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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgactgtattcatataccagagttaccttctcttagaagttggtacatcaagcaactaattctggttacttatggtttgacatgtttctgctttatgcagGCTGCCATTGTGAATTCTCAGACTCTTGAAGAGGTTGCTAGACTTGAAAAG

Basic information

species Glycine max
transcript GLYMA10G24350.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G24350.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os02g13990.3 (Oryza sativa), 3'ss of exon 5
---tgactgtattcatataccagagttaccttctcttagaagttggtacatcaagcaactaattctggttacttatggtttgacatgtttctgctttatgcagGCTGCCATTGTGAATTCTCAGACTCTTGAAGAGGTTGCTAGACTTGAAAAG
   ||  | |     | |      || |   |||  ||    | |    ||    ||||||  |      | | | ||||| |||   || | |  | |||||||||||||||||||||||||||| ||||| |||||||| || |||||||||
atatgtgtatggctctctgttgatgtcaatatcttctatgtatggtggtatagtacaactacctgcaaa-attcaaggtttaacaa--ttattccatctgcagGCTGCCATTGTGAATTCTCAGACACTTGAGGAGGTTGCAAGGCTTGAAAAG

upper sequence: GLYMA10G24350.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv01s0150g00590.t01 (Vitis vinifera), 3'ss of exon 5
--tgactgtattcatataccagagttaccttctcttagaagttggtacatcaagcaactaattctggttacttatggtttga---catgtttctgctttatgcagGCTGCCATTGTGAATTCTCAGACTCTTGAAGAGGTTGCTAGACTTGAAAAG
  | ||| ||||| | |  ||| |  | || |   |     |   | |||        | |   |    | | ||| |||     ||| |||     || ||||||| || ||||||||||| |||||||||||||||||||| || |||||||||
ttttact-tattctt-tgtcagtgaaagctgcatct---tttctcttcattgcatgcttgaacttaaaaattcatgttttccgtccatattttgttgttgtgcagGCCGCAATTGTGAATTCACAGACTCTTGAAGAGGTTGCAAGGCTTGAAAAG
















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|58016033|gb|CX702775.1|CX702775
EST:     AGATGCCCAAAGTCGTTGCTCCTACACCTGAGCAAATTATTGCTATTAAG                         GCTGCCATTGTGAATTCTCAGACTCTTGAAGAGGTTGCTAGACTTGAAAAG
genomic: AGATGCCCAAAGTCGTTGCTCCTACACCTGAGCAAATTATTGCTATTAAGgtacaatgat ... ctttatgcagGCTGCCATTGTGAATTCTCAGACTCTTGAAGAGGTTGCTAGACTTGAAAAG
EST: gi|193670506|gb|FK610376.1|FK610376
EST:     AGATGCCCAAAGTCGTTGCNCCTACACCTGAGCAAATTATTGCTATTAAG                         GCTGCCATTGTGAATTCTCAGACTCTTGAAGAGGTTGCTAGACTTGAAAAG
genomic: AGATGCCCAAAGTCGTTGCTCCTACACCTGAGCAAATTATTGCTATTAAGgtacaatgat ... ctttatgcagGCTGCCATTGTGAATTCTCAGACTCTTGAAGAGGTTGCTAGACTTGAAAAG
EST: gi|151403344|gb|EV273154.1|EV273154
EST:     AGATGCCCAAAGTCGTTGCTCCTACACCTGAGCAAATTATTGCTATTAAG                         GCTGCCATTGTGAATTCTCAGACTCTTGAAGAGGTTGCTAGACTTGAAAAG
genomic: AGATGCCCAAAGTCGTTGCTCCTACACCTGAGCAAATTATTGCTATTAAGgtacaatgat ... ctttatgcagGCTGCCATTGTGAATTCTCAGACTCTTGAAGAGGTTGCTAGACTTGAAAAG
EST: gi|213605917|gb|DB983622.1|DB983622
EST:     AGATGCCCAAAGTCGTTGCTCCTACACCTGAGCAAATTATTGCTATTAAG                         GATTG-CATTGTGAATTCTCAGACTCTTGAAGAGGTTGCTAGACTTGAAAA
genomic: AGATGCCCAAAGTCGTTGCTCCTACACCTGAGCAAATTATTGCTATTAAGgtacaatgat ... ctttatgcagG-CTGCCATTGTGAATTCTCAGACTCTTGAAGAGGTTGCTAGACTTGAAAA
EST: gi|192309061|gb|FG999036.1|FG999036
EST:     TGAGCAAATTATTGCTATTAAG                         GCTGCCATTGTGAATTTTCAGACTCTTGAAGAGGTTGCTAGACTTGAAAAG
genomic: TGAGCAAATTATTGCTATTAAGgtacaatgat ... ctttatgcagGCTGCCATTGTGAATTCTCAGACTCTTGAAGAGGTTGCTAGACTTGAAAAG
EST: gi|26268201|gb|CA819264.1|CA819264
EST:     AGATGCCCAAAGTCGTTGCTCCTACACCTGAGCAAATTATTGCTATTAAG                         GCTGCCATTGTGAATTCTCAGACTCTTGAAGAGGTTGCTAGACTTGAAAAG
genomic: AGATGCCCAAAGTCGTTGCTCCTACACCTGAGCAAATTATTGCTATTAAGgtacaatgat ... ctttatgcagGCTGCCATTGTGAATTCTCAGACTCTTGAAGAGGTTGCTAGACTTGAAAAG
EST: gi|10252487|gb|BE820253.1|BE820253
EST:     GCCCAAAGTCGTTGCTCCTACACCTGAGCAAATTATTGCTATTAAG                         GCTGCCATTGTGAATTCTCAGACTCTTGAAGAGGTTGCTAGACTTGAAAAG
genomic: GCCCAAAGTCGTTGCTCCTACACCTGAGCAAATTATTGCTATTAAGgtacaatgat ... ctttatgcagGCTGCCATTGTGAATTCTCAGACTCTTGAAGAGGTTGCTAGACTTGAAAAG
EST: gi|58023144|gb|CX709885.1|CX709885
EST:     AGATGCCCAAAGTCGTTGCTCCTACACCTGAGCAAATTATTGCTATTAAG                         GCTGCCATTGTGAATTCTCAGACTCTTGAAGAGGTTGCTAGACTTGAAAAG
genomic: AGATGCCCAAAGTCGTTGCTCCTACACCTGAGCAAATTATTGCTATTAAGgtacaatgat ... ctttatgcagGCTGCCATTGTGAATTCTCAGACTCTTGAAGAGGTTGCTAGACTTGAAAAG
EST: gi|15203108|gb|BI425876.1|BI425876
EST:     AGATGCCCAAAGTCGTTGCTCCTACACCTGAGCAAATTATTGCTATTAAG                         GCTGCCATTGTGAATTCTCAGACTCTTGATTTTGTTGCTAGACTTGAAAAG
genomic: AGATGCCCAAAGTCGTTGCTCCTACACCTGAGCAAATTATTGCTATTAAGgtacaatgat ... ctttatgcagGCTGCCATTGTGAATTCTCAGACTCTTGAAGAGGTTGCTAGACTTGAAAAG
EST: gi|23052917|gb|BU577408.1|BU577408
EST:     AGATGCCCAAAGTCGTTGCTCCTACACCTGAGCAAATTATTGCTATTAAG                         GCTGCCATTGTGAATTCTCAGACTCTTGAAGAGGTTGCTAGACTTGAAAAG
genomic: AGATGCCCAAAGTCGTTGCTCCTACACCTGAGCAAATTATTGCTATTAAGgtacaatgat ... ctttatgcagGCTGCCATTGTGAATTCTCAGACTCTTGAAGAGGTTGCTAGACTTGAAAAG
EST: gi|6951211|gb|AW423340.1|AW423340
EST:     GCCCAAAGTCGTTGCTCCTACACCTGAGCAAATTATTGCTATTAAG                         GCTGCCATTGTGAATTCTCAGACTCTTGAAGAGGTTGCTAGACTTGAAAAG
genomic: GCCCAAAGTCGTTGCTCCTACACCTGAGCAAATTATTGCTATTAAGgtacaatgat ... ctttatgcagGCTGCCATTGTGAATTCTCAGACTCTTGAAGAGGTTGCTAGACTTGAAAAG
EST: gi|13790409|gb|BG653000.1|BG653000
EST:     AGATGCCCAAAGTCGTTGCTCCTACACCTGAGCAAATTATTGCTATTAAG                         GCTGCCATTGTGAATTCTCAGACTCTTGAAGAGGTTGCTAGACTTGAAAAG
genomic: AGATGCCCAAAGTCGTTGCTCCTACACCTGAGCAAATTATTGCTATTAAGgtacaatgat ... ctttatgcagGCTGCCATTGTGAATTCTCAGACTCTTGAAGAGGTTGCTAGACTTGAAAAG
EST: gi|193564897|gb|FK520096.1|FK520096
EST:     AGATGCCCAAAGTCGTTGCTCCTACACCTGAGCAAATTATTGCTATTAAG                         GCTGCCATTGTGAATTCTCAGACTCTTGAAGAGGTTGCTAGACTTGAAAAG
genomic: AGATGCCCAAAGTCGTTGCTCCTACACCTGAGCAAATTATTGCTATTAAGgtacaatgat ... ctttatgcagGCTGCCATTGTGAATTCTCAGACTCTTGAAGAGGTTGCTAGACTTGAAAAG
EST: gi|8282401|gb|BE019962.1|BE019962
EST:     AGATGCCCAAAGTCGTTGCTCCTACACCTGAGCAAATTATTGCTATTAAG                         GCTGCCATTGTGAATTCTCAGACTCTTGAAGAGGTTGCTAGACTTGAAAAG
genomic: AGATGCCCAAAGTCGTTGCTCCTACACCTGAGCAAATTATTGCTATTAAGgtacaatgat ... ctttatgcagGCTGCCATTGTGAATTCTCAGACTCTTGAAGAGGTTGCTAGACTTGAAAAG
EST: gi|192320514|gb|FK011924.1|FK011924
EST:     AGATGCCCAAAGTCGTTGCTCCTACACCTGAGCAAATTATTGCTATTAAG                         GCTGCCATTGTGAATTTTCAGACTCTTGAAGAGGTTGCTAGACTTGAAAAG
genomic: AGATGCCCAAAGTCGTTGCTCCTACACCTGAGCAAATTATTGCTATTAAGgtacaatgat ... ctttatgcagGCTGCCATTGTGAATTCTCAGACTCTTGAAGAGGTTGCTAGACTTGAAAAG
EST: gi|214008290|gb|DB989832.1|DB989832
EST:     AGATGCCCAAAGTCGTTGCTCCTACACCTGAGCAAATTATTGCTATTAAG                         GCTGCCATTGTGAATTCTCAGACTCTTGAAGAGGTTGCTAGACTTGAAAAG
genomic: AGATGCCCAAAGTCGTTGCTCCTACACCTGAGCAAATTATTGCTATTAAGgtacaatgat ... ctttatgcagGCTGCCATTGTGAATTCTCAGACTCTTGAAGAGGTTGCTAGACTTGAAAAG
EST: gi|16344759|gb|BI970354.1|BI970354
EST:     AGATGCCCAAAGTCGTTGCTCCTACACCTGAGCAAATTATTGCTATTAAG                         GCTGCCATTGTGAATTCTCAGACTCTTGAAGAGGTTGCTAGACTTGAAAAG
genomic: AGATGCCCAAAGTCGTTGCTCCTACACCTGAGCAAATTATTGCTATTAAGgtacaatgat ... ctttatgcagGCTGCCATTGTGAATTCTCAGACTCTTGAAGAGGTTGCTAGACTTGAAAAG
EST: gi|193602036|gb|FK558817.1|FK558817
EST:     AGATGCCCAAAGTCGTTGCTCCTACACCTGAGCAAATTATTGCTATTAAG                         GCTGCCATTGTGAATTCTCAGACTCTTGAAGAGGTTGCTAGACTTGAAAAG
genomic: AGATGCCCAAAGTCGTTGCTCCTACACCTGAGCAAATTATTGCTATTAAGgtacaatgat ... ctttatgcagGCTGCCATTGTGAATTCTCAGACTCTTGAAGAGGTTGCTAGACTTGAAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catcaagcaactaattctggttacttatggtttgacatgtttctgctttatgcagGCTGCCATTGTGAATTCTCAGACTCTTGAAGAGGTTGCTAGACTTGAAAAG
                                       tttctgcttt  CT-rich tract
        aactaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgactgtattcatataccagagttaccttctcttagaagttggtacatcaagcaactaattctggttacttatggtttgacatgtttctgctttatgcagGCTGCCATTGTGAATTCTCAGACTCTTGAAGAGGTTGCTAGACTTGAAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
-gactgta
- - - - - catatac
- - - - - - - - - - - - -ccttctc
- - - - - - - - - - - - - - - - - - - gttggta
- - - - - - - - - - - - - - - - - - - - - - - -tcaagca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tctggtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tggtttg