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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggatatattttattctttgatggttccctgactgttgtagttactgaataaacttcattccatgcagGCTTTCAAAATAATTGTGACTGATCCTGATACTGTTTTAAGTACTCTCACTCGTGAAGTTAAGGAAGTTGGCCCTGACGGGCAAGAG

Basic information

species Glycine max
transcript GLYMA11G35600.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G35600.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv13s0067g01710.t01 (Vitis vinifera), 3'ss of exon 2
-------------------------------------------------------------------gtaaggatatattttattctttg------atggttcc--ctgactgttgtagttactgaataaacttcattccatgcagGCTTTCAAAATAATTGTGACTGATCCTGATACTGTTTTAAGTACTCTCACTCGTGAAGTTAAGGAAGTTGGCCCTGACGGGCAAGAG
                                                                   ||  || |   || | ||||||        |  || |  || |      |  || ||   ||   ||   |   ||||||| || || ||||||||||||||||||||| | ||| | | | | ||||||||||||||||| |||||||||||||| || || |||
gtgagattatttatcactttattggaggtttttttatgtttttttttttgtgggggcggggggatgggtgggggtcctttcttttctttttctcttgtatttacagctaagaaccttttttcctttttaccttttggttgttgcagGCATTTAAGATAATTGTGACTGATCCTGATTCAGTTCTGAATTCCCTCACTCGTGAAGTTAAAGAAGTTGGCCCTGATGGACAGGAG
















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|6070400|gb|AW099787.1|AW099787
EST:     ATATTCACATTGGATGGCCTTTGTATCGCAAATATGGTCATGCTTTTGAG                         GCTCTCAAAATAATTGTGACTGATCCTGATACTGTTTTAAGTACTCTC
genomic: ATATTCACATTGGATGGCCTTTGTATCGCAAATATGGTCATGCTTTTGAGgtaaggatat ... ttccatgcagGCTTTCAAAATAATTGTGACTGATCCTGATACTGTTTTAAGTACTCTC
EST: gi|193623725|gb|FK575537.1|FK575537
EST:     ATATTCACATTGGATGGCCTTTGTATCGCAAATATGGTCATGCTTTTGAG                         GCTTTCAAAATAATTGTGACTGATCCTGATACTGTTTTAAGTACTCTC
genomic: ATATTCACATTGGATGGCCTTTGTATCGCAAATATGGTCATGCTTTTGAGgtaaggatat ... ttccatgcagGCTTTCAAAATAATTGTGACTGATCCTGATACTGTTTTAAGTACTCTC
EST: gi|208137298|gb|GD934602.1|GD934602
EST:     AATATGGTCATGCTTTTGAG                         GCTTTCAAAATAATTGTGACTGATCCTGATACTGTTTTAAGTACTCTCACT
genomic: AATATGGTCATGCTTTTGAGgtaaggatat ... ttccatgcagGCTTTCAAAATAATTGTGACTGATCCTGATACTGTTTTAAGTACTCTCACT
EST: gi|151396190|gb|EV266067.1|EV266067
EST:     ATATTCACATTGGATGGTCTTTGTATCGCAAATATGGTCATGCTTTTGAG                         GCTTTCAAAATAATTGTGACTGATCCTGATACTGTTTTAAGTACTCTCACT
genomic: ATATTCACATTGGATGGCCTTTGTATCGCAAATATGGTCATGCTTTTGAGgtaaggatat ... ttccatgcagGCTTTCAAAATAATTGTGACTGATCCTGATACTGTTTTAAGTACTCTCACT
EST: gi|7284298|gb|AW596892.1|AW596892
EST:     ATATTCACATTGGATGGCCTTTGTATCGCAAATATGGTCATGCTTTTGAG                         GCTTTCAAAATAATTGTGACTGATCCTGATACTGTTTTAAGTACTCTC
genomic: ATATTCACATTGGATGGCCTTTGTATCGCAAATATGGTCATGCTTTTGAGgtaaggatat ... ttccatgcagGCTTTCAAAATAATTGTGACTGATCCTGATACTGTTTTAAGTACTCTC
EST: gi|298190105|gb|HO032226.1|HO032226
EST:     ATATTCACATTGGATGGCCTTTGTATCGCAAATATGGTCATGCTTTTGAG                         GCTTTCAAAATAATTGTGACTGATCCTGATACTGTTTTAAGTACTCTCACT
genomic: ATATTCACATTGGATGGCCTTTGTATCGCAAATATGGTCATGCTTTTGAGgtaaggatat ... ttccatgcagGCTTTCAAAATAATTGTGACTGATCCTGATACTGTTTTAAGTACTCTCACT
EST: gi|254323854|gb|GR840387.1|GR840387
EST:     ATATTCACATTGGATGGCCTTTGTATCGCAAATATGGTCATGCTTTTGAG                         GCTTTCAAAATAATTGTGACTGATCCTGATACTGTTTTAAGTACTCTCACT
genomic: ATATTCACATTGGATGGCCTTTGTATCGCAAATATGGTCATGCTTTTGAGgtaaggatat ... ttccatgcagGCTTTCAAAATAATTGTGACTGATCCTGATACTGTTTTAAGTACTCTCACT
EST: gi|192306825|gb|FK002995.1|FK002995
EST:     ATATTCACATTGGATGGCCTTTGTATCGCAAATATGGTCATGCTTTTGAG                         GCTTTCAAAATAATTGTGACTGATCCTGATACTGTTTTAAGTACTCTCACT
genomic: ATATTCACATTGGATGGCCTTTGTATCGCAAATATGGTCATGCTTTTGAGgtaaggatat ... ttccatgcagGCTTTCAAAATAATTGTGACTGATCCTGATACTGTTTTAAGTACTCTCACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctttgatggttccctgactgttgtagttactgaataaacttcattccatgcagGCTTTCAAAATAATTGTGACTGATCCTGATACTGTTTTAAGTACTCTCACTCGTGAAGTTAAGGAAGTTGGCCCTGACGGGCAAGAG
             ccctgac  putative branch site (score: 3)
                                        cttcattcc  putative PPT
                                  aataaactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaggatatattttattctttgatggttccctgactgttgtagttactgaataaacttcattccatgcagGCTTTCAAAATAATTGTGACTGATCCTGATACTGTTTTAAGTACTCTCACTCGTGAAGTTAAGGAAGTTGGCCCTGACGGGCAAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA