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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgtccctgtctacaaatttccatcaataattagtcttaaaaaatcaaatttggttcattgttctgcctcatcttttttgaaaaatcatataaggtttattttcaatggtttttaacttttcatttcttaatctatttcgtttctactagGGAGGAGGATGGTGCAACAATGTCACTACTTGCCTTGCTCGCAAGACCAATCGTCTAGGTTCATCTAAGCAAATGGCGAAGCAAATTGCCTTTTCAGGAA

Basic information

species Glycine max
transcript GLYMA01G35480.3
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G35480.3 (Glycine max), 3'ss of exon 3
lower sequence: Vv02s0087g00400.t01 (Vitis vinifera), 3'ss of exon 3
gtgtgtccctgtctacaaatttccatcaataattagtcttaaaaaatcaaatttggttcattgttctgcctcatcttttttgaaaaatcatataaggtttattttcaatggtttt----taacttttcatttcttaatctatttcgtttc--tactagGGAGGAGGATGGTGCAACAATGTCACTACTTGCCTTGCTCGCAAGACCAATCGTCTAGGTTCATCTAAGCAAATGGCGAAGCAAATTGCCTTTTCAGGAA
                                                         | |||| | |  |  |  ||    | |||||   | ||  ||| |     |||    |    || | | | || || | || |||  | |||   ||  |||||||||||||||||||||||| | | |||||||||||||| | |  ||| ||| |||||||||| |||||||||| |||||||||||| || || || |
---------------------------------------------------------tgattggtttctcagaaattaga-ggaaaatggaagaaaatttttgagtcatgcaactggcatagcatataatctcatcatttatggctttttgatatcagGGAGGAGGATGGTGCAACAATGCCTCAACTTGCCTTGCTCGTAGGGACAACCGTTTAGGTTCATCGAAGCAAATGGTGAAGCAAATTGCTTTCTCTGGGA
















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|13311525|gb|BG405176.1|BG405176
EST:     TTGATAAGGGATTTGGATCAGGGATTAACAATTGGTTGGTTGCATTTGAG                         GGAGGAGGATGGTGCAACAATGTCACTACTTGCCTTGCTCGCAAGACCAAT
genomic: TTGATAAGGGATTTGGATCAGGGATTAACAATTGGTTGGTTGCATTTGAGgtgtgtccct ... tttctactagGGAGGAGGATGGTGCAACAATGTCACTACTTGCCTTGCTCGCAAGACCAAT
EST: gi|151394706|gb|EV264577.1|EV264577
EST:     TTGATAAGGGATTTGGATCAGGGATTAACAATTGGTTGGTTGCATTTGAG                         GGAGGAGGATGGTGCAACAATGTCACTACTTGCCTTGCTCGCAAGACCAAT
genomic: TTGATAAGGGATTTGGATCAGGGATTAACAATTGGTTGGTTGCATTTGAGgtgtgtccct ... tttctactagGGAGGAGGATGGTGCAACAATGTCACTACTTGCCTTGCTCGCAAGACCAAT
EST: gi|13311486|gb|BG405137.1|BG405137
EST:     TTGATAAGGGATTTGGATCAGGGATTAACAATTGGTTGGTTGCATTTGAG                         GGAGGAGGATGGTGCAACAATGTCACTACTTGCCTTGCTCGCAAGACCAAT
genomic: TTGATAAGGGATTTGGATCAGGGATTAACAATTGGTTGGTTGCATTTGAGgtgtgtccct ... tttctactagGGAGGAGGATGGTGCAACAATGTCACTACTTGCCTTGCTCGCAAGACCAAT
EST: gi|213605459|gb|DB966952.1|DB966952
EST:     TTGATAAGGGATTTGGATCAGGGATTAACAATTGGTTGGTTGCATTTGAG                         GGAGGAGGATGGTGCAACAATGTCACTACTTGCCTTGCTCGCAAGACCAAT
genomic: TTGATAAGGGATTTGGATCAGGGATTAACAATTGGTTGGTTGCATTTGAGgtgtgtccct ... tttctactagGGAGGAGGATGGTGCAACAATGTCACTACTTGCCTTGCTCGCAAGACCAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttattttcaatggtttttaacttttcatttcttaatctatttcgtttctactagGGAGGAGGATGGTGCAACAATGTCACTACTTGCCTTGCTCGCAAGACCAATCGTCTAGGTTCATCTAAGCAAATGGCGAAGCAAATTGCCTTTTCAGGAA
                                    tctatttcgtttct  CT-rich tract
              tttttaacttttcatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtgtccctgtctacaaatttccatcaataattagtcttaaaaaatcaaatttggttcattgttctgcctcatcttttttgaaaaatcatataaggtttattttcaatggtttttaacttttcatttcttaatctatttcgtttctactagGGAGGAGGATGGTGCAACAATGTCACTACTTGCCTTGCTCGCAAGACCAATCGTCTAGGTTCATCTAAGCAAATGGCGAAGCAAATTGCCTTTTCAGGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA