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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcaaatgcagagcaatttgtttgtcaatgttgttaacttaatgcaatatttaagtattttatagcctgaccaacgctcaaattttgtgccttgtatgcagGCTGTTTGCACTGAAGCTGGAATGTTTGCTTTGAGGGAGCGGAGGGTACACGTGACTCAGGAGGATTTTGAGATGGCCGTGGCGAAGGTGATGAAAAAGG

Basic information

species Glycine max
transcript GLYMA07G00420.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G00420.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os02g11050.1 (Oryza sativa), 3'ss of exon 8
gcaaatgcagagcaatttgtttgtcaatgttgt-taacttaatgcaata-tttaagtattttatagcctgaccaac--gctcaaattttgtgcc-ttgtatgcagGCTGTTTGCACTGAAGCTGGAATGTTTGCTTTGAGGGAGCGGAGGGTACACGTGACTCAGGAGGATTTTGAGATGGCCGTGGCGAAGGTGATGAAAAAGG
     | || | |||| ||  | |  |    |    |   || |  |||  |    ||  || |   |   | |      |||  || | |  | |  | | ||||| || ||||| |||||||||||||||||| |  | ||| | ||||| || || || || ||||| ||||||||||| ||||||||||||||||| || |
-----ttcaaaacaatgtgcatatatacacagcactatagaacgtcatagctcctataccttgtgatcatgcaactttattcactttctctttcatcatcttcagGCGGTCTGCACAGAAGCTGGAATGTTTGCTCTTCGTGAGAGAAGGGTGCATGTAACACAAGAGGACTTTGAGATGGCAGTGGCGAAGGTGATGAAGAAAG

upper sequence: GLYMA07G00420.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G107362_T04 (Zea mays), 3'ss of exon 8
-gcaaatgcagagca--atttgtttgtcaatgttgttaa-cttaatgcaatatttaagtattttatagcctgaccaacgctcaaattttgtgccttgtatgcagGCTGTTTGCACTGAAGCTGGAATGTTTGCTTTGAGGGAGCGGAGGGTACACGTGACTCAGGAGGATTTTGAGATGGCCGTGGCGAAGGTGATGAAAAAGG
    |||||  |  |  |    ||||| |  ||| |    | ||  ||  | | |  || ||| | |   |  ||     |  | |||| ||   |   | ||||| || ||||| || ||||||||||||||| |  | ||| | ||||| ||||| || |||||||| || |||||||| ||||| ||||||||||| || |
tttcaatgcttattaccaagcatttgtgatcgttatagttcctatagctttgtgtttgtgtttcagactttttcc----tttcatttttttggtgttggttcagGCCGTCTGCACAGAGGCTGGAATGTTTGCTCTTCGTGAGAGAAGGGTGCACGTTACCCAGGAGGACTTCGAGATGGCAGTGGCCAAGGTGATGAAGAAAG

upper sequence: GLYMA07G00420.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G137528_T01 (Zea mays), 3'ss of exon 8
gcaaatgcagagcaatttgtttgtcaatgttgttaacttaatgcaatatttaagtattttatagcctgaccaacgctcaaattttgtgccttg--tatgcagGCTGTTTGCACTGAAGCTGGAATGTTTGCTTTGAGGGAGCGGAGGGTACACGTGACTCAGGAGGATTTTGAGATGGCCGTGGCGAAGGTGATGAAAAAGG
|    |  |   || ||  | ||   |   ||||  ||   |    | |  |  |  | |  |  |  |  |||| | ||  ||| |   |||  | | ||||| || || || || ||||||||||||||| |  | ||| | ||||| ||||| || |||||||| || |||||||| ||||| ||||||||||| || |
gtttgttaaatccacttcatctgatga-actgtttgctgcctctcgtttcaatcttgtgttgattcgaagtaacgtttaacattttttttttggctgttcagGCCGTCTGTACAGAGGCTGGAATGTTTGCTCTCCGTGAGAGAAGGGTGCACGTTACACAGGAGGACTTCGAGATGGCAGTGGCCAAGGTGATGAAGAAAG

upper sequence: GLYMA07G00420.1 (Glycine max), 3'ss of exon 8
lower sequence: AT5G20000.1 (Arabidopsis thaliana), 3'ss of exon 8
gcaaatgcagagcaatttgtttgtcaatgttgttaacttaatgcaatatttaagtattttatagcctgaccaacgctcaaattttgtgcc-ttgtatgcagGCTGTTTGCACTGAAGCTGGAATGTTTGCTTTGAGGGAGCGGAGGGTACACGTGACTCAGGAGGATTTTGAGATGGCCGTGGCGAAGGTGATGAAAAAGG
                      || | ||||  |   |   |||     |   ||  | |  |  ||| |   | || |  ||||  |   ||     |||||||| ||||| || || || ||||||||  |  | ||| |||| ||||| ||||||||||| || ||||||||||| ||||||||||| ||||| || |
----------------------gtaagtgtttctctgtccctgcttctgtcttgttctctccaatctgtctctctctaatgtttttggttattacggtcagGCTGTATGCACGGAGGCGGGCATGTTTGCACTTCGTGAGAGGAGAGTACATGTGACTCAGGAAGACTTTGAGATGGCTGTGGCGAAGGTAATGAAGAAAG

upper sequence: GLYMA07G00420.1 (Glycine max), 3'ss of exon 8
lower sequence: AT5G19990.1 (Arabidopsis thaliana), 3'ss of exon 8
gcaaatgcagagcaatttgtttgtcaatgttgttaacttaatgcaatatttaagtattttatagcctgaccaacgctcaaattttgtgccttgtatg--cagGCTGTTTGCACTGAAGCTGGAATGTTTGCTTTGAGGGAGCGGAGGGTACACGTGACTCAGGAGGATTTTGAGATGGCCGTGGCGAAGGTGATGAAAAAGG
           | ||  ||||| || || |   ||  |  ||    |  |       | || |   || |   | || |  |||| ||  |  || |  |||||||| ||||| || || |||||||||||| || | ||| |||| ||||||||||| || || || ||||||||||| ||||| ||||| ||||| || |
-----------gtaaagtgttt-tctatttctctacttctatcttgttct------ctctacattttgcctctctcttatgtttt-tggttaatacggtcagGCTGTGTGCACGGAGGCGGGAATGTTTGCTCTGCGTGAGAGGAGAGTACACGTGACACAAGAAGACTTTGAGATGGCGGTGGCCAAGGTAATGAAGAAAG

upper sequence: GLYMA07G00420.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv04s0008g04690.t01 (Vitis vinifera), 3'ss of exon 8
-gcaaatgcagagcaatttgtttgtcaa-tgttgttaacttaatgcaatatttaagtattttatagcctgaccaacgctcaaattttgtgcc-ttgtatgcagGCTGTTTGCACTGAAGCTGGAATGTTTGCTTTGAGGGAGCGGAGGGTACACGTGACTCAGGAGGATTTTGAGATGGCCGTGGCGAAGGTGATGAAAAAGG
   || | |  |    |     | |||| ||  ||    |   ||   | | |    |  | | ||| || | ||  || || |||| |    |||| ||||||| || ||||| |||||||||||||||||| | |||||| |||| ||||| ||||| || || |||||||||||||| ||||| ||||||||||||||||
actaagtccttattcttcatcatatcaagtgcggtcggttatctgttttgtcttctaacatca-agcatgtctaa--ctaaacttttatataattgtttgcagGCGGTATGCACAGAAGCTGGAATGTTTGCTCTAAGGGAGAGGAGAGTACATGTGACACAAGAAGATTTTGAGATGGCAGTGGCAAAGGTGATGAAAAAGG

upper sequence: GLYMA07G00420.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv09s0002g05800.t01 (Vitis vinifera), 3'ss of exon 8
gcaaatgcagagcaatttgtttgtcaatgttgttaact-taatgcaa--tatttaagtattttatagcctgaccaacgctcaaatt------ttgtgcctt-gtatgcagGCTGTTTGCACTGAAGCTGGAATGTTTGCTTTGAGGGAGCGGAGGGTACACGTGACTCAGGAGGATTTTGAGATGGCCGTGGCGAAGGTGATGAAAAAGG
       | ||      ||  |    | ||| || | | ||||| ||   |||||    ||  ||||       | | |||  |||      |||  | || || ||||||| || ||||| ||||| || |||||||||||||||||| ||||||| ||||| || ||||| ||||| |||||||| || || || |||||||| ||||
-------ctgactttcctgccttcataggtttttgaatataatggaaaccatttac---ttgcatagatctgatacctctcggattgagcatttgaacttttgtttgcagGCGGTATGCACAGAAGCAGGGATGTTTGCTTTGAGGGAGAGGAGGGTTCACGTAACACAGGAAGATTTCGAGATGGCTGTAGCCAAAGTGATGAAGAAGG

upper sequence: GLYMA07G00420.1 (Glycine max), 3'ss of exon 8
lower sequence: PP1S245_17V6.1 (Physcomitrella patens), 3'ss of exon 8
------------------------------gcaaatgcagagcaatttgtttgtcaatgttgttaacttaatgcaatatttaagtattttatagcctgaccaacgctcaaattttgtgccttgtatgcagGCTGTTTGCACTGAAGCTGGAATGTTTGCTTTGAGGGAGCGGAGGGTACACGTGACTCAGGAGGATTTTGAGATGGCCGTGGCGAAGGTGATGAAAAAGG
                                   ||||     |     || |   || | ||   ||  |    |||||   | ||||     || |         ||  |||||||  |  || |||||||| ||||| ||||| || ||||||||| |  | || ||| | ||||| || || || ||||||||||| ||| | ||||||||||||||||| ||||
gttcctactaaagagtcgttgttttgtcacatttctgcaattagacacagttttttgtgctttttcttttcttttctatttgtttgtttttc--tcttaatgtttaataatctttgtgctgt-cattcagGCTGTGTGCACAGAAGCAGGCATGTTTGCTCTACGTGAACGGCGTGTACATGTAACACAAGAGGATTTTGAAATGTCTGTGGCGAAGGTGATGAAGAAGG

upper sequence: GLYMA07G00420.1 (Glycine max), 3'ss of exon 8
lower sequence: PP1S7016_1V6.1 (Physcomitrella patens), 3'ss of exon 3
---------------------------------------gcaaatgcagagcaatttgtttgtcaatgttgttaacttaatgcaatatttaagtattttatagcctgaccaacgctcaaattttgtgccttgtatgcagGCTGTTTGCACTGAAGCTGGAATGTTTGCTTTGAGGGAGCGGAGGGTACACGTGACTCAGGAGGATTTTGAGATGGCCGTGGCGAAGGTGATGAAAAAGG
                                           || |  || ||  || | |    | ||||      | |    |||||||  |||||      |     |  || |  |||| |  |||  || |||||||| ||||| || ||||| ||||||||| |  | || ||| | ||||| ||||| || ||||| || |||||||| ||||| ||||||||||| ||||
gtagctacaaacctacagtatctagggtttatttctggtagtgatacgaaggaagctgctagaggcttttgt------attatgttatttaaa-attttggctgttcgtttatactaattttttattgcttcaat-cagGCTGTATGCACAGAGGCTGGCATGTTTGCTCTACGTGAACGGCGTGTACATGTGACACAAGAGGACTTCGAGATGGCTGTGGCTAAGGTGATGAAGAAGG

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|214009603|gb|DB988312.1|DB988312
EST:     TGAAGAAGATTGCCGAGAAGATGAATGGAGCATCTGGTGCTGAACTTAAG                         GCTGTTTGCACTGAAGCTGGAATGTTTGCTTTGAGGGAGCGGAGGGTACAC
genomic: TGAAGAAGATTGCCGAGAAGATGAATGGAGCATCTGGTGCTGAACTTAAGgtatactcta ... ttgtatgcagGCTGTTTGCACTGAAGCTGGAATGTTTGCTTTGAGGGAGCGGAGGGTACAC
EST: gi|214008199|gb|DB987076.1|DB987076
EST:     GAGAAGATGAATGGAGCATCTGGTGCTGAACTTAAG                         GCTGTTTGCACTGAAGCTGGAATGTTTGCTTTGAGGGAGCGGAGGGTACAC
genomic: GAGAAGATGAATGGAGCATCTGGTGCTGAACTTAAGgtatactcta ... ttgtatgcagGCTGTTTGCACTGAAGCTGGAATGTTTGCTTTGAGGGAGCGGAGGGTACAC
EST: gi|193564595|gb|FK521432.1|FK521432
EST:     TGAAGAAGATTGCCGAGAAGATGAATGGAGCATCTGGTGCTGAACTTAAG                         GCTGTTTGCACTGAAGCTGGAATGTTTGCTTTGAGGGAGCGGAGGGTACAC
genomic: TGAAGAAGATTGCCGAGAAGATGAATGGAGCATCTGGTGCTGAACTTAAGgtatactcta ... ttgtatgcagGCTGTTTGCACTGAAGCTGGAATGTTTGCTTTGAGGGAGCGGAGGGTACAC
EST: gi|192332825|gb|FK026826.1|FK026826
EST:     TGAAGAAGATTGCCGAGAAGATGAATGGAGCATCTGGTGCTGAACTTAAG                         GCTGTTTGCACTGAAGCTGGAATGTTTGCTTTGAGGGAGCGGAGGGTACAC
genomic: TGAAGAAGATTGCCGAGAAGATGAATGGAGCATCTGGTGCTGAACTTAAGgtatactcta ... ttgtatgcagGCTGTTTGCACTGAAGCTGGAATGTTTGCTTTGAGGGAGCGGAGGGTACAC
EST: gi|192332826|gb|FK026827.1|FK026827
EST:     TGAAGAAGATTGCCGAGAAGATGAATGGAGCATCTGGTGCTGAACTTAAG                         GCTGTTTGCACTGAAGCTGGAATGTTTGCTTTGAGGGAGCGGAGGGTACAC
genomic: TGAAGAAGATTGCCGAGAAGATGAATGGAGCATCTGGTGCTGAACTTAAGgtatactcta ... ttgtatgcagGCTGTTTGCACTGAAGCTGGAATGTTTGCTTTGAGGGAGCGGAGGGTACAC
EST: gi|17022699|gb|BM093733.1|BM093733
EST:     TGAAGAAGATTGCCGAGAAGATGAATGGAGCATCTGGTGCTGAACTTAAG                         GCTGTTTGCACTGAAGCTGGAATGTTTGCTTTGAGGGAGCGGAGGGTACAC
genomic: TGAAGAAGATTGCCGAGAAGATGAATGGAGCATCTGGTGCTGAACTTAAGgtatactcta ... ttgtatgcagGCTGTTTGCACTGAAGCTGGAATGTTTGCTTTGAGGGAGCGGAGGGTACAC
EST: gi|254318622|gb|GR832790.1|GR832790
EST:     TGAAGAAGATTGCCGAGAAGATGAATGGAGCATCTGGTGCTGAACTTAAG                         GCTGTTTGCACTGAAGCTGGAATGTTTGCTTTGAGGGAGCGGAGGGTACAC
genomic: TGAAGAAGATTGCCGAGAAGATGAATGGAGCATCTGGTGCTGAACTTAAGgtatactcta ... ttgtatgcagGCTGTTTGCACTGAAGCTGGAATGTTTGCTTTGAGGGAGCGGAGGGTACAC
EST: gi|193404796|gb|FK369625.1|FK369625
EST:     TGAAGAAGATTGCCGAGAAGATGAATGGAGCATCTGGTGCTGAACTTAAG                         GCTGTTTGCACTGAAGCTGGAATGTTTGCTTTGAGGGAGCGGAGGGTACAC
genomic: TGAAGAAGATTGCCGAGAAGATGAATGGAGCATCTGGTGCTGAACTTAAGgtatactcta ... ttgtatgcagGCTGTTTGCACTGAAGCTGGAATGTTTGCTTTGAGGGAGCGGAGGGTACAC
EST: gi|209727795|gb|BW658719.1|BW658719
EST:     TGAAGAAGATTGCCGAGAAGATGAATGGAGCATCTGGTGCTGAACTTAAG                         GCTGTTTGCACTGAAGCTGGAATGTTTGCTTTGAGGGAGCGGAGGGTACAC
genomic: TGAAGAAGATTGCCGAGAAGATGAATGGAGCATCTGGTGCTGAACTTAAGgtatactcta ... ttgtatgcagGCTGTTTGCACTGAAGCTGGAATGTTTGCTTTGAGGGAGCGGAGGGTACAC
EST: gi|16344411|gb|BI970006.1|BI970006
EST:     TGAAGAAGATTGCCGAGAAGATGAATGGAGCATCTGGTGCTGAACTTAAG                         GCTGTTTGCACTGAAGCTGGAATGTTTGCTTTGAGGGAGCGGAGGGTACAC
genomic: TGAAGAAGATTGCCGAGAAGATGAATGGAGCATCTGGTGCTGAACTTAAGgtatactcta ... ttgtatgcagGCTGTTTGCACTGAAGCTGGAATGTTTGCTTTGAGGGAGCGGAGGGTACAC
EST: gi|16344478|gb|BI970073.1|BI970073
EST:     TGAAGAAGATTGCCGAGAAGATGAATGGAGCATCTGGTGCTGAACTTAAG                         GCTGTTTGCACTGAAGCTGGAATGTTTGCTTTGAGGGAGCGGAGGGTACAC
genomic: TGAAGAAGATTGCCGAGAAGATGAATGGAGCATCTGGTGCTGAACTTAAGgtatactcta ... ttgtatgcagGCTGTTTGCACTGAAGCTGGAATGTTTGCTTTGAGGGAGCGGAGGGTACAC
EST: gi|254318623|gb|GR832791.1|GR832791
EST:     TGAAGAAGATTGCCGAGAAGATGAATGGAGCATCTGGTGCTGAACTTAAG                         GCTGTTTGCACTGAAGCTGGAATGTTTGCTTTGAGGGAGCGGAGGGTACAC
genomic: TGAAGAAGATTGCCGAGAAGATGAATGGAGCATCTGGTGCTGAACTTAAGgtatactcta ... ttgtatgcagGCTGTTTGCACTGAAGCTGGAATGTTTGCTTTGAGGGAGCGGAGGGTACAC
EST: gi|15589592|gb|BI674208.1|BI674208
EST:     TGAAGAAGATTGCCGAGAAGATGAATGGAGCATCTGGTGCTGAACTTAAG                         GCTGTTTGCACTGAAGCTGGAATGTTTGCTTTGAGGGAGCGGAGGGTACAC
genomic: TGAAGAAGATTGCCGAGAAGATGAATGGAGCATCTGGTGCTGAACTTAAGgtatactcta ... ttgtatgcagGCTGTTTGCACTGAAGCTGGAATGTTTGCTTTGAGGGAGCGGAGGGTACAC
EST: gi|7924399|gb|AW830425.1|AW830425
EST:     TGAAGAAGATTGCCGAGAAGATGAATGGAGCATCTGGTGCTGAACTTAAG                         GCTGTTTGCACTGAAGCTGGAATGTTTGCTTTGAGGGAGCGGAGGGTACAC
genomic: TGAAGAAGATTGCCGAGAAGATGAATGGAGCATCTGGTGCTGAACTTAAGgtatactcta ... ttgtatgcagGCTGTTTGCACTGAAGCTGGAATGTTTGCTTTGAGGGAGCGGAGGGTACAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatttaagtattttatagcctgaccaacgctcaaattttgtgccttgtatgcagGCTGTTTGCACTGAAGCTGGAATGTTTGCTTTGAGGGAGCGGAGGGTACACGTGACTCAGGAGGATTTTGAGATGGCCGTGGCGAAGGTGATGAAAAAGG
                  gcctgac  putative branch site (score: 3)
     taagtattttata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcaaatgcagagcaatttgtttgtcaatgttgttaacttaatgcaatatttaagtattttatagcctgaccaacgctcaaattttgtgccttgtatgcagGCTGTTTGCACTGAAGCTGGAATGTTTGCTTTGAGGGAGCGGAGGGTACACGTGACTCAGGAGGATTTTGAGATGGCCGTGGCGAAGGTGATGAAAAAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
-caaatgc
- - - - - - - - -tgtttgt
- - - - - - - - - - - - caatgtt
- - - - - - - - - - - - - - - - - - - -aatgcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agcctga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccaacgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tttgtgc