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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatattctttataacacaagttgcatgctagtttgtttggtttttttccatatgctgaagataccagttcttctctgattttatgctatgctatttaaagGTTGAGAATCAGGAGGGAGTCCTGAATTTTGACGAAATCCTGCGGGAGACTGATGCATTCATGGTGGCACGTGGTGATCTTGGAATGGAGATCCCAGTAG

Basic information

species Glycine max
transcript GLYMA05G09310.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G09310.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G008714_T01 (Zea mays), 3'ss of exon 2
tatattctttataac-acaagttgcatgctagtttgtttggtttttttccatatgctg--aagataccagttcttctctgattttatgctatgctatttaaagGTTGAGAATCAGGAGGGAGTCCTGAATTTTGACGAAATCCTGCGGGAGACTGATGCATTCATGGTGGCACGTGGTGATCTTGGAATGGAGATCCCAGTAG
|  ||  |  || |  | ||  | |||  |||    | || |  | ||   |||||||  | |   |   ||| | ||  ||  |||| | | |  | |  ||||||| || || ||||| ||  | || ||||| || ||| || ||||||||||||| || ||||| ||  | |||||||||||||||||||| || || |
ttcatattacatcatgataatgtacata-tagaacttatgatcgtgttggttatgctgtcatggatctgattcctttc--atgatatggtttccgctatgcagGTTGAAAACCAAGAGGGTGTTGTAAACTTTGATGAGATCTTGAGGGAGACTGATGCTTTTATGGTTGCTAGAGGTGATCTTGGAATGGAGATTCCTGTTG

upper sequence: GLYMA05G09310.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G63680.1 (Arabidopsis thaliana), 3'ss of exon 3
tatattctttataacacaa-gttgcatgctagtttgtttggtttttttccatatgctgaagataccagttcttctctgattttatgctatgctatttaaagGTTGAGAATCAGGAGGGAGTCCTGAATTTTGACGAAATCCTGCGGGAGACTGATGCATTCATGGTGGCACGTGGTGATCTTGGAATGGAGATCCCAGTAG
               |||| ||| ||   || ||   |||    |        |  | ||| ||  | |     |   |||||    |||  ||||  ||||||||||| || || |||||||||||||| || || ||  |||| || ||||||||||||||||| || |||||||||||||| |||||||| ||  |||
-------------gtacaaagttacaccttatttcacttgtggctaaagttggttttaaaggtaggattgtgattagaatttt----tatcttatt--aagGTTGAGAACCAAGAAGGAGTCCTGAATTTCGATGAGATTTTGCGTGAAACTGATGCATTCATGGTTGCTCGTGGTGATCTTGGGATGGAGATTCCGATAG

upper sequence: GLYMA05G09310.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv10s0071g01060.t01 (Vitis vinifera), 3'ss of exon 2
----tatattctttataacacaagttgcatgctagtttgtttggtttttttccatatgctgaa-gataccagttcttctctgattttatgctatgctatttaaagGTTGAGAATCAGGAGGGAGTCCTGAATTTTGACGAAATCCTGCGGGAGACTGATGCATTCATGGTGGCACGTGGTGATCTTGGAATGGAGATCCCAGTAG
     | |||  | |        | | | |    |  ||||| |  ||| |   |   ||||| ||||    || |||| ||   ||  |||     ||||  |||||||||| || ||||| ||  | || || || |||||  | || ||||||||  | |||||||| || || |||||||| ||||||||||||||||| |
atgagaaattactgagtttctgtggttcttcaaggagtgttttgcatttcttggt-cactgaatgatatgtttttttctttg---ttgagctgaaa-attttcagGTTGAGAACCAAGAGGGTGTTATCAACTTCGATGAAATATTACGTGAGACTGACTCCTTCATGGTTGCCCGAGGTGATCTCGGAATGGAGATCCCAGTGG

upper sequence: GLYMA05G09310.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv08s0056g00190.t01 (Vitis vinifera), 3'ss of exon 2
------tatattctttataacacaagttgcatgctagtttgtttggttttttt-ccatatgctgaagataccagttcttctctgattttatgctatgctatttaaagGTTGAGAATCAGGAGGGAGTCCTGAATTTTGACGAAATCCTGCGGGAGACTGATGCATTCATGGTGGCACGTGGTGATCTTGGAATGGAGATCCCAGTAG
      |  ||  ||  |    ||| |||| | |  |||| |||| |   | |  ||||  || | |  | |     |||| ||       ||| |  |   | ||||| ||||| |||||||| ||  | || ||||| ||||| ||||| ||||| ||| |||| ||||| || ||||||||||||||||||||||||||||| |
gcttatttcatggttggttgtgcaatttgcttacatgtttctttgataaatatgtcatagcctcatggcatcttcctttctgtg-------gctgtaattcctgaagGTGGAGAACCAGGAGGGTGTTATCAACTTTGATGAAATACTGCGTGAGACCGATTCATTTATGGTTGCCCGTGGTGATCTTGGAATGGAGATCCCAGTGG

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|16279454|gb|BI943445.1|BI943445
EST:     TCCGCAAGGTTCTGGGGCCACATGCAAAGAATATTCAGTTGATGTCAAAG                         GTTGAGAATCAGGAGGGAGTCCTGAATTTTGACGAAATCCTGCGGGAGACT
genomic: TCCGCAAGGTTCTGGGGCCACATGCAAAGAATATTCAGTTGATGTCAAAGgtattttttg ... ctatttaaagGTTGAGAATCAGGAGGGAGTCCTGAATTTTGACGAAATCCTGCGGGAGACT
EST: gi|208033021|gb|GD831296.1|GD831296
EST:     TCCGCAAGGTTCTGGGGCCACATGCAAAGAATATTCAGTTGATGTCAAAG                         GTTGAGAATCAGGAGGGAGT
genomic: TCCGCAAGGTTCTGGGGCCACATGCAAAGAATATTCAGTTGATGTCAAAGgtattttttg ... ctatttaaagGTTGAGAATCAGGAGGGAGT
EST: gi|16281628|gb|BI944585.1|BI944585
EST:     TCCGCAAGGTTCTGGGGCCACATGCAAAGAATATTCAGTTGATGTCAAAG                         GTTGAGAATCAGGAGGGAGTCCTGAATTTTGACGAAATCCTGCGGGAGACT
genomic: TCCGCAAGGTTCTGGGGCCACATGCAAAGAATATTCAGTTGATGTCAAAGgtattttttg ... ctatttaaagGTTGAGAATCAGGAGGGAGTCCTGAATTTTGACGAAATCCTGCGGGAGACT
EST: gi|7685861|gb|AW756509.1|AW756509
EST:     TCCGCAAGGTTCTGGGGCCACATGCAAAGAATATTCAGTTGATGTCAAAG                         GTTGAGACTCAGGAGGGAGTCCTGAATGTTGACGAGATCCTGCGGGAGACT
genomic: TCCGCAAGGTTCTGGGGCCACATGCAAAGAATATTCAGTTGATGTCAAAGgtattttttg ... ctatttaaagGTTGAGAATCAGGAGGGAGTCCTGAATTTTGACGAAATCCTGCGGGAGACT
EST: gi|192300401|gb|FG987888.1|FG987888
EST:     TCCGCAAGGTTCTGGGGCCACATGCAAAGAATATTCAGTTGATGTCAAAG                         GTTGAGAATCAGGAGGGAGTCCTGAATTTTGACGAAATCCTGCGGGAGACT
genomic: TCCGCAAGGTTCTGGGGCCACATGCAAAGAATATTCAGTTGATGTCAAAGgtattttttg ... ctatttaaagGTTGAGAATCAGGAGGGAGTCCTGAATTTTGACGAAATCCTGCGGGAGACT
EST: gi|193388042|gb|FK354257.1|FK354257
EST:     GCAAGGTTCTGGGGCCACATGCAAAGAATATTCAGTTGATGTCAAAG                         GTTGAGAATCAGGAGGGAGTCCTGAATTTTGACGAAATCCTGCGGGAGACT
genomic: GCAAGGTTCTGGGGCCACATGCAAAGAATATTCAGTTGATGTCAAAGgtattttttg ... ctatttaaagGTTGAGAATCAGGAGGGAGTCCTGAATTTTGACGAAATCCTGCGGGAGACT
EST: gi|193367355|gb|FK329507.1|FK329507
EST:     TCCGCAAGGTTCTGGGGCCACATGCAAAGAATATTCAGTTGATGTCAAAG                         GTTGAGAATCAGGAGGGAGTCCTGAATTTTGACGAAATCCTGCGGGAGACT
genomic: TCCGCAAGGTTCTGGGGCCACATGCAAAGAATATTCAGTTGATGTCAAAGgtattttttg ... ctatttaaagGTTGAGAATCAGGAGGGAGTCCTGAATTTTGACGAAATCCTGCGGGAGACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttccatatgctgaagataccagttcttctctgattttatgctatgctatttaaagGTTGAGAATCAGGAGGGAGTCCTGAATTTTGACGAAATCCTGCGGGAGACTGATGCATTCATGGTGGCACGTGGTGATCTTGGAATGGAGATCCCAGTAG
                           ctctgat  putative branch site (score: 4)
                                              tatttaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatattctttataacacaagttgcatgctagtttgtttggtttttttccatatgctgaagataccagttcttctctgattttatgctatgctatttaaagGTTGAGAATCAGGAGGGAGTCCTGAATTTTGACGAAATCCTGCGGGAGACTGATGCATTCATGGTGGCACGTGGTGATCTTGGAATGGAGATCCCAGTAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - aacacaag
- - - - - - - - - - - gcatgct
- - - - - - - - - - - - - - - - ttgtttg
- - - - - - - - - - - - - - - - - - - - - - - - - - tgctgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgctatg