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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattgtttcattatttaacccattactccaaaattatgatattttcttttgctaatcattgcataaaaggaagataaatgattagacgtgtttcttgcggattttcagATATTGAGATGTGGCCCACCACCTATGAACAAGGCCATGGCTGCACACCTTGAAGCCCTTGGATATGCTTCTGAGATGCAGTTCCAGTTCTGATTCTCTT

Basic information

species Glycine max
transcript GLYMA03G00920.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G00920.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os05g40990.1 (Oryza sativa), 3'ss of exon 8
--------------------------gtaattgtttcattatttaacccattactccaaaattatgatattttcttttgctaatcattgcata---aaaggaagataaatgattagacgtgtttcttgcggattttcagATATTGAGATGTGGCCCACCACCTATGAACAAGGCCATGGCTGCACACCTTGAAGCCCTTGGATATGCTTCTGAGATGCAGTTCCAGTTCTGATTCTCTT
                          ||  | |  |   |  |  | |    |  | | ||||   |         |||      ||| |||     ||| | || |  ||  |     ||| |  |      ||||||||||||||||| || || || || |||||||| |||||||||| |||||| ||    ||||| ||  |    || ||||||||||| |||| |  |||  
gtaggtgtcacattgtgatgtcttctgtggtagcgtgccttctggaacttggaaccgacaattgctaagagaatagttgaagtgtattccatctaccaagcaggacatctgtgtgacaatgtatggttgctcctttcagATATTGAGATGCGGACCTCCTCCCATGAACAAAGCCATGGCTGAACACCTGGAGAATCTTGGCTACACGAAGGAAATGCAGTTCCAATTCTAAGCCTCCA

upper sequence: GLYMA03G00920.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G133213_T01 (Zea mays), 3'ss of exon 8
gtaattgtttcattat-ttaacccattactccaaaattatgat--attttcttttgctaatcattgcataaaaggaagataaatgattagacgtgtttcttgcggattttcagATATTGAGATGTGGCCCACCACCTATGAACAAGGCCATGGCTGCACACCTTGAAGCCCTTGGATATGCTTCTGAGATGCAGTTCCAGTTCTGATTCTCTT
|| | | ||   |  | ||      | | | ||  || | |||  ||| | | ||    ||  ||| ||  ||             | ||| ||||||         ||||||||  |||||||||| || || || ||||||||||||||||||||||||||||| |  ||    ||  |    ||||||||||||||||||| |      |
gtgaatcttgagtcttatttttttttcagttcactatgaagatcgattgtgtattctctattcttgtatctaacc-----------tgagatgtgtttaccta----tttcagATCCTGAGATGTGGTCCTCCTCCGATGAACAAGGCCATGGCTGCACACCTTGACGAGCTCAACTACACAAAGGAGATGCAGTTCCAGTTCTAAGCAATGT

upper sequence: GLYMA03G00920.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G422581_T01 (Zea mays), 3'ss of exon 3
gtaattgtttcat--tatttaacccattactccaaaattatgatattttcttttgctaatcattgcataaaaggaagataaatgattagacgtgtttcttgcggattttcagATATTGAGATGTGGCCCACCACCTATGAACAAGGCCATGGCTGCACACCTTGAAGCCCTTGGATATGCTTCTGAGATGCAGTTCCAGTTCTGATTCTCTT
|| | | ||   |  |||||    || | | | |  |  ||   ||| | | ||    ||  ||| ||  ||             | ||| ||||||         ||||||||  |||||||||| || || || ||||||||||||||||||||||||||||| |  ||    ||  |    ||||||||||||||||||| |      |
gtgaatcttgagtcttatttttttcagttcactatgaagatcg-attgtgtattctctattcttgtatctaacc-----------tgagatgtgtttaccta----tttcagATCCTGAGATGTGGTCCTCCTCCGATGAACAAGGCCATGGCTGCACACCTTGACGAGCTCAACTACACAAAGGAGATGCAGTTCCAGTTCTAAGCAATGT

upper sequence: GLYMA03G00920.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G127972_T01 (Zea mays), 3'ss of exon 3
gtaattgtttcat--tatttaacccattactccaaaattatgat--attttcttttgctaatcattgcataaaaggaagataaatgattagacgtgtttcttgcggattttcagATATTGAGATGTGGCCCACCACCTATGAACAAGGCCATGGCTGCACACCTTGAAGCCCTTGGATATGCTTCTGAGATGCAGTTCCAGTTCTGATTCTCTT
|| | | ||   |  |||||      | | | ||  || | |||  ||| | | ||    ||  ||| ||  ||             | ||| ||||||         ||||||||  |||||||||| || || || ||||||||||||||||||||||||||||| |  ||    ||  |    ||||||||||||||||||| |      |
gtgaatcttgagtcttattttttttttcagttcactatgaagatcgattgtgtattctctattcttgtatctaacc-----------tgagatgtgtttaccta----tttcagATCCTGAGATGTGGTCCTCCTCCGATGAACAAGGCCATGGCTGCACACCTTGACGAGCTCAACTACACAAAGGAGATGCAGTTCCAGTTCTAAGCAATGT

upper sequence: GLYMA03G00920.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G076206_T01 (Zea mays), 3'ss of exon 5
--gtaattgtttcattatttaacccattactccaaaattatgat-attttcttttgctaatcattgcataaaaggaa--gataaatgattagacgtgtttcttgcggattttcagATATTGAGATGTGGCCCACCACCTATGAACAAGGCCATGGCTGCACACCTTGAAGCCCTTGGATATGCTTCTGAGATGCAGTTCCAGTTCTGATTCTCTT
  | |   |  | |||   |   |  | | | ||  || | |||  |  |  |||    ||  ||| || |  | |    |      ||   || ||| | |  |    ||||||||  | || ||||| || ||  | ||||||||||||||||||||||||||||| |  ||    ||  |    ||||||||||||||||||| |    |  
gtgaatcaggcttattgccttttctttcagttcactatgaggattgtcatgatttctctattcttgtatgattgtatctaacctggaatcttacatgtgtttaccta--tttcagATCCTAAGGTGTGGTCCTCCTTCGATGAACAAGGCCATGGCTGCACACCTTGACGAGCTCAACTACACGAAGGAGATGCAGTTCCAGTTCTAAGCAACGC

upper sequence: GLYMA03G00920.1 (Glycine max), 3'ss of exon 8
lower sequence: AT5G17770.1 (Arabidopsis thaliana), 3'ss of exon 8
gtaattgtttcattatttaacccattactccaaaattatgatattttcttttgctaatcattgcataaaaggaagataaatgat-tagacgtgtttcttgcg-gattttcagATATTGAGATGTGGCCCACCACCTATGAACAAGGCCATGGCTGCACACCTTGAAGCCCTTGGATATGCTTCTGAGATGCAGTTCCAGTTCTGATTCTCTT
     ||    |  || |||  ||||  |  | ||||     ||||| |  ||   | |||    |  |||   |      ||| ||    || ||| ||    | || |||||  | ||||| || ||||| || ||||||||||||||||||||| |||||||||| || |||||  || | |||||||| |||||||||||||     |
-----tgcaagagaatgtaa--cattgataaacaatt----catttt-tggtgaggagcatatggtttaagatggtgtgtcgatctaagtatggttcatgtttaaattgcagATCCTAAGATGCGGACCACCGCCAATGAACAAGGCCATGGCTGCAAACCTTGAAGCTCTGGGATACTCTCCGGAGATGCAATTCCAGTTCTGATCTGAAT

upper sequence: GLYMA03G00920.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv08s0056g01150.t01 (Vitis vinifera), 3'ss of exon 8
gtaattgtttcattatttaacccattactccaaaattatgatattttcttttgcta-atcattgcataaaaggaagataaatgattagacgtgtttcttgcggattttcagATATTGAGATGTGGCCCACCACCTATGAACAAGGCCATGGCTGCACACCTTGAAGCCCTTGGATATGCTTCTGAGATGCAGTTCCAGTTCTGATTCTCTT
    | | ||   |  |     |||  |  |||||   |   |  |  |  |   | ||||| |  |        | |  ||| |||  |   |||  | |  || | |||||  |  ||||||| |||||||| ||||||||||||||||| ||   |||  | |   |||||||  |   |||||||||||||||||||| ||  | ||
---gtaggtttgcttctgggttcatgcccacaaaacccttgaacatgttagtctcatatcatggtctgg------gcttgatgtttaacc---tttgatccaaatctgcagATTCTCCGATGTGGTCCACCACCCATGAACAAGGCCATGGCCGCCATCCTCAACGATATTGGATACACAGATGAGATGCAGTTCCAGTTCTAATCATGTT

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|13251953|gb|BG362856.1|BG362856
EST:     CAAAGGAGATGATTCAAACCCATTGCCCTGCTCCAGCACAAGATATTAAG                         ATATTGAGATGTGGCCCACCACCTATGAACAAGGCCATGGCTGCACACCTT
genomic: CAAAGGAGATGATTCAAACCCATTGCCCTGCTCCAGCACAAGATATTAAGgtaattgttt ... ggattttcagATATTGAGATGTGGCCCACCACCTATGAACAAGGCCATGGCTGCACACCTT
EST: gi|58021619|gb|CX708360.1|CX708360
EST:     CAAAGGAGATGATTCAAACCCATTGCCCTGCTCCAGCACAAGATATTAAG                         ATATTGAGATGTGGCCCACCACCTATGAACAAGGCCATGGCTGCACACCTT
genomic: CAAAGGAGATGATTCAAACCCATTGCCCTGCTCCAGCACAAGATATTAAGgtaattgttt ... ggattttcagATATTGAGATGTGGCCCACCACCTATGAACAAGGCCATGGCTGCACACCTT
EST: gi|298184687|gb|HO029900.1|HO029900
EST:     CAAAGGAGATGATTCAAACCCATTGCCCTGCTCCAGCACAAGATATTAAG                         ATATTGAGATGTGGCCCACCACCTATGAACAAGGCCATGGCTGCACACCTT
genomic: CAAAGGAGATGATTCAAACCCATTGCCCTGCTCCAGCACAAGATATTAAGgtaattgttt ... ggattttcagATATTGAGATGTGGCCCACCACCTATGAACAAGGCCATGGCTGCACACCTT
EST: gi|193684767|gb|FK622291.1|FK622291
EST:     CAAAGGAGATGATTCAAACCCATTGCCCTGCTCCAGCACAAGATATTAAG                         ATATTGAGATGTGGCCCACCACCTATGAACAAGGCCATGGCTGCACACCTT
genomic: CAAAGGAGATGATTCAAACCCATTGCCCTGCTCCAGCACAAGATATTAAGgtaattgttt ... ggattttcagATATTGAGATGTGGCCCACCACCTATGAACAAGGCCATGGCTGCACACCTT
EST: gi|151403993|gb|EV273803.1|EV273803
EST:     CAAAGGAGATGATTCAAACCCATTGCCCTGCTCCAGCACA-GATATTA-G                         ATATTGAGATGTGGCCCACCACCTATGAACAAG-C-ATGGCTGCACACCTT
genomic: CAAAGGAGATGATTCAAACCCATTGCCCTGCTCCAGCACAAGATATTAAGgtaattgttt ... ggattttcagATATTGAGATGTGGCCCACCACCTATGAACAAGGCCATGGCTGCACACCTT
EST: gi|56173100|gb|CV997226.1|CV997226
EST:     CAAAGGAGATGATTCAAACCCATTGCCCTGCTCCAGCACATGATATTAAG                         ATATTGAGATGTGGCCCACCACCTATGAACAAGGCCATGGCTGCACACCTT
genomic: CAAAGGAGATGATTCAAACCCATTGCCCTGCTCCAGCACAAGATATTAAGgtaattgttt ... ggattttcagATATTGAGATGTGGCCCACCACCTATGAACAAGGCCATGGCTGCACACCTT
EST: gi|151399348|gb|EV269219.1|EV269219
EST:     CAAAGGAGATGATTCAAACCCATTGCCCTGCTCCAGCACAAGATATTAAG                         ATATTGAGATGTGGCCCACCACCTATGAACAAG-CCATGGCTGCACACCTT
genomic: CAAAGGAGATGATTCAAACCCATTGCCCTGCTCCAGCACAAGATATTAAGgtaattgttt ... ggattttcagATATTGAGATGTGGCCCACCACCTATGAACAAGGCCATGGCTGCACACCTT
EST: gi|193576645|gb|FK533728.1|FK533728
EST:     CAAAGGAGATGATTCAAACCCATTGCCCTGCTCCAGCACAAGATATTAAG                         ATATTGAGATGTGGCCCACCACCTATGAACAAGGCCATGGCTGCACACCTT
genomic: CAAAGGAGATGATTCAAACCCATTGCCCTGCTCCAGCACAAGATATTAAGgtaattgttt ... ggattttcagATATTGAGATGTGGCCCACCACCTATGAACAAGGCCATGGCTGCACACCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatcattgcataaaaggaagataaatgattagacgtgtttcttgcggattttcagATATTGAGATGTGGCCCACCACCTATGAACAAGGCCATGGCTGCACACCTTGAAGCCCTTGGATATGCTTCTGAGATGCAGTTCCAGTTCTGATTCTCTT
 tgctaat  putative branch site (score: 2)
                                                ttttc  putative PPT
                 aagataaatgatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattgtttcattatttaacccattactccaaaattatgatattttcttttgctaatcattgcataaaaggaagataaatgattagacgtgtttcttgcggattttcagATATTGAGATGTGGCCCACCACCTATGAACAAGGCCATGGCTGCACACCTTGAAGCCCTTGGATATGCTTCTGAGATGCAGTTCCAGTTCTGATTCTCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG