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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cattgctttgcacacttagtgttggaaaatatgatattaatgtcgtataataatacataaaagaaatgatgatttgaattggtttcctttctgtccgcagCACACTTCATTGAGCCCAGATGGGAAACTGGTTGTGATTGTTGGAGACAACCCAGAAGGGATACTAGTGGATTCTCAAACTGGAAAG

Basic information

species Glycine max
transcript GLYMA07G40060.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G40060.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os08g38880.6 (Oryza sativa), 3'ss of exon 6
--------------------------------------------------------------------------------------cattgctttgcacacttagtgttggaaaatatgatattaatgtcgtataataatacata----aaagaaatgatgatttgaattggtttcct-ttctgtcc---gcagCACACTTCATTGAGCCCAGATGGGAAACTGGTTGTGATTGTTGGAGACAACCCAGAAGGGATACTAGTGGATTCTCAAACTGGAAAG
                                                                                      ||||    |    ||| | || |     | | |||  |    |   || |  | | | |    || |   |  |||||| |  | |   | | || | | |   ||||||||| ||||||||||| ||||| ||||| ||||  |||||||| |||||||| |||||  |  |||| ||| || |  | ||||| 
gtaagcctttacttcattcatcaaactgtttatatctatatcttgttttatttattggatactcccaagtcctaatctattcgccacattcaagtcactactgaatgctttgctaaa-gattcttgcattccatgaggaaagaaagcctaatgttttattgatttaatcttgccccttgttttataccatgcagCACACATCATTGAGCCCGGATGGTAAACTTGTTGCTATTGTTGGGGACAACCCTGAAGGACTTATAGTCGATACTAATTCAGGAAAA

upper sequence: GLYMA07G40060.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv00s1206g00020.t01 (Vitis vinifera), 3'ss of exon 4
---cattgctttgcacacttagtgttggaaaatatgatattaatgtcgtataataatacataaaagaaatgatgatttgaattggtttcctttctgtccgcagCACACTTCATTGAGCCCAGATGGGAAACTGGTTGTGATTGTTGGAGACAACCCAGAAGGGATACTAGTGGATTCTCAAACTGGAAAG
    |    | |  |     |  |   |  | | ||  ||     |  |     || | ||||  | | | ||   ||   ||  | ||| ||||||   ||||| || || ||||| |||||||| || ||  |||| |||||||| ||||||||||| || ||||| ||||| ||||| |||||||||
ctagaggattgttgaggtacatggccagccagtttggcat-gtcctaatcactgaacaaataagtgtactaatatgttc--tttatgtcccttctgtttacagCATACCTCTTTGAGTCCAGATGGTAAGCTTCTTGTCATTGTTGGTGACAACCCAGATGGAATACTGGTGGACTCTCAGACTGGAAAG
















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|193536718|gb|FK490042.1|FK490042
EST:     TGGAAAGATTTCAGCTTTCCAAGCATTTCTCCTTCTCATGGCCCGTAAAT                         CACACTTCATTGAG
genomic: TGGAAAGATTTCAGCTTTCCAAGCATTTCTCCTTCTCATGGCCCGTAAATgtaagtaata ... ctgtccgcagCACACTTCATTGAG
EST: gi|207807077|gb|GD778014.1|GD778014
EST:     TGGAAAGATTTCAGCTTTCCAAGCATTTCTCCTTCTCATGGCCCGTAAAT                         CACACTTCATTGAGCCCAGATGGGAAA
genomic: TGGAAAGATTTCAGCTTTCCAAGCATTTCTCCTTCTCATGGCCCGTAAATgtaagtaata ... ctgtccgcagCACACTTCATTGAGCCCAGATGGGAAA
EST: gi|208246755|gb|GE044367.1|GE044367
EST:     TGGAAAGATTTCAGCTTTCCAAGCATTTCTCCTTCTCATGGCCCGTAAAT                         CACACTTCATTGAGCCCAGATGGGAAA
genomic: TGGAAAGATTTCAGCTTTCCAAGCATTTCTCCTTCTCATGGCCCGTAAATgtaagtaata ... ctgtccgcagCACACTTCATTGAGCCCAGATGGGAAA
EST: gi|58022343|gb|CX709084.1|CX709084
EST:     TGGAAAGATTTCAGCTTTCCAAGCATTTCTCCTTCTCATGGCCCGTAAAT                         CACACTTCATTGAGCCCAGATGGGAAACTGGTTGTGATTGTTGGAGACAAC
genomic: TGGAAAGATTTCAGCTTTCCAAGCATTTCTCCTTCTCATGGCCCGTAAATgtaagtaata ... ctgtccgcagCACACTTCATTGAGCCCAGATGGGAAACTGGTTGTGATTGTTGGAGACAAC
EST: gi|58024987|gb|CX711728.1|CX711728
EST:     TGGAAAGATTTCAGCTTTCCAAGCATTTCTCCTTCTCATGGCCCGTAAAT                         CACACTTCATTGAGCCCAGATGGGAAACTGGTTGTGATTGTTGGAGACAAC
genomic: TGGAAAGATTTCAGCTTTCCAAGCATTTCTCCTTCTCATGGCCCGTAAATgtaagtaata ... ctgtccgcagCACACTTCATTGAGCCCAGATGGGAAACTGGTTGTGATTGTTGGAGACAAC
EST: gi|193584456|gb|FK543278.1|FK543278
EST:     TGGAAAGATTTCAGCTTTCCAAGCATTTCTCCTTCTCATGGCCCGTAAAT                         CACACTTCATTGAGCCCAGATGGGAAACTGGTTGTGATTGTTGGAGACAAC
genomic: TGGAAAGATTTCAGCTTTCCAAGCATTTCTCCTTCTCATGGCCCGTAAATgtaagtaata ... ctgtccgcagCACACTTCATTGAGCCCAGATGGGAAACTGGTTGTGATTGTTGGAGACAAC
EST: gi|193689306|gb|FK632665.1|FK632665
EST:     ATTTCAGCTTTCCAAGCATTTCTCCTTCTCATGGCCCGTAAAT                         CACACTTCATTGAGCCCAGATGGGAAACTGGTTGTGATTGTTGGAGACAAC
genomic: ATTTCAGCTTTCCAAGCATTTCTCCTTCTCATGGCCCGTAAATgtaagtaata ... ctgtccgcagCACACTTCATTGAGCCCAGATGGGAAACTGGTTGTGATTGTTGGAGACAAC
EST: gi|193490569|gb|FK456394.1|FK456394
EST:     TGGAAAGATTTCAGCTTTCCAAGCATTTCTCCTTCTCATGGCCCGTAAAT                         CACACTTCATTGAGCCCAGATGGGAAACTGGTTGTGATTGTTGGAGACAAC
genomic: TGGAAAGATTTCAGCTTTCCAAGCATTTCTCCTTCTCATGGCCCGTAAATgtaagtaata ... ctgtccgcagCACACTTCATTGAGCCCAGATGGGAAACTGGTTGTGATTGTTGGAGACAAC
EST: gi|58022583|gb|CX709324.1|CX709324
EST:     TGGAAAGATTTCAGCTTTCCAAGCATTTCTCCTTCTCATGGCCCGTAAAT                         CACACTTCATTGAGCCCAGATGGGAAACTGGTTGTGATTGTTGGAGACAAC
genomic: TGGAAAGATTTCAGCTTTCCAAGCATTTCTCCTTCTCATGGCCCGTAAATgtaagtaata ... ctgtccgcagCACACTTCATTGAGCCCAGATGGGAAACTGGTTGTGATTGTTGGAGACAAC
EST: gi|193348336|gb|FK309544.1|FK309544
EST:     TGGAAAGATTTCAGCTTTCCAAGCATTTCTCCTTCTCATGGCCCGTAAAT                         CACACTTCATTGAGCCCAGATGGGAAACTGGTTGTGATTGTTGGAGACAAC
genomic: TGGAAAGATTTCAGCTTTCCAAGCATTTCTCCTTCTCATGGCCCGTAAATgtaagtaata ... ctgtccgcagCACACTTCATTGAGCCCAGATGGGAAACTGGTTGTGATTGTTGGAGACAAC
EST: gi|57575083|gb|CX548058.1|CX548058
EST:     TGGAAAGATTTCAGCTTTCCAAGCATTTCTCCTTCTCATGGCCCGTAAAT                         CACACTTCATTGAGCCCAGATGGGAAACTGGTTGTGATTGTTGGAGACAAC
genomic: TGGAAAGATTTCAGCTTTCCAAGCATTTCTCCTTCTCATGGCCCGTAAATgtaagtaata ... ctgtccgcagCACACTTCATTGAGCCCAGATGGGAAACTGGTTGTGATTGTTGGAGACAAC
EST: gi|192332288|gb|FK023937.1|FK023937
EST:     CTCCTTCTCATGGCCCGTAAAT                         CACACTTCATTGAGCCCAGATGGGAAACTGGTTGTGATTGTTGGAGACAAC
genomic: CTCCTTCTCATGGCCCGTAAATgtaagtaata ... ctgtccgcagCACACTTCATTGAGCCCAGATGGGAAACTGGTTGTGATTGTTGGAGACAAC
EST: gi|207732145|gb|GD706680.1|GD706680
EST:     TGGAAAGATTTCAGCTTTCCAAGCATTTCTCCTTCTCATGGCCCGTAAAT                         CACACTTCATTGAGCCCAGATGGGAAACTGGTTGTGATTGTTGGAGACAAC
genomic: TGGAAAGATTTCAGCTTTCCAAGCATTTCTCCTTCTCATGGCCCGTAAATgtaagtaata ... ctgtccgcagCACACTTCATTGAGCCCAGATGGGAAACTGGTTGTGATTGTTGGAGACAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tataataatacataaaagaaatgatgatttgaattggtttcctttctgtccgcagCACACTTCATTGAGCCCAGATGGGAAACTGGTTGTGATTGTTGGAGACAACCCAGAAGGGATACTAGTGGATTCTCAAACTGGAAAG
                                     tttcctttctgtccgc  CT-rich tract
     taatacataaaagaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cattgctttgcacacttagtgttggaaaatatgatattaatgtcgtataataatacataaaagaaatgatgatttgaattggtttcctttctgtccgcagCACACTTCATTGAGCCCAGATGGGAAACTGGTTGTGATTGTTGGAGACAACCCAGAAGGGATACTAGTGGATTCTCAAACTGGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA