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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtcattggaatttttacttattttacatttataatgaagtagataagtcacgtgtcactaatttgtaatttcactgcaagGTTGTTGAACTTCCCATGCTTCATCCAGAGAAATTTGTCAAGCTTGGGATTGATCCTCCAAAGGGTGTTCTTTGTTATGGCCCCCCAGGAACTGGGAAAA

Basic information

species Glycine max
transcript GLYMA07G05220.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G05220.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os02g54340.1 (Oryza sativa), 3'ss of exon 6
-------------------------------------gtaag-tcattggaatttttacttattttacatttataatgaagtagataagtcacgtgtcactaatttgtaatt--tcactgcaagGTTGTTGAACTTCCCATGCTTCATCCAGAGAAATTTGTCAAGCTTGGGATTGATCCTCCAAAGGGTGTTCTTTGTTATGGCCCCCCAGGAACTGGGAAAA
                                     | ||  |   |     || | | |        ||  |  || | |   |  |  |  |     |   |  | |||  |   |   |||||||||| |||||||||||||| |||||||| |||||||||||||| ||||||||||||||||| || ||||| |||||||| || |||||||| ||||
gtatactaatcttttttcagttcatatcccttgtcgtgcaaacttgctcatccttgtgcatcaggctagttagttttggacttattttgctatttactgtttgctaattattgtttgttcatagGTTGTTGAGCTTCCCATGCTTCACCCAGAGAAGTTTGTCAAGCTTGGTATTGATCCTCCAAAGGGGGTCCTTTGCTATGGCCCTCCTGGAACTGGCAAAA

upper sequence: GLYMA07G05220.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G181359_T01 (Zea mays), 3'ss of exon 6
--------------gtaagtcattggaatttttacttatttta-catttataatgaagtagataagtcacgtgtcactaatttgtaatttcactgcaagGTTGTTGAACTTCCCATGCTTCATCCAGAGAAATTTGTCAAGCTTGGGATTGATCCTCCAAAGGGTGTTCTTTGTTATGGCCCCCCAGGAACTGGGAAAA
               |   || |  ||  |   || || |  | |||   || | | |    ||  |    |         |||||  ||   |||| ||||||||||||||| |||||||| ||||| || |||||||||||||| |||||||||||||| || || ||||| |||||||| || || ||||| || |
gtatgtgatccttttttcttcttgtgagctggcacatactgcatcatagttagttacgggactagtttggttactctgtgcttgtaccttttttgca-gGTTGTTGAACTTCCTATGCTTCACCCAGAAAAGTTTGTCAAGCTTGGTATTGATCCTCCAAAAGGCGTCCTTTGCTATGGCCCACCTGGCACTGGCAAGA

upper sequence: GLYMA07G05220.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G110185_T04 (Zea mays), 3'ss of exon 5
----------gtaagtcattg-gaatttttacttatttta-catttataatgaagtagataagtcacgtgtcactaatttgtaatttcactgcaagGTTGTTGAACTTCCCATGCTTCATCCAGAGAAATTTGTCAAGCTTGGGATTGATCCTCCAAAGGGTGTTCTTTGTTATGGCCCCCCAGGAACTGGGAAAA
           |   || ||| ||  |   |  || |  | ||    || ||| | |  ||  |    |   | |   | ||| | |   |||| ||||||||||||||| |||||||| ||||| || |||||||||||||| ||||| ||||| || ||||| ||||| |||||||| || || ||||| || |
gtatgtggtccttcttccttgtgagctgggaaatactgcatcacagttagtgatggatctattttgtttactatttgct-gtactatttttgca-gGTTGTTGAACTTCCTATGCTTCACCCAGAAAAGTTTGTCAAGCTTGGTATTGACCCTCCGAAAGGTGTCCTTTGCTATGGCCCACCTGGTACTGGCAAGA

upper sequence: GLYMA07G05220.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv09s0002g00170.t01 (Vitis vinifera), 3'ss of exon 6
----------------------------------------------------gtaagtcattgg-aatttttacttattttacatttataatgaagtagataagtcacgtgtc-actaat--ttgtaatttcactgcaagGTTGTTGAACTTCCCATGCTTCATCCAGAGAAATTTGTCAAGCTTGGGATTGATCCTCCAAAGGGTGTTCTTTGTTATGGCCCCCCAGGAACTGGGAAAA
                                                        ||| ||    |||   |  || |||    |  |    |  |   |   || | |||   || ||  || ||| ||     | |||| ||||| || || ||||| || || ||||| ||||| |||||||| ||||||||||| ||||||||||| || ||||| || || ||||| || ||||
gtgtgtatattctttttacatttttttttgtcagatcatatatgcatttacaccgtgtctttcttgattaacagctagtttttgatcctgtgaacttctgtccttctcttgtttgctgatatttataactttggctctagGTGGTTGAGCTCCCTATGCTCCACCCTGAGAAGTTTGTGAAGCTTGGAATTGATCCTCCTAAGGGTGTTCTCTGCTATGGTCCTCCTGGAACCGGTAAAA

upper sequence: GLYMA07G05220.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ13722 (Selaginella moellendorffii), 3'ss of exon 6
gtaagtcattggaatttttacttattttacatttataatgaagtagataagtcacgtgtcactaatttgtaatttcac-tgca-agGTTGTTGAACTTCCCATGCTTCATCCAGAGAAATTTGTCAAGCTTGGGATTGATCCTCCAAAGGGTGTTCTTTGTTATGGCCCCCCAGGAACTGGGAAAA
                           ||  |  |  ||     |  |   |  |  |||    || |  | ||| ||    | ||||||| || ||||| ||||| ||||| ||||| ||| |||||||||| || |||||||| || || |||||||| || ||||| || |||||||||||||
--------------------------gtaactacaccattttacatttggtttcctcgtcgacgatcttaacttttacgcatatagGTTGTAGAGCTTCCTATGCTCCATCCTGAGAAGTTTATCAAGCTTGGAATCGATCCTCCCAAAGGAGTTCTTTGCTACGGCCCTCCGGGAACTGGGAAAA

upper sequence: GLYMA07G05220.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ29161 (Selaginella moellendorffii), 3'ss of exon 6
gtaagtcattggaatttttacttattttacatttataatgaagtagataagtcacgtgtcactaatttgtaatttcac-tgca-agGTTGTTGAACTTCCCATGCTTCATCCAGAGAAATTTGTCAAGCTTGGGATTGATCCTCCAAAGGGTGTTCTTTGTTATGGCCCCCCAGGAACTGGGAAAA
                           ||  |  |  ||     |  |   |  |  |||    || |  | ||| ||    | ||||||| || ||||| ||||| || || || || ||| |||||||||| || |||||||| || || |||||||| || ||||| || |||||||||||||
--------------------------gtaactacaccattttacatttggttttctcgtcgacgatcttaacttttacgcatatagGTTGTAGAGCTTCCTATGCTCCACCCTGAAAAGTTTATCAAGCTTGGAATCGATCCTCCCAAAGGAGTTCTTTGCTACGGCCCTCCGGGAACTGGGAAAA

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|207733086|gb|GD710938.1|GD710938
EST:     CATATAATGATGTTGGCGGTTGTAAGGAGCAGATTGAAAAGNTGCGAGAA                         GTTGTTGAACTT
genomic: CATATAATGATGTTGGCGGTTGTAAGGAGCAGATTGAAAAGATGCGAGAAgtaagtcatt ... tcactgcaagGTTGTTGAACTT
EST: gi|19937368|gb|BQ081261.1|BQ081261
EST:     GCAGATTGAAAAGATGCGAGAA                         GTTGTTGAACTTCCCATGCTTCATCCAGAGAAATTTGTCAAGCTTGGGATT
genomic: GCAGATTGAAAAGATGCGAGAAgtaagtcatt ... tcactgcaagGTTGTTGAACTTCCCATGCTTCATCCAGAGAAATTTGTCAAGCTTGGGATT
EST: gi|192302201|gb|FG997281.1|FG997281
EST:     CATATAATGATGTTGGCGGTTGTAAGGAGCAGATTGAAAAGATGCGAGAA                         GTTGTTGAACTTCCCATGCTTCATCCAGAGAAATTTGTCAAGCTTGGGATT
genomic: CATATAATGATGTTGGCGGTTGTAAGGAGCAGATTGAAAAGATGCGAGAAgtaagtcatt ... tcactgcaagGTTGTTGAACTTCCCATGCTTCATCCAGAGAAATTTGTCAAGCTTGGGATT
EST: gi|16277271|gb|BI942294.1|BI942294
EST:     CATATAATGATGTTGGCGGTTGTAAGGAGCAGATTGAAAAGATGCGAGAA                         GTTGTTGAACTTCCCATGCTTCATCCAGAGAAATTTGTCAAGCTTGGGATT
genomic: CATATAATGATGTTGGCGGTTGTAAGGAGCAGATTGAAAAGATGCGAGAAgtaagtcatt ... tcactgcaagGTTGTTGAACTTCCCATGCTTCATCCAGAGAAATTTGTCAAGCTTGGGATT
EST: gi|57575942|gb|CX548913.1|CX548913
EST:     TTGTAAGGAGCAGATTGAAAAGATGCGAGAA                         GTTGTTG-ACTTTCCCATGTTTCATCCAGAGAAATTGGTCAAGCTTGGGAT
genomic: TTGTAAGGAGCAGATTGAAAAGATGCGAGAAgtaagtcatt ... tcactgcaagGTTGTTGAAC-TTCCCATGCTTCATCCAGAGAAATTTGTCAAGCTTGGGAT
EST: gi|208236095|gb|GE030659.1|GE030659
EST:     CATATAATGATGTTGGCGGTTGTAAGGAGCAGATTGAAAAGATGCGAGAA                         GTTGTTGAACTTCCCATGCTTCATCCAGAGAAATTTGTCAAG
genomic: CATATAATGATGTTGGCGGTTGTAAGGAGCAGATTGAAAAGATGCGAGAAgtaagtcatt ... tcactgcaagGTTGTTGAACTTCCCATGCTTCATCCAGAGAAATTTGTCAAG
EST: gi|16346898|gb|BI972493.1|BI972493
EST:     CATATAATGATGTTGGCGGTTGTAAGGAGCAGATTGAAAAGATGCGAGAA                         GTTGTTGAACTTCCCATGCTTCATCCAGAGAAATTTGTCAAGCTTGGGATT
genomic: CATATAATGATGTTGGCGGTTGTAAGGAGCAGATTGAAAAGATGCGAGAAgtaagtcatt ... tcactgcaagGTTGTTGAACTTCCCATGCTTCATCCAGAGAAATTTGTCAAGCTTGGGATT
EST: gi|58024535|gb|CX711276.1|CX711276
EST:     CATATAATGATGTTGGCGGTTGTAAGGAGCAGATTGAAAAGATGCGAGAA                         GTTGTTGAACTTCCCATGCTTCATCCAGAGAAATTTGTCAAGCTTGGGATT
genomic: CATATAATGATGTTGGCGGTTGTAAGGAGCAGATTGAAAAGATGCGAGAAgtaagtcatt ... tcactgcaagGTTGTTGAACTTCCCATGCTTCATCCAGAGAAATTTGTCAAGCTTGGGATT
EST: gi|193407658|gb|FK374476.1|FK374476
EST:     CATATAATGATGTTGGCGGTTGTAAGGAGCAGATTGAAAAGATGCGAGAA                         GTTGTTGAACTTCCCATGCTTCATCCAGAGAAATTTGTCAAGCTTGGGATT
genomic: CATATAATGATGTTGGCGGTTGTAAGGAGCAGATTGAAAAGATGCGAGAAgtaagtcatt ... tcactgcaagGTTGTTGAACTTCCCATGCTTCATCCAGAGAAATTTGTCAAGCTTGGGATT
EST: gi|209717333|gb|BW659036.1|BW659036
EST:     CATATAATGATGTTGGCGGTTGTAAGGAGCAGATTGAAAAGATGCGAGAA                         GTTGTTGAACTTCCCATGCTTCATCCAGAGAAATTTGTCAAGCTTGGGATT
genomic: CATATAATGATGTTGGCGGTTGTAAGGAGCAGATTGAAAAGATGCGAGAAgtaagtcatt ... tcactgcaagGTTGTTGAACTTCCCATGCTTCATCCAGAGAAATTTGTCAAGCTTGGGATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catttataatgaagtagataagtcacgtgtcactaatttgtaatttcactgcaagGTTGTTGAACTTCCCATGCTTCATCCAGAGAAATTTGTCAAGCTTGGGATTGATCCTCCAAAGGGTGTTCTTTGTTATGGCCCCCCAGGAACTGGGAAAA
                              cactaat  putative branch site (score: 2)
                                           tttcact  putative PPT
                               actaatttgtaattt  TA-rich tract