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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttgcttattttcaccatgttgtaaattgtaaatatttatatcctgtttttgaaattctgttggaggtttacatattaattgtaatgttggcccctgcagGCCTCAGGTAACTATAGCAACGGCCATAATCTTTTGTCATCGGTTCTTTCTTCGACAATCTCATGCAAAGAATGACCGAAGG

Basic information

species Glycine max
transcript GLYMA20G02860.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G02860.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G308570_T02 (Zea mays), 3'ss of exon 10
-gttgcttattttcaccatgttgtaaattgtaaatatttatatcctgtttttgaaattctgttggaggtttacatattaattgtaatgttggcccc----tgcagGCCTCAGGTAACTATAGCAACGGCCATAATCTTTTGTCATCGGTTCTTTCTTCGACAATCTCATGCAAAGAATGACCGAAGG
   ||| | ||    | | ||| ||   |||   | |||   |     | ||  |  | ||    |  ||||    |  | ||  |   |  | ||    || |||||||| || || || || || || ||| | || ||||||||||| |||||||| ||||||||||| || |||||| || ||
gcctgcatgttactgc-acgttttatgatgtct-tgtttgagttgaaatcttttatatatgc--aatttttattcttctaatgcca-actaactccataatgtagGCCTCAAGTGACAATTGCTACTGCTATAGTGTTCTGTCATCGGTTTTTTCTTCGTCAATCTCATGCGAAAAATGACAGACGG

upper sequence: GLYMA20G02860.1 (Glycine max), 3'ss of exon 2
lower sequence: AC233979.1_FGT009 (Zea mays), 3'ss of exon 1
gttgcttattttcaccatgttgtaaattgtaaatatttatatcctgttt---ttgaaattctgttggaggtttacatattaattgtaatgttggc--------ccctgcagGCCTCAGGTAACTATAGCAACGGCCATAATCTTTTGTCATCGGTTCTTTCTTCGACAATCTCATGCAAAGAATGACCGAAGG
         |  |  |||| |            |  | ||||| |||||   ||||||   | ||      | |  | ||  || ||||| ||             || || ||||| || || || || || || ||| | || |||||||||||||||||||| ||||| ||||| || |||||| || ||
---------tgcctgcatgctactg--cacgggttgtgatatcttgtttgagttgaaaccttttttatatgtaatttttttcttctaatgctgatgaactttgtaatgtagACCTCAAGTGACAATTGCTACTGCTATAGTGTTCTGTCATCGGTTCTTTCTTCGTCAATCGCATGCCAAAAATGACAGACGG

upper sequence: GLYMA20G02860.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G45190.1 (Arabidopsis thaliana), 3'ss of exon 2
gttgcttattttcaccatgttgtaaattgtaaatatttatatcctgtttttgaaattctgttggaggtttacatattaattg--taatgttggcccctg--cagGCCTCAGGTAACTATAGCAACGGCCATAATCTTTTGTCATCGGTTCTTTCTTCGACAATCTCATGCAAAGAATGACCGAAGG
      | | || |   || | |   | || |   ||| |    ||||     | |||  ||   || |  | |   || |   | || | |    |    ||| || ||||| || ||||| || || |||||||| |||||||| |||||  |||| ||||| ||||||||||||||| |||||
---cactgtcttaattttgct-tttgtagtcatggtttctgcattgttcagagatttcaatttttggctctcttggaaagtcgctgatatagttttccaatcagTCCCCAGGTTACAATAGCTACAGCGATAATCTTCTGTCATCGATTCTTCTTTCGCCAATCACATGCAAAGAATGACAGAAGG

upper sequence: GLYMA20G02860.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G45190.2 (Arabidopsis thaliana), 3'ss of exon 4
gttgcttattttcaccatgttgtaaattgtaaatatttatatcctgtttttgaaattctgttggaggtttacatattaattg--taatgttggcccctg--cagGCCTCAGGTAACTATAGCAACGGCCATAATCTTTTGTCATCGGTTCTTTCTTCGACAATCTCATGCAAAGAATGACCGAAGG
     ||| |||  |  | |||||    || |   ||| |    ||||     | |||  ||   || |  | |   || |   | || | |    |    ||| || ||||| || ||||| || || |||||||| |||||||| |||||  |||| ||||| ||||||||||||||| |||||
-----ttaattttgc--ttttgta----gtcatggtttctgcattgttcagagatttcaatttttggctctcttggaaagtcgctgatatagttttccaatcagtccccagGTTACAATAGCTACAGCGATAATCTTCTGTCATCGATTCTTCTTTCGCCAATCACATGCAAAGAATGACAGAAGG

upper sequence: GLYMA20G02860.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv00s0125g00270.t01 (Vitis vinifera), 3'ss of exon 1
----gttgcttattttcaccatgttgtaaattgtaaatatttatatcctgtttttgaaattctgttggaggtttacatattaattgtaatgttggcccc--tgcagGCCTCAGGTAACTATAGCAACGGCCATAATCTTTTGTCATCGGTTCTTTCTTCGACAATCTCATGCAAAGAATGACCGAAGG
         || |||| | ||   |   |||| || |     || |  | || |   |||  |  |  |   | ||||    |||  ||   |||   |  ||||| || |||||||||||||| || || ||||| ||||||||||||||||||||| | |||||||| |||||||||||| |||||
ccataacatttttttttatcagaat---aattatataa---catttttttttatcagaataattatataccataacatgaatattagaaatctggtttcattgcagACCCCAGGTAACTATAGCCACAGCAATAATATTTTGTCATCGGTTCTTTCTTTGCCAATCTCACGCAAAGAATGACAGAAGG

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|207766610|gb|GD738798.1|GD738798
EST:     CGCAAGTCATACTGCACATTCTTGCAGGATTTAGGCATGAGACTTAAAGT                         GCCTCAGGTAACTATAGCAACGGCCATAATACTTTT
genomic: CGCAAGTCATACTGCACATTCTTGCAGGATTTAGGCATGAGACTTAAAGTgtgagtttgg ... gcccctgcagGCCTCAGGTAACTATAGCAACGGCCATAAT-CTTTT
EST: gi|208067704|gb|GD864882.1|GD864882
EST:     CGCAAGTCATACTGCACATTCTTGCAGGATTTAGGCATGAGACTTAAAGT                         GCCTCAGGTAACTATAGCAACGGCCATAATCTTTTGTCATCGGTTCTTTCT
genomic: CGCAAGTCATACTGCACATTCTTGCAGGATTTAGGCATGAGACTTAAAGTgtgagtttgg ... gcccctgcagGCCTCAGGTAACTATAGCAACGGCCATAATCTTTTGTCATCGGTTCTTTCT
EST: gi|193466882|gb|FK430735.1|FK430735
EST:     AGTCATACTGCACATTTCTTGAACAAGGATTTAGGCATGAGACTTAAAGT                         GCCTCAGGTAACTATAGCAACGGCCATAATCTTTTGTCATCGGTTCTTTCT
genomic: AGTCATACTGCACA-TTCTTG--C-AGGATTTAGGCATGAGACTTAAAGTgtgagtttgg ... gcccctgcagGCCTCAGGTAACTATAGCAACGGCCATAATCTTTTGTCATCGGTTCTTTCT
EST: gi|193363879|gb|FK329685.1|FK329685
EST:     CGCAAGTCATACTGCACATTCTTGCAGGATTTAGGCATGAGACTTAAAGT                         GCCTCAGGTAACTATAGCAACGGCCATAATCTTTTGTCATCGGTTCTTTCT
genomic: CGCAAGTCATACTGCACATTCTTGCAGGATTTAGGCATGAGACTTAAAGTgtgagtttgg ... gcccctgcagGCCTCAGGTAACTATAGCAACGGCCATAATCTTTTGTCATCGGTTCTTTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttttgaaattctgttggaggtttacatattaattgtaatgttggcccctgcagGCCTCAGGTAACTATAGCAACGGCCATAATCTTTTGTCATCGGTTCTTTCTTCGACAATCTCATGCAAAGAATGACCGAAGG
                            tattaat  putative branch site (score: 2)
                                              cccctgc  putative PPT
                      tttacatattaattgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgcttattttcaccatgttgtaaattgtaaatatttatatcctgtttttgaaattctgttggaggtttacatattaattgtaatgttggcccctgcagGCCTCAGGTAACTATAGCAACGGCCATAATCTTTTGTCATCGGTTCTTTCTTCGACAATCTCATGCAAAGAATGACCGAAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
gttgctt
- - - - - -tcaccat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttggagg