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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catttcattaattcaaacattgactagattttattgttcgcgtaattgttgcttgtttcacaaatgggatttccattgattgttgtctgtgaattctcagTAAGGGTTCTAAGTCTGGTGCTTCGATGAAGTGTGCTGGTTGTCAAGGAACTGGTATGAAGGTTTCTATAAGACATCTTGGCCCGTCCATGATTCAGCAG

Basic information

species Glycine max
transcript GLYMA11G17930.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G17930.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os03g57340.1 (Oryza sativa), 3'ss of exon 3
-catttcattaattcaaacattgactagattttattgttcgcgtaattgttgcttgtttcacaaatgggatttccattgattgttgtctgtgaattct-cagTAAGGGTTCTAAGTCTGGTGCTTCGATGAAGTGTGCTGGTTGTCAAGGAACTGGTATGAAGGTTTCTATAAGACATCTTGGCCCGTCCATGATTCAGCAG
  || |||| |  |    | ||   | | |  ||    | || |||        ||||| || | |  ||| ||     | |||| | ||   ||  | ||| ||||| || || ||||||||||| ||||||||  |||||||||||||  |||||||||||||    ||  | ||  | || ||    ||||||||||| 
gtatgtcatcagctt---ccttttgtgggtcctaaatattgcataaac------tgtttgactattctgatatctcac-actgttctgtgctcatcttgcagCAAGGGCTCGAAATCTGGTGCTTCCATGAAGTGCTCTGGTTGTCAAGGTTCTGGTATGAAGGTCCAAATTCGCCAGTTGGGGCCAGGAATGATTCAGCAA

upper sequence: GLYMA11G17930.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G028218_T01 (Zea mays), 3'ss of exon 3
catttcattaattcaaacattgactagattttattgttcgcgtaattgttgcttgtttcacaaatgggatttcca----ttgattgt-tgtctgtgaattctcagTAAGGGTTCTAAGTCTGGTGCTTCGATGAAGTGTGCTGGTTGTCAAGGAACTGGTATGAAGGTTTCTATAAGACATCTTGGCCCGTCCATGATTCAGCAG
   |   | |  | || |    ||   |   |        |  ||||      || ||   | ||  ||||   |     ||||||| ||  ||| |     |||||||||||| |||||||| ||||||  || ||||||||||||||||||  ||||  | |||||    ||  | ||  | || ||    ||||||||||| 
--gtaggtcatctgaatccacaacacaaggatgccaaaaactcaattacaatatgctttctatattagattcttaggatctgattgtgtgcttgtaatcgtgcagTAAGGGTTCCAAGTCTGGAGCTTCGTCGAGGTGTGCTGGTTGTCAAGGTTCTGGCTTCAAGGTCCAAATCCGGCAGTTGGGACCTGGAATGATTCAGCAA

upper sequence: GLYMA11G17930.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G029079_T01 (Zea mays), 3'ss of exon 5
catttcattaattcaaacattgactagattttattgttcgcgtaattgttgcttgtttcacaaatgggatttcca----ttgattgt-tgtctgtgaattctcagTAAGGGTTCTAAGTCTGGTGCTTCGATGAAGTGTGCTGGTTGTCAAGGAACTGGTATGAAGGTTTCTATAAGACATCTTGGCCCGTCCATGATTCAGCAG
     | | ||||       ||  |  |   ||       |  ||||   |  || ||   | ||  ||||   |     | ||||| ||  ||| |     |||||||||||| |||||||| ||||||  || ||||||||||||||||||  ||||  | |||||    ||  | ||  | || ||    ||||||||||| 
-----cttgaatttgccttctggttcaaggataccaaaaactcaattacagtatgctttctatattagattcttaggatctcattgtgtgcttgtaatcatgcagTAAGGGTTCCAAGTCTGGAGCTTCGTCGAGGTGTGCTGGTTGTCAAGGTTCTGGCTTCAAGGTCCAAATCCGGCAGTTGGGACCTGGAATGATTCAGCAA

upper sequence: GLYMA11G17930.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G434839_T01 (Zea mays), 3'ss of exon 10
catttcattaattcaaacattgactagattttattgttcgcgtaattgttgcttgtttcacaaatgggatttcca----ttgattgt-tgtctgtgaattctcagTAAGGGTTCTAAGTCTGGTGCTTCGATGAAGTGTGCTGGTTGTCAAGGAACTGGTATGAAGGTTTCTATAAGACATCTTGGCCCGTCCATGATTCAGCAG
       | |  | || |    ||   |   |        |  ||||   |  || ||   | ||  ||||   |     | ||||| ||  ||| |     |||||||||||| |||||||| ||||||  || |||||||||||||||| |  ||||  | |||||    ||  | ||  | || ||    ||||||||||| 
-----ggtcatctgaatccacaacacaaggatgccaaaaactcaattacagtatgctttctatattagattcttaggatctcattgtgtgcttgtaatcgtgcagTAAGGGTTCCAAGTCTGGAGCTTCGTCGAGGTGTGCTGGTTGTCAATGTTCTGGCTTCAAGGTCCAAATCCGGCAGTTGGGACCTGGAATGATTCAGCAA

upper sequence: GLYMA11G17930.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv06s0080g01230.t01 (Vitis vinifera), 3'ss of exon 3
catttcattaattcaaacattgact-agattttattgttcgcgtaattgttgcttgtttcacaaatggg-atttccattgattgttgtc-tgtgaattct--cagTAAGGGTTCTAAGTCTGGTGCTTCGATGAAGTGTGCTGGTTGTCAAGGAACTGGTATGAAGGTTTCTATAAGACATCTTGGCCCGTCCATGATTCAGCAG
    | | ||||||    ||  ||| | |||||||  |      | ||  |  || || | |   |  |   ||  || |   ||| || ||| ||   |  ||| || || || || ||||| || || || ||||||  ||||||||||||  |||| ||||||||||| || ||||| |||||||| || ||||||||||||
---gtgagtaattctgtgatgcactcaaattttataatgatttcatttactttttattgccctgctatgtgcttatatgggaggttatcatgtaaacaatgacagAAAAGGGTCAAAATCTGGAGCATCAATAAAGTGTAATGGTTGTCAAGGGTCTGGGATGAAGGTTTCAATTAGACAACTTGGCCCCTCTATGATTCAGCAG

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|207842272|gb|GD817628.1|GD817628
EST:     TCTAAGAAGCTCTCCCTCTCCAGAAATGTCATATGCTCCAAGTGCACTGG                         TAAGGGTTCTAAGTCTGGTGCTTCGATAGAAAGTGTGCTGGT
genomic: TCTAAGAAGCTCTCCCTCTCCAGAAATGTCATATGCTCCAAGTGCACTGGgtgagtgaat ... gaattctcagTAAGGGTTCTAAGTCTGGTGCTTCGAT-GAA-GTGTGCTGGT
EST: gi|38192432|gb|CF921638.1|CF921638
EST:     TCTAAGAAGCTCTCCCTCTCCAGAAATGTCATATGCTCCAAGTGCACTGG                         TAAGGGTTCTAAGTCTGGTGCTTCGATGAAGTGTGCTGGTTGTCAAGGAAC
genomic: TCTAAGAAGCTCTCCCTCTCCAGAAATGTCATATGCTCCAAGTGCACTGGgtgagtgaat ... gaattctcagTAAGGGTTCTAAGTCTGGTGCTTCGATGAAGTGTGCTGGTTGTCAAGGAAC
EST: gi|254346520|gb|GR856242.1|GR856242
EST:     TCTAAGAAGCTCTCCCTCTCCAGAAATGTCATATGCTCCAAGTGCACTGG                         TAAGGGTTCTAAGTCTGGTGCTTCGATGAAGTGTGCTGGTTGTCAAGGAAC
genomic: TCTAAGAAGCTCTCCCTCTCCAGAAATGTCATATGCTCCAAGTGCACTGGgtgagtgaat ... gaattctcagTAAGGGTTCTAAGTCTGGTGCTTCGATGAAGTGTGCTGGTTGTCAAGGAAC
EST: gi|208039461|gb|GD836243.1|GD836243
EST:     TCTAAGAAGCTCTCCCTCTCCAGAAATGTCATATGCTCCAAGTGCACTGG                         TAAGGGTTCTAAGTCTGGTGCTTCGATGAAGTGTGCTGGTTGTCAAGGAAC
genomic: TCTAAGAAGCTCTCCCTCTCCAGAAATGTCATATGCTCCAAGTGCACTGGgtgagtgaat ... gaattctcagTAAGGGTTCTAAGTCTGGTGCTTCGATGAAGTGTGCTGGTTGTCAAGGAAC
EST: gi|16106325|gb|BI894065.1|BI894065
EST:     TCTAAGAAGCTCTCCCTCTCCAGAAATGTCATATGCTCCAAGTGCACTGG                         TAAGGGTTCTAAGTCTGGTGCTTCGATGAAGTGTGCTGGTTGTCAAGGAAC
genomic: TCTAAGAAGCTCTCCCTCTCCAGAAATGTCATATGCTCCAAGTGCACTGGgtgagtgaat ... gaattctcagTAAGGGTTCTAAGTCTGGTGCTTCGATGAAGTGTGCTGGTTGTCAAGGAAC
EST: gi|209696486|gb|BW672828.1|BW672828
EST:     TCTAAGAAGCTCTCCCTCTCCAGAAATGTCATATGCTCCAAGTGCACTGG                         TAAGGGTTCTAAGTCTGGTGCTTCGATGAAGTGTGCTGGTTGTCAAGGAAC
genomic: TCTAAGAAGCTCTCCCTCTCCAGAAATGTCATATGCTCCAAGTGCACTGGgtgagtgaat ... gaattctcagTAAGGGTTCTAAGTCTGGTGCTTCGATGAAGTGTGCTGGTTGTCAAGGAAC
EST: gi|213600517|gb|DB960065.1|DB960065
EST:     TCTAAGAAGCTCTCCCTCTCCAGAAATGTCATATGCTCCAAGTGCACTGG                         TAAGGGTTCTAAGTCTGGTGCTTCGATGAAGTGTGCTGGTTGTCAAGGAA
genomic: TCTAAGAAGCTCTCCCTCTCCAGAAATGTCATATGCTCCAAGTGCACTGGgtgagtgaat ... gaattctcagTAAGGGTTCTAAGTCTGGTGCTTCGATGAAGTGTGCTGGTTGTCAAGGAA
EST: gi|209714486|gb|BW684862.1|BW684862
EST:     TCTAAGAAGCTCTCCCTCTCCAGAAATGTCATATGCTCCAAGTGCACTGG                         TAAGGGTTCTAAGTCTGGTGCTTCGATGAAGTGTGCTGGT
genomic: TCTAAGAAGCTCTCCCTCTCCAGAAATGTCATATGCTCCAAGTGCACTGGgtgagtgaat ... gaattctcagTAAGGGTTCTAAGTCTGGTGCTTCGATGAAGTGTGCTGGT
EST: gi|209723723|gb|BW662591.1|BW662591
EST:     TCTAAGAAGCTCTCCCTCTCCAGAAATGTCATATGCTCCAAGTGCACTGG                         TAAGGGTTCTAAGTCTGGTGCTTCGATGAAGTGTGCTGGTT
genomic: TCTAAGAAGCTCTCCCTCTCCAGAAATGTCATATGCTCCAAGTGCACTGGgtgagtgaat ... gaattctcagTAAGGGTTCTAAGTCTGGTGCTTCGATGAAGTGTGCTGGTT
EST: gi|208257655|gb|GE055306.1|GE055306
EST:     TCTAAGAAGCTCTCCCTCTCCAGAAATGTCATATGCTCCAAGTGCACTGG                         TAAGGGTTCTAAGTCTGGTGCTTCGATGAAGTGTGCTGGTTGTCAAGGAAC
genomic: TCTAAGAAGCTCTCCCTCTCCAGAAATGTCATATGCTCCAAGTGCACTGGgtgagtgaat ... gaattctcagTAAGGGTTCTAAGTCTGGTGCTTCGATGAAGTGTGCTGGTTGTCAAGGAAC
EST: gi|213619545|gb|DB957246.1|DB957246
EST:     TCTAAGAAGCTCTCCCTCTCCAGAAATGTCATATGCTCCAAGTGCACTGG                         TAAGGGTTCTAAGTCTG
genomic: TCTAAGAAGCTCTCCCTCTCCAGAAATGTCATATGCTCCAAGTGCACTGGgtgagtgaat ... gaattctcagTAAGGGTTCTAAGTCTG
EST: gi|193420309|gb|FK392167.1|FK392167
EST:     TCTAAGAAGCTCTCCCTCTCCAGAAATGTCATATGCTCCAAGTGCACTGG                         TAAGGGTTCTAAGTCTGGTGCTTCGATGAAGTGTGCTGGTTGTCAAGGAAC
genomic: TCTAAGAAGCTCTCCCTCTCCAGAAATGTCATATGCTCCAAGTGCACTGGgtgagtgaat ... gaattctcagTAAGGGTTCTAAGTCTGGTGCTTCGATGAAGTGTGCTGGTTGTCAAGGAAC
EST: gi|254324916|gb|GR834341.1|GR834341
EST:     TCTAAGAAGCTCTCCCTCTCCAGAAATGTCATATGCTCCAAGTGCACTGG                         TAAGGGTTCTAAGTCTGGTGCTTCGATGAAGTGTGCTGGTTGTCAAGGAAC
genomic: TCTAAGAAGCTCTCCCTCTCCAGAAATGTCATATGCTCCAAGTGCACTGGgtgagtgaat ... gaattctcagTAAGGGTTCTAAGTCTGGTGCTTCGATGAAGTGTGCTGGTTGTCAAGGAAC
EST: gi|17963719|gb|BM270465.1|BM270465
EST:     TCTAAGAAGCTCTCCCTCTCCAGAAATGTCATATGCTCCAAGTGCACTGG                         TAAGGGTTCTAAGTCTGGTGCTTCGATGAAGTGTGCTGTTTGTCAAGGAAC
genomic: TCTAAGAAGCTCTCCCTCTCCAGAAATGTCATATGCTCCAAGTGCACTGGgtgagtgaat ... gaattctcagTAAGGGTTCTAAGTCTGGTGCTTCGATGAAGTGTGCTGGTTGTCAAGGAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgttgcttgtttcacaaatgggatttccattgattgttgtctgtgaattctcagTAAGGGTTCTAAGTCTGGTGCTTCGATGAAGTGTGCTGGTTGTCAAGGAACTGGTATGAAGGTTTCTATAAGACATCTTGGCCCGTCCATGATTCAGCAG
                            cattgat  putative branch site (score: 4)
                                                ttctc  putative PPT
                             attgatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catttcattaattcaaacattgactagattttattgttcgcgtaattgttgcttgtttcacaaatgggatttccattgattgttgtctgtgaattctcagTAAGGGTTCTAAGTCTGGTGCTTCGATGAAGTGTGCTGGTTGTCAAGGAACTGGTATGAAGGTTTCTATAAGACATCTTGGCCCGTCCATGATTCAGCAG

- - - - - - -caaacat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttgtc