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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atctctgagaactgttaaaatatatagcttgtttatagtacatgtgctttcttggatttgagtacttaaatcatgattttttttttggtttgaattgcagCCTGGTTATGAACGTCTATGCTGCTTGGGGTGTATGCAGCCACGCAATCACAATTTTGCCACCACTTGTGTTTGCAGAGTTCCCAAGAACCTTAGGGAGG

Basic information

species Glycine max
transcript GLYMA07G15700.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G15700.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os12g05410.1 (Oryza sativa), 3'ss of exon 3
--atctctgagaactgttaaaatatata-gcttgtttatagtacatgtgctttcttggatttgagtacttaaatcatgattttttttttggtttgaattgcagCCTGGTTATGAACGTCTATGCTGCTTGGGGTGTATGCAGCCACGCAATCACAATTTTGCCACCACTTGTGTTTGCAGAGTTCCCAAGAACCTTAGGGAGG
  |||||  |      ||  |    |||   ||  |  || |   |||| |    |     ||   |  | | | |   |||||   |||| |  |||||||||  || ||||| ||||| |||||| || | ||||| ||| ||||  | ||||| ||||| ||||| ||||||||||| ||||| ||| |||| ||||| |
aaatctcacatgcacattggacctcatatatttagtcttaatgt-tgtggtccaatttgcatggccaactgactgagtttttttgcattggat--aattgcagCAAGGCTATGAGCGTCTCTGCTGCCTGCGCTGTATCCAGACACGAGACCACAACTTTGCGACCACCTGTGTTTGCAGGGTTCCTAAGCACCTAAGGGAAG

upper sequence: GLYMA07G15700.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv05s0020g01520.t01 (Vitis vinifera), 3'ss of exon 3
atctctgagaactg-ttaaaatata--tagcttgtttatagtacatgtgctttcttggatttgagtacttaaatcatgattttttttttgg---tttgaattgcagCCTGGTTATGAACGTCTATGCTGCTTGGGGTGTATGCAGCCACGCAATCACAATTTTGCCACCACTTGTGTTTGCAGAGTTCCCAAGAACCTTAGGGAGG
       | ||| |  | | || |   ||  || | || |  | |   ||     || ||||   |    |||      ||||  |  |     |||||||||||||| |||||||||||||| ||||||||| | || ||||| |||||  ||||||| ||||||||||| ||||| ||| | || |||||| |||| |||||||
------aaaaacaggctgatatttgcttaatttctctaaaagataaaagcaaagatgaatttacatctccaaaatccttttttaatgatatgcttttgaattgcagCCAGGTTATGAACGTCTCTGCTGCTTGAGATGCATGCAACCACGGGATCACAACTTTGCCACCACATGTGTGTGCCGGGTCCCCAAGCACCTAAGGGAGG
















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|208248646|gb|GE044101.1|GE044101
EST:     GTTTAGATCAAGGATATGCTGACCACAATCTAATTGCAAAATGGAAGAAG                         CCTGGTTATGAACGTCT
genomic: GTTTAGATCAAGGATATGCTGACCACAATCTAATTGCAAAATGGAAGAAGgtacctaaat ... tgaattgcagCCTGGTTATGAACGTCT
EST: gi|151408524|gb|EV278332.1|EV278332
EST:     GTTTAGATCAAGGATATGCTGACCACAATCTAATTGCAAAATGGAAGAAG                         CCCGGTTATGAACGTCTATGCTGCTTGGGGTGTATGCAGCCACGCAATCAC
genomic: GTTTAGATCAAGGATATGCTGACCACAATCTAATTGCAAAATGGAAGAAGgtacctaaat ... tgaattgcagCCTGGTTATGAACGTCTATGCTGCTTGGGGTGTATGCAGCCACGCAATCAC
EST: gi|207699666|gb|GD678937.1|GD678937
EST:     GTTTAGATCAAGGATATGCTGACCACAATCTAATTGCAAAATGGAAGAAG                         CCTGGTTATGAACGTCTATGCTGCTTGGGGTGTATGCAGCCACGCAATCAC
genomic: GTTTAGATCAAGGATATGCTGACCACAATCTAATTGCAAAATGGAAGAAGgtacctaaat ... tgaattgcagCCTGGTTATGAACGTCTATGCTGCTTGGGGTGTATGCAGCCACGCAATCAC
EST: gi|38192606|gb|CF921812.1|CF921812
EST:     GTTTAGATCAAGGATATGCTGACCACAATCTAATTGCAAAATGGAAGAAG                         CCTGGTTATGAACGTCTATGCTGCTTGGGGTGTATGCAGCCACGCAATCAC
genomic: GTTTAGATCAAGGATATGCTGACCACAATCTAATTGCAAAATGGAAGAAGgtacctaaat ... tgaattgcagCCTGGTTATGAACGTCTATGCTGCTTGGGGTGTATGCAGCCACGCAATCAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctttcttggatttgagtacttaaatcatgattttttttttggtttgaattgcagCCTGGTTATGAACGTCTATGCTGCTTGGGGTGTATGCAGCCACGCAATCACAATTTTGCCACCACTTGTGTTTGCAGAGTTCCCAAGAACCTTAGGGAGG
                               ttttttttttggttt  CT-rich tract
                 tacttaaatcatgatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atctctgagaactgttaaaatatatagcttgtttatagtacatgtgctttcttggatttgagtacttaaatcatgattttttttttggtttgaattgcagCCTGGTTATGAACGTCTATGCTGCTTGGGGTGTATGCAGCCACGCAATCACAATTTTGCCACCACTTGTGTTTGCAGAGTTCCCAAGAACCTTAGGGAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - gcttgtt
- - - - - - - - - - - - - - - - - - -gtacatg
- - - - - - - - - - - - - - - - - - - - - - tgctttc
- - - - - - - - - - - - - - - - - - - - - - - - - - -ggatttg