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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgcttattcataagtttttgttttccataatttatggttcaagggcagttgatccatttttcgtattgattgcttaagatgatatcctgttggtatatagGTTTGGTCGAAAGTGATCCAGAAGGTGCACTTGCTGGTTTTGCTGAGGTAGTGCGCATGGAACAAGAGAAGGCAGAATG

Basic information

species Glycine max
transcript GLYMA03G00670.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G00670.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv08s0040g00430.t01 (Vitis vinifera), 3'ss of exon 2
tgcttattcataagtttttgttttccataatttatgg-ttcaagggcagttgatc--catttttcgtattgattgctta-----agatgatatcctgttggtatatagGTTTGGTCGAAAGTGATCCAGAAGGTGCACTTGCTGGTTTTGCTGAGGTAGTGCGCATGGAACAAGAGAAGGCAGAATG
     |||  ||| ||   ||| |   |   || |||  | | ||    ||| |   ||  ||||  ||  || | ||       ||    ||    || ||  | ||||||||| || | |||||||||||||||||||||||| |||||||| ||||| |||||||||| |||||||||||| ||
----aatttgtaaattccagttat---tgccttgtggacttatggatttttgttttgcaaatttcaaatgaatggttttcctctggagctcatttcctttgt-cacagGTTTGGTTGAGACTGATCCAGAAGGTGCACTTGCTGGCTTTGCTGAAGTAGTTCGCATGGAACCAGAGAAGGCAGAGTG
















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|298189914|gb|HO038317.1|HO038317
EST:     GCAAGAGGAACAGGATGTTGATATTGAGAATCAATATTACAATTCAAAAG                         GTTTGGTCGAAAGTGATCCAGAAGGTGCACTTGCTGGTTTTGCTGAGGTAG
genomic: GCAAGAGGAACAGGATGTTGATATTGAGAATCAATATTACAATTCAAAAGgtatttccct ... tggtatatagGTTTGGTCGAAAGTGATCCAGAAGGTGCACTTGCTGGTTTTGCTGAGGTAG
EST: gi|151398925|gb|EV268796.1|EV268796
EST:     GCAAGAGGAACAGGATGTTGATATTGAGAATCAATATTACAATTCAAAAG                         GTTTGGTCGAAAGTGATCCAGAAGGTGCACTTGCTGGTTTTACTGAGGTAG
genomic: GCAAGAGGAACAGGATGTTGATATTGAGAATCAATATTACAATTCAAAAGgtatttccct ... tggtatatagGTTTGGTCGAAAGTGATCCAGAAGGTGCACTTGCTGGTTTTGCTGAGGTAG
EST: gi|192307527|gb|FK002045.1|FK002045
EST:     GCAAGAGGAACAGGATGTTGATATTGAGAATCAATATTACAATTCAAAAG                         GTTTGGTCGAAAGTGATCCAGAAGGTGCACTTGCTGGTTTTGCTGAGGTAG
genomic: GCAAGAGGAACAGGATGTTGATATTGAGAATCAATATTACAATTCAAAAGgtatttccct ... tggtatatagGTTTGGTCGAAAGTGATCCAGAAGGTGCACTTGCTGGTTTTGCTGAGGTAG
EST: gi|298189905|gb|HO038308.1|HO038308
EST:     GCAAGAGGAACAGGATGTTGATATTGAGAATCAATATTACAATTCATAAG                         GTTTGGTCGAAAGTGATCCAAAAAGTGCACTTGCTGGTTTTGCTGAGGTAG
genomic: GCAAGAGGAACAGGATGTTGATATTGAGAATCAATATTACAATTCAAAAGgtatttccct ... tggtatatagGTTTGGTCGAAAGTGATCCAGAAGGTGCACTTGCTGGTTTTGCTGAGGTAG
EST: gi|151398223|gb|EV268101.1|EV268101
EST:     GCAAGAGGAACAGGATGTTGATATTGAGAATCAATATTACAATTCAAAAG                         GTTTGATCGAAAGTGATCCAGAAGGTGCACTTGCTGGTTTTGCTGAGGTAG
genomic: GCAAGAGGAACAGGATGTTGATATTGAGAATCAATATTACAATTCAAAAGgtatttccct ... tggtatatagGTTTGGTCGAAAGTGATCCAGAAGGTGCACTTGCTGGTTTTGCTGAGGTAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagttgatccatttttcgtattgattgcttaagatgatatcctgttggtatatagGTTTGGTCGAAAGTGATCCAGAAGGTGCACTTGCTGGTTTTGCTGAGGTAGTGCGCATGGAACAAGAGAAGGCAGAATG
                  tattgat  putative branch site (score: 3)
                                       tcctgtt  putative PPT
                  tattgatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgcttattcataagtttttgttttccataatttatggttcaagggcagttgatccatttttcgtattgattgcttaagatgatatcctgttggtatatagGTTTGGTCGAAAGTGATCCAGAAGGTGCACTTGCTGGTTTTGCTGAGGTAGTGCGCATGGAACAAGAGAAGGCAGAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
tgcttat
- - - - - - - - - - - - - - - - - - - - - - gcagttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgattgc