTCGATTGATAGCCTTGAGAAGGAACGGGATTTC
genomic: GCCGGAAACCCTGCCTATGAAGAAAAGgtatttttgt ... gttgatgcagATAACAGAGTTGAAGTTGTCGATTGATAGCCTTGAGAAGGAACGGGATTTC
EST: gi|151393328|gb|EV263203.1|EV263203
EST:     AGGTTGCGAGAGCAGCACCTTCTGCCGGAAACCCTGCCTATGAAGAAAAG                         ATAACAGAGTTGAAGTTGTCGATTGATAGCCTTGAGAAAGAACGGGATTTC
genomic: AGGTTGCGAGAGCAGCACCTTCTGCCGGAAACCCTGCCTATGAAGAAAAGgtatttttgt ... gttgatgcagATAACAGAGTTGAAGTTGTCGATTGATAGCCTTGAGAAGGAACGGGATTTC
EST: gi|192296791|gb|FG993089.1|FG993089
EST:     AGGTTGCGAGAGCAGCACCTTCTGCCGGAAACCCTGCCTATGAAGAAAAG                         ATAACAGAGTTGAAGTTGTCGATTGATAGCCTTGAGAAGGAACGGGATTTC
genomic: AGGTTGCGAGAGCAGCACCTTCTGCCGGAAACCCTGCCTATGAAGAAAAGgtatttttgt ... gttgatgcagATAACAGAGTTGAAGTTGTCGATTGATAGCCTTGAGAAGGAACGGGATTTC
EST: gi|7685270|gb|AW755918.1|AW755918
EST:     AGGTTGCGAGAGCAGCACCTTCTGCCGGAAACCCTGCCTATGAAGAAAAG                         ATAACAGAGTTGAAGTTGTCGATTGATAGCCTTGAGAAGGAACGGGATTTC
genomic: AGGTTGCGAGAGCAGCACCTTCTGCCGGAAACCCTGCCTATGAAGAAAAGgtatttttgt ... gttgatgcagATAACAGAGTTGAAGTTGTCGATTGATAGCCTTGAGAAGGAACGGGATTTC
EST: gi|192301066|gb|FG987991.1|FG987991
EST:     AGGTTGCGAGAGCAGCACCTTCTGCCGGAAACCCTGCCTATGAAGAAAAG                         ATAACAGAGTTGAAGTTGTCGATTGATAGCCTTGAGAAAGGAACGGGATTT
genomic: AGGTTGCGAGAGCAGCACCTTCTGCCGGAAACCCTGCCTATGAAGAAAAGgtatttttgt ... gttgatgcagATAACAGAGTTGAAGTTGTCGATTGATAGCCTTGAGAA-GGAACGGGATTT
EST: gi|22929992|gb|BU547131.1|BU547131
EST:     AGGTTGCGAGAGCAGCACCTTCTGCCGGAAACCCTGCCTATGAAGAAAAG                         ATAACAGAGTTGAAGTTGTCGATTGATAGCCTTGAGAAGGAACGGGATTTC
genomic: AGGTTGCGAGAGCAGCACCTTCTGCCGGAAACCCTGCCTATGAAGAAAAGgtatttttgt ... gttgatgcagATAACAGAGTTGAAGTTGTCGATTGATAGCCTTGAGAAGGAACGGGATTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaattatcaaatgaataatggaagtatattgctcttacagttgaagttgatgcagATAACAGAGTTGAAGTTGTCGATTGATAGCCTTGAGAAGGAACGGGATTTCTACTTTGCAAAGCTGAGAGATATTGAGATACTGTGCCAGACTCCTGAGA
     atcaaatgaataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatttttgttttcccgtcgaaagaattatcaaatgaataatggaagtatattgctcttacagttgaagttgatgcagATAACAGAGTTGAAGTTGTCGATTGATAGCCTTGAGAAGGAACGGGATTTCTACTTTGCAAAGCTGAGAGATATTGAGATACTGTGCCAGACTCCTGAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA