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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aattctgcccatttttcttctaaccctgaaaggagagtttgaactttggactcttgtgcattttcttttaaattctttgaaccttggactcttgtggcagTACTCCTATTTTTACTGGTGATGGGGAAGGTGGAAGTGGTTTTGCAGCAGCTGCTGCTGCAGCAGCAGCAGGCGGTGTATCTGGATTTGAGTTTGGTGTT

Basic information

species Glycine max
transcript GLYMA02G05250.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G05250.2 (Glycine max), 3'ss of exon 5
lower sequence: Vv04s0023g03620.t01 (Vitis vinifera), 3'ss of exon 5
-----------aattctgcccatttttcttctaaccctgaaaggagagtttg--aactttggactcttgtgcattttcttttaaattctttgaaccttggactcttgtggcagTACTCCTATTTTTACTGGTGATGGGGAAGGTGGAAGTGGTTTTGCAGCAGCTGCTGCTGCAGCAGCAGCAGGCGGTGTATCTGGATTTGAGTTTGGTGTT
           | ||       ||||| || | |  ||   | || | | |   || ||  |||  |      |  |||| || |||||||     |||    ||  ||||||||| || || || || || ||||||||||||||||||||||||||||||||||| || ||||||||||| || |||||  |||| ||||| |||||||| 
gtaactggtcaactttcattttttttttttttcattctcgcatgacattgtagaaaattatgacagtgtaatttcatcttatatattcttttg-ttttgtttcctcatggcagTACACCCATCTTCACAGGGGATGGGGAAGGTGGAAGTGGTTTTGCAGCAGCTGCCGCCGCAGCAGCAGCTGGTGGTGTGGCTGGTTTTGATTTTGGTGTG

upper sequence: GLYMA02G05250.2 (Glycine max), 3'ss of exon 5
lower sequence: PP1S14_318V6.2 (Physcomitrella patens), 3'ss of exon 5
aattctgcccatttttcttctaaccctgaaaggagagtttgaactttggactcttg-tgcattttcttttaaat------tctttgaaccttggactcttgtggcagTACTCCTATTTTTACTGGTGATGGGGAAGGTGGAAGTGGTTTTGCAGCAGCTGCTGCTGCAGCAGCAGCAGGCGGTGTATCTGGATTTGAGTTTGGTGTT
          || || |||  ||  ||||  |       ||  || | |     || |   ||||  | | |        ||| | |    |||   ||    ||||| || |||| |||||||||||||| |||||||||||||| ||||| ||||||||||| ||| | || || |  | ||    |||   ||    |||||  
-------atgatcttactttgaattctgatggtttgtactggcctcttggtaaatgatatgttttggtatcaccagtctctctctaatttatggttactccacgcagTTCTTCTATCTTTACTGGTGATGGAGAAGGTGGAAGTGGATTTGCTGCAGCTGCTGCCGCATCTGCTGCCGCGGCTGCCGTTGGTGGTGGAGGTGGTGCA
















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|193700720|gb|FK635573.1|FK635573
EST:     ATTGTTCATGTTCCATCTGGTCCAAACGCTCTTTCTGATGTACTAATAAG                         TACTCCTATTTTTACTGGTGATGGAGAAGGTGGAAGTGGTTTTGCAGCAGC
genomic: ATTGTTCATGTTCCATCTGGTCCAAACGCTCTTTCTGATGTACTAATAAGgttagtggtt ... cttgtggcagTACTCCTATTTTTACTGGTGATGGGGAAGGTGGAAGTGGTTTTGCAGCAGC
EST: gi|193672270|gb|FK617590.1|FK617590
EST:     ATTGTTCATGTTCCATCTGGTCCAAACGCTCTTTCTGATGTACTAATAAG                         TACTCCTATTTTTACTGGTGATGGAGAAGGTGGAAGTGGTTTTGCAGCAGC
genomic: ATTGTTCATGTTCCATCTGGTCCAAACGCTCTTTCTGATGTACTAATAAGgttagtggtt ... cttgtggcagTACTCCTATTTTTACTGGTGATGGGGAAGGTGGAAGTGGTTTTGCAGCAGC
EST: gi|193478287|gb|FK445760.1|FK445760
EST:     ATTGTTCATGTTCCATCTGGTCCAAACGCTCTTTCTGATGTACTAATAAG                         TACTCCTATTTTTACTGGTGATGGAGAAGGTGGAAGTGGTTTTGCAGCAGC
genomic: ATTGTTCATGTTCCATCTGGTCCAAACGCTCTTTCTGATGTACTAATAAGgttagtggtt ... cttgtggcagTACTCCTATTTTTACTGGTGATGGGGAAGGTGGAAGTGGTTTTGCAGCAGC
EST: gi|254335038|gb|GR844823.1|GR844823
EST:     ATTGTTCATGTTCCATCTGGTCCAAACGCTCTTTCTGATGTACTAATAAG                         TACTCCTATTTTTACTGGTGATGGGGAAGGTGGAAGTGGTTTTGCAGCAGC
genomic: ATTGTTCATGTTCCATCTGGTCCAAACGCTCTTTCTGATGTACTAATAAGgttagtggtt ... cttgtggcagTACTCCTATTTTTACTGGTGATGGGGAAGGTGGAAGTGGTTTTGCAGCAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggactcttgtgcattttcttttaaattctttgaaccttggactcttgtggcagTACTCCTATTTTTACTGGTGATGGGGAAGGTGGAAGTGGTTTTGCAGCAGCTGCTGCTGCAGCAGCAGCAGGCGGTGTATCTGGATTTGAGTTTGGTGTT
                                           ctcttgt  CT-rich tract
              attttcttttaaattc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aattctgcccatttttcttctaaccctgaaaggagagtttgaactttggactcttgtgcattttcttttaaattctttgaaccttggactcttgtggcagTACTCCTATTTTTACTGGTGATGGGGAAGGTGGAAGTGGTTTTGCAGCAGCTGCTGCTGCAGCAGCAGCAGGCGGTGTATCTGGATTTGAGTTTGGTGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - ctgccca
- - - - - - - - - -ctaaccc
- - - - - - - - - - - - - - - - - gagtttg
- - - - - - - - - - - - - - - - - - - - - - - - - -tcttgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccttgga