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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ataaaaaatatatttaaacaagaaaaacgtttgaccttgaagacagaatgagaatgagtccaaacatacctaattagttgtgtatgatttgaatgcacagGGATGGAGCAGATGTAAGGGGATACTTTGCGTGGTCATTACTAGACAACTTTGAATGGGCTCAAGGTTATACAAAACGCTTTGGATTGGTCTATGTAGAT

Basic information

species Glycine max
transcript GLYMA11G16220.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G16220.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv00s0220g00070.t01 (Vitis vinifera), 3'ss of exon 11
ataaaaaatatatttaaacaagaaaaacgtttgaccttgaagacagaatgagaatgag----tccaaacatacctaattag-ttgtgtatgatttgaat---gcacagGGATGGAGCAGATGTAAGGGGATACTTTGCGTGGTCATTACTAGACAACTTTGAATGGGCTCAAGGTTATACAAAACGCTTTGGATTGGTCTATGTAGAT
       | | |||||||| ||  ||     | | |  | | | | ||| | |||  |    ||     ||      |  | ||||    | || | |    | ||||||||||||  ||||| |||||||||||||| ||||| ||||||||||||||||||||| |||||||||| || ||||| || || ||||| || || || 
---ttttacaaatttaaacgagtgaa-----taaaccaggaaaaaaaataataattgggtgttctgtttatggaacgtggggttgttgggggttgggacttgggacagGGATGGAGTTGATGTGAGGGGATACTTTGCATGGTCGTTACTAGACAACTTTGAATGGTCTCAAGGTTACACCAAACGTTTCGGTTTGGTTTACGTGGAC
















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|254323235|gb|GR840040.1|GR840040
EST:     AGAGTTCGCTATTTCAAAGGATATCTTGCGTCAGTTGCTCAGGCTATAAA                         GGATGGAGCAGATGTAAGGGGATACTTTGCGTGGTCATTACTAGACAACTT
genomic: AGAGTTCGCTATTTCAAAGGATATCTTGCGTCAGTTGCTCAGGCTATAAAgtgagtttgc ... gaatgcacagGGATGGAGCAGATGTAAGGGGATACTTTGCGTGGTCATTACTAGACAACTT
EST: gi|207811707|gb|GD785952.1|GD785952
EST:     AGAGTTCGCTATTTCAAAGGATATCTTGCGTCAGTTGCTCAGGCTATAAA                         GGATGGAGCAGATGTAAGGGG
genomic: AGAGTTCGCTATTTCAAAGGATATCTTGCGTCAGTTGCTCAGGCTATAAAgtgagtttgc ... gaatgcacagGGATGGAGCAGATGTAAGGGG
EST: gi|193684458|gb|FK623554.1|FK623554
EST:     AGAGTTCGCTATTTCAAAGGATATCTTGCGTCAGTTGCTCAGGCTATAAA                         GGATGGAGCAGATGTAAGGGGATACTTTGCGTGGTCATTACTAGACAACTT
genomic: AGAGTTCGCTATTTCAAAGGATATCTTGCGTCAGTTGCTCAGGCTATAAAgtgagtttgc ... gaatgcacagGGATGGAGCAGATGTAAGGGGATACTTTGCGTGGTCATTACTAGACAACTT
EST: gi|208058216|gb|GD860235.1|GD860235
EST:     AGAGTTCGCTATTTCAAAGGATATCTTGCGTCAGTTGCTCAGGCTATAAA                         GGATGGAGCAGATGTAAGGGG
genomic: AGAGTTCGCTATTTCAAAGGATATCTTGCGTCAGTTGCTCAGGCTATAAAgtgagtttgc ... gaatgcacagGGATGGAGCAGATGTAAGGGG
EST: gi|16343782|gb|BI969377.1|BI969377
EST:     AGAGTTCGCTATTTCAAAGGATATCTTGCGTCAGTTGCTCAGGCTATAAA                         GGATGGAGCAGATGTAAGGGGATACTTTGCGTGGTCATTACTAGACAACTT
genomic: AGAGTTCGCTATTTCAAAGGATATCTTGCGTCAGTTGCTCAGGCTATAAAgtgagtttgc ... gaatgcacagGGATGGAGCAGATGTAAGGGGATACTTTGCGTGGTCATTACTAGACAACTT
EST: gi|207713670|gb|GD695345.1|GD695345
EST:     AGAGTTCGCTATTTCAAAGGATATCTTGCGTCAGTTGCTCAGGCTATAAA                         GGATGGAGCAGA
genomic: AGAGTTCGCTATTTCAAAGGATATCTTGCGTCAGTTGCTCAGGCTATAAAgtgagtttgc ... gaatgcacagGGATGGAGCAGA
EST: gi|208143435|gb|GD942453.1|GD942453
EST:     AGAGTTCGCTATTTCAAAGGATATCTTGCGTCAGTTGCTCAGGCTATAAA                         GGATGGAGCAGATGTAAGGGGATACTTTGCGTGGTCATTACTAGACAACTT
genomic: AGAGTTCGCTATTTCAAAGGATATCTTGCGTCAGTTGCTCAGGCTATAAAgtgagtttgc ... gaatgcacagGGATGGAGCAGATGTAAGGGGATACTTTGCGTGGTCATTACTAGACAACTT
EST: gi|13478588|gb|BG508004.1|BG508004
EST:     AGAGTTCGCTATTTCAAAGGATATCTTGCGTCAGTTGCTCAGGCTATAAA                         GGATGGAGCAGATGTAAGGGGATACTTTGCGTGGTCATTACTAGACAACTT
genomic: AGAGTTCGCTATTTCAAAGGATATCTTGCGTCAGTTGCTCAGGCTATAAAgtgagtttgc ... gaatgcacagGGATGGAGCAGATGTAAGGGGATACTTTGCGTGGTCATTACTAGACAACTT
EST: gi|193493539|gb|FK460989.1|FK460989
EST:     AGAGTTCGCTATTTCAAAGGATATCTTGCGTCAGTTGCTCAGGCTATAAA                         GGATGGAGCAGATGTAAGGGGATACTTTGCGTGGTCATTACTAGACAACTT
genomic: AGAGTTCGCTATTTCAAAGGATATCTTGCGTCAGTTGCTCAGGCTATAAAgtgagtttgc ... gaatgcacagGGATGGAGCAGATGTAAGGGGATACTTTGCGTGGTCATTACTAGACAACTT
EST: gi|7685569|gb|AW756217.1|AW756217
EST:     AGAGTTCGCTATTTCAAAGGATATCTTGCGTCAGTTGCTCAGGCTATAAA                         GGATGGAGCAGATGTAAGGGGATACTTTGCGTGGTCATTACTAGACAACTT
genomic: AGAGTTCGCTATTTCAAAGGATATCTTGCGTCAGTTGCTCAGGCTATAAAgtgagtttgc ... gaatgcacagGGATGGAGCAGATGTAAGGGGATACTTTGCGTGGTCATTACTAGACAACTT
EST: gi|14990778|gb|BI316451.1|BI316451
EST:     AGAGTTCGCTATTTCAAAGGATAACTTGCGTCAGTTGCTCAGGCTATAAA                         GGATGGAGCAGATGTAAGGGGATACTTTGCGTGGTCATTACTAGACAACTT
genomic: AGAGTTCGCTATTTCAAAGGATATCTTGCGTCAGTTGCTCAGGCTATAAAgtgagtttgc ... gaatgcacagGGATGGAGCAGATGTAAGGGGATACTTTGCGTGGTCATTACTAGACAACTT
EST: gi|58019646|gb|CX706388.1|CX706388
EST:     AGAGTTCGCTATTTCAAAGGATATCTTGCGTCAGTTGCTCAGGCTATAAA                         GGATGGAGCAGATGTAAGGGGATACTTTGCGTGGTCATTACTAGACAACTT
genomic: AGAGTTCGCTATTTCAAAGGATATCTTGCGTCAGTTGCTCAGGCTATAAAgtgagtttgc ... gaatgcacagGGATGGAGCAGATGTAAGGGGATACTTTGCGTGGTCATTACTAGACAACTT
EST: gi|208186897|gb|GD987139.1|GD987139
EST:     AGAGTTCGCTATTTCAAAGGATATCTTGCGTCAGTTGCTCAGGCTATAAA                         GGATGGAGCAGAT
genomic: AGAGTTCGCTATTTCAAAGGATATCTTGCGTCAGTTGCTCAGGCTATAAAgtgagtttgc ... gaatgcacagGGATGGAGCAGAT
EST: gi|7591313|gb|AW707049.1|AW707049
EST:     AGAGTTCGCTATNTCAAAGGATATCTTGCGTCAGTTGCTCAGGCTATAAA                         GGATGGAGCAGATGTAAGGNGATACTNTGCGTGGTCATTACTAGACAACTN
genomic: AGAGTTCGCTATTTCAAAGGATATCTTGCGTCAGTTGCTCAGGCTATAAAgtgagtttgc ... gaatgcacagGGATGGAGCAGATGTAAGGGGATACTTTGCGTGGTCATTACTAGACAACTT
EST: gi|207746658|gb|GD719209.1|GD719209
EST:     AGAGTTCGCTATTTCAAAGGATATCTTGCGTCAGTTGCTCAGGCTATAAA                         GGATGGAGCAGATG
genomic: AGAGTTCGCTATTTCAAAGGATATCTTGCGTCAGTTGCTCAGGCTATAAAgtgagtttgc ... gaatgcacagGGATGGAGCAGATG
EST: gi|58022640|gb|CX709381.1|CX709381
EST:     AGAGTTCGCTATTTCAAAGGATATCTTGCGTCAGTTGCTCAGGCTATAAA                         GGATGGAGCAGATGTAAGGGGATACTTTGCGTGGTCATTACTAGACAACTT
genomic: AGAGTTCGCTATTTCAAAGGATATCTTGCGTCAGTTGCTCAGGCTATAAAgtgagtttgc ... gaatgcacagGGATGGAGCAGATGTAAGGGGATACTTTGCGTGGTCATTACTAGACAACTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaatgagaatgagtccaaacatacctaattagttgtgtatgatttgaatgcacagGGATGGAGCAGATGTAAGGGGATACTTTGCGTGGTCATTACTAGACAACTTTGAATGGGCTCAAGGTTATACAAAACGCTTTGGATTGGTCTATGTAGAT
                      acctaat  putative branch site (score: 3)
                         taattagtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ataaaaaatatatttaaacaagaaaaacgtttgaccttgaagacagaatgagaatgagtccaaacatacctaattagttgtgtatgatttgaatgcacagGGATGGAGCAGATGTAAGGGGATACTTTGCGTGGTCATTACTAGACAACTTTGAATGGGCTCAAGGTTATACAAAACGCTTTGGATTGGTCTATGTAGAT

- aaaaaat
- - - - - - - - - -aagaaaa
- - - - - - - - - - - - - - - - - ccttgaa
- - - - - - - - - - - - - - - - - - - - - - -gaatgag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccaaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtatga