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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgttttccatgctctcatcaataatgttcttttggtattcaaaatgcttttgtgacatagtgaatgactaaatgctctacatacagGTAGCGATGAAGCTTGCTCCTGATAGGAAGAAATTCATGGAGGTGATACAAGGCACTGGTGATATCAGTGCTGATATACAGAAATTTTGTACTGACTTTT

Basic information

species Glycine max
transcript GLYMA10G32590.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G32590.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os07g26460.1 (Oryza sativa), 3'ss of exon 5
---------gtaatgttttccatgctctcatcaataatg-ttcttttggtattcaaaatgcttttgtgacatagtgaatgacta--aatgctctacatacagGTAGCGATGAAGCTTGCTCCTGATAGGAAGAAATTCATGGAGGTGATACAAGGCACTGGTGATATCAGTGCTGATATACAGAAATTTTGTACTGACTTTT
          || | || |         ||   ||  |   |  | |||| ||  ||    | || | | |||| || |  |||  ||| |   |  | ||||| || || ||||||||||| || |||||||||||||||||| | ||    ||| | ||||||||||  || || ||  |||| |||||| |    || |
tgaacatgattagtcttctttccatggccacagattgtaactagtatggtcttgcaagca-tattattatatag-gagtatctaacaatccctgagtttcagGTTGCCATAAAGCTTGCTCCAGACAGGAAGAAATTCATGGAGATCATTAGTGGCTCAGGTGATATCAACGCAGACATCGAGAAGTTTTGTGCAACTTTCT

upper sequence: GLYMA10G32590.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv05s0049g01330.t01 (Vitis vinifera), 3'ss of exon 5
gtaatgttttccatgctctcatcaataatgttcttttggtattcaaaatgctt--ttgtgacatagtgaatgactaaatgctctacatacagGTA---------GCGATGAAGCTTGCTCCTGATAGGAAGAAATTCATGGAGGTGATACAAGGCACTGGTGATATCAGTGCTGATATACAGAAATTTTGTACTGACTTTT
 |    || ||  |  |    | || |   ||||| |     |  || |      || | ||||   || |  ||        || |||| ||||         || |||||||||||||| ||||||||||| |||||||| ||||||   || || |||||| ||| |||||| ||  ||   ||||| ||   ||| |
-ttcaattctctgttttacagttaaaataattcttgtatcccttgaattagccaattttaacatctggactttcttggcttgttatatactggtataacagCTTGCTATGAAGCTTGCTCCAGATAGGAAGAAGTTCATGGACGTGATATCGGGTACAGGTGATGTCAATGCTGACATGGAGGCTTTTTGCACAAGCTTCT
















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|298173249|gb|HO020233.1|HO020233
EST:     ACAAGACTCTAAAGAAGTGGCATGGCTGGCTTGCAAGTTCAAGCTTCAGT                         GTAGCGATGAAGCTTGCTCCTGA
genomic: ACAAGACTCTAAAGAAGTGGCATGGCTGGCTTGCAAGTTCAAGCTTCAGTgtaatgtttt ... ctacatacagGTAGCGATGAAGCTTGCTCCTGA
EST: gi|208331138|gb|GE130941.1|GE130941
EST:     ACAAGACTCTAAAGAAGTGGCATGGCTGGCTTGCAAGTTCAAGCTTCAGT                         GTAGCGATGAAGCTTGCTCCTGATAGGAAGAAATTCATGGAGGTGATACAA
genomic: ACAAGACTCTAAAGAAGTGGCATGGCTGGCTTGCAAGTTCAAGCTTCAGTgtaatgtttt ... ctacatacagGTAGCGATGAAGCTTGCTCCTGATAGGAAGAAATTCATGGAGGTGATACAA
EST: gi|151409417|gb|EV279225.1|EV279225
EST:     ACAAGACTCTAAAGAAGTGGCATGGCTGGCTTGCAAGTTCAAGCTTCAGT                         GTAGCGATGAAGCTTGCTCCTGATAGGAAGAAATTCATGGAGGTGATACAA
genomic: ACAAGACTCTAAAGAAGTGGCATGGCTGGCTTGCAAGTTCAAGCTTCAGTgtaatgtttt ... ctacatacagGTAGCGATGAAGCTTGCTCCTGATAGGAAGAAATTCATGGAGGTGATACAA
EST: gi|151412396|gb|EV282208.1|EV282208
EST:     CAAGGCTCTAAAGAAGTGGCATGGCTGGCTTTGCAAGTTCAAGCTTCAGT                         GTAGCGATGAAGCTTGCTCCTGATAGGAAGAAATTCATGGAGGTGATACAA
genomic: CAAGACTCTAAAGAAGTGGCATGGCTGGCTT-GCAAGTTCAAGCTTCAGTgtaatgtttt ... ctacatacagGTAGCGATGAAGCTTGCTCCTGATAGGAAGAAATTCATGGAGGTGATACAA
EST: gi|213615020|gb|DB957058.1|DB957058
EST:     ACAAGACTCTAAAGAAGTGGCATGGCTGGCTTGCAAGTTCAAGCTTCAGT                         GTAGCGATGAAGCTTGCTCCTGATAGGAAGAAATTCATGGAGGTGATACAA
genomic: ACAAGACTCTAAAGAAGTGGCATGGCTGGCTTGCAAGTTCAAGCTTCAGTgtaatgtttt ... ctacatacagGTAGCGATGAAGCTTGCTCCTGATAGGAAGAAATTCATGGAGGTGATACAA
EST: gi|254340633|gb|GR854361.1|GR854361
EST:     ACAAGACTCTAAAGAAGTGGCATGGCTGGCTTGCAAGTTCAAGCTTCAGT                         GTAGCGATGAAGCTTGCTCCTGATAGGAAGAAATTCATGGAGGTGATACAA
genomic: ACAAGACTCTAAAGAAGTGGCATGGCTGGCTTGCAAGTTCAAGCTTCAGTgtaatgtttt ... ctacatacagGTAGCGATGAAGCTTGCTCCTGATAGGAAGAAATTCATGGAGGTGATACAA
EST: gi|298197177|gb|HO041920.1|HO041920
EST:     ACAAGACTCTAAAGAAGTGGCATGGCTGGCTTGCAAGTTCAAGCTTCAGT                         GTAGCGATGAAGCTTGCTCCTGATAGGA
genomic: ACAAGACTCTAAAGAAGTGGCATGGCTGGCTTGCAAGTTCAAGCTTCAGTgtaatgtttt ... ctacatacagGTAGCGATGAAGCTTGCTCCTGATAGGA
EST: gi|151411234|gb|EV281045.1|EV281045
EST:     ACAAGACTCTAAAGAAGTGGCATGGCTGGCTTGCAAGTTCAAGCTTCAGT                         GTAGCGATGAAGCTTGCTCCTGATAGGAAGAAATTCATGGGAGGTGATACA
genomic: ACAAGACTCTAAAGAAGTGGCATGGCTGGCTTGCAAGTTCAAGCTTCAGTgtaatgtttt ... ctacatacagGTAGCGATGAAGCTTGCTCCTGATAGGAAGAAATTCATGG-AGGTGATACA
EST: gi|192326692|gb|FK018879.1|FK018879
EST:     ACAAGACTCTAAAGAAGTGGCATGGCTGGCTTGCAAGTTCAAGCTTCAGT                         GTAGCGATGAAGCTTGCTCCTGATAGGAAGAAATTCATGGAGGTGATACAA
genomic: ACAAGACTCTAAAGAAGTGGCATGGCTGGCTTGCAAGTTCAAGCTTCAGTgtaatgtttt ... ctacatacagGTAGCGATGAAGCTTGCTCCTGATAGGAAGAAATTCATGGAGGTGATACAA
EST: gi|209707561|gb|BW680931.1|BW680931
EST:     ACAAGACTCTAAAGAAGGGGCATGGCTGGCTTGCAAGTTCAAGCTTCAGT                         GTAGCGATGAAGCTTGCTCCTGATAGGAAGAAATTCATGGAGGTGATACAA
genomic: ACAAGACTCTAAAGAAGTGGCATGGCTGGCTTGCAAGTTCAAGCTTCAGTgtaatgtttt ... ctacatacagGTAGCGATGAAGCTTGCTCCTGATAGGAAGAAATTCATGGAGGTGATACAA
EST: gi|10231207|gb|BE800023.1|BE800023
EST:     ACAAGACTCTAAAGAAGTGGCATGGCTGGCTTGCAAGTTCAAGCTTCAGT                         GTAGCGATGAAGCTTGCTCCTGATAGGAAGAAATTCATGGAGGTGATACAA
genomic: ACAAGACTCTAAAGAAGTGGCATGGCTGGCTTGCAAGTTCAAGCTTCAGTgtaatgtttt ... ctacatacagGTAGCGATGAAGCTTGCTCCTGATAGGAAGAAATTCATGGAGGTGATACAA
EST: gi|254340634|gb|GR854362.1|GR854362
EST:     ACAAGACTCTAAAGAAGTGGCATGGCTGGCTTGCAAGTTCAAGCTTCAGT                         GTAGCGATGAAGCTTGCTCCTGATAGGAAGAAATTCATGGAGGTGATACAA
genomic: ACAAGACTCTAAAGAAGTGGCATGGCTGGCTTGCAAGTTCAAGCTTCAGTgtaatgtttt ... ctacatacagGTAGCGATGAAGCTTGCTCCTGATAGGAAGAAATTCATGGAGGTGATACAA
EST: gi|208167521|gb|GD965159.1|GD965159
EST:     ACAAGACTCTAAAGAAGTGGCATGGCTGGCTTGCAAGTTCAAGCTTCAGT                         GTAGCGATGAAGCTTGCTCCTGATAGGAAGAAATTCATGGAGGTGATACAA
genomic: ACAAGACTCTAAAGAAGTGGCATGGCTGGCTTGCAAGTTCAAGCTTCAGTgtaatgtttt ... ctacatacagGTAGCGATGAAGCTTGCTCCTGATAGGAAGAAATTCATGGAGGTGATACAA
EST: gi|209707562|gb|BW680932.1|BW680932
EST:     ACAAGACTCTAAAGAAGGGGCATGGCTGGCTTGCAAGTTCAAGCTTCAGT                         GTAGCGATGAAGCTTGCTCCTGATAGGAAGAAATTCATGGAGGTGATACAA
genomic: ACAAGACTCTAAAGAAGTGGCATGGCTGGCTTGCAAGTTCAAGCTTCAGTgtaatgtttt ... ctacatacagGTAGCGATGAAGCTTGCTCCTGATAGGAAGAAATTCATGGAGGTGATACAA
EST: gi|151408958|gb|EV278766.1|EV278766
EST:     ACAAGACTCTAAAGAAGCGGCATGGCTGGCTTGCAAGTTCAAGCTTCAGT                         GTAGCGATGAAGCTTGCTCCTGATAGGAAGAAATTCATGGAGGTGATACAA
genomic: ACAAGACTCTAAAGAAGTGGCATGGCTGGCTTGCAAGTTCAAGCTTCAGTgtaatgtttt ... ctacatacagGTAGCGATGAAGCTTGCTCCTGATAGGAAGAAATTCATGGAGGTGATACAA
EST: gi|58025262|gb|CX712003.1|CX712003
EST:     ACAAGACTCTAAAGAAGTGGCATGGCTGGCTTGCAAGTTCAAGCTTCAGT                         GTAGCGATGAAGCTTGCTCNTGATAGGAAGAAATTCATGGAGGTGATACAA
genomic: ACAAGACTCTAAAGAAGTGGCATGGCTGGCTTGCAAGTTCAAGCTTCAGTgtaatgtttt ... ctacatacagGTAGCGATGAAGCTTGCTCCTGATAGGAAGAAATTCATGGAGGTGATACAA
EST: gi|192324104|gb|FK019395.1|FK019395
EST:     ACAAGACTCTAAAGAAGTGGCATGGCTGGCTTGCAAGTTCAAGCTTCAGT                         GTAGCGATGAAGCTTGCTCCTGATAGGAAGAAATTCATGGAGGTGATACAA
genomic: ACAAGACTCTAAAGAAGTGGCATGGCTGGCTTGCAAGTTCAAGCTTCAGTgtaatgtttt ... ctacatacagGTAGCGATGAAGCTTGCTCCTGATAGGAAGAAATTCATGGAGGTGATACAA
EST: gi|192295514|gb|FG988088.1|FG988088
EST:     ACAAGACTCTAAAGAAGTGGCATGGCTGGCTTGCAAGTTCAAGCTTCAGT                         GTAGCGATGAAGCTTGCTCCTGATAGGAAGAAATTCATGGAGGTGATACAA
genomic: ACAAGACTCTAAAGAAGTGGCATGGCTGGCTTGCAAGTTCAAGCTTCAGTgtaatgtttt ... ctacatacagGTAGCGATGAAGCTTGCTCCTGATAGGAAGAAATTCATGGAGGTGATACAA
EST: gi|12773166|gb|BG238093.1|BG238093
EST:     ACAAGACTCTAAAGAAGTGGCATGGCTGGCTTGCAAGTTCAAGCTTCAGT                         GTAGCGATGAAGCTTGCTCCTGATAGGAAGAAATTCATGGAGGTGATACAA
genomic: ACAAGACTCTAAAGAAGTGGCATGGCTGGCTTGCAAGTTCAAGCTTCAGTgtaatgtttt ... ctacatacagGTAGCGATGAAGCTTGCTCCTGATAGGAAGAAATTCATGGAGGTGATACAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggtattcaaaatgcttttgtgacatagtgaatgactaaatgctctacatacagGTAGCGATGAAGCTTGCTCCTGATAGGAAGAAATTCATGGAGGTGATACAAGGCACTGGTGATATCAGTGCTGATATACAGAAATTTTGTACTGACTTTT
                                  gactaaa  putative branch site (score: 2)
     attcaaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatgttttccatgctctcatcaataatgttcttttggtattcaaaatgcttttgtgacatagtgaatgactaaatgctctacatacagGTAGCGATGAAGCTTGCTCCTGATAGGAAGAAATTCATGGAGGTGATACAAGGCACTGGTGATATCAGTGCTGATATACAGAAATTTTGTACTGACTTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT