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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgctggttttctatgttgtgaagtcggttctgatactagtcagtgtgttgaattctgttgctaaatttactatctaaagctatattttgggtatttcagTCTCTTGCACAGCAGTACAGCTCCGAGTTCCTTCAATCAGAGCTTGAGAGGACACGCATTAACACAGCATGCTTTGCAGAATCTATTCCTTTGGACTCTT

Basic information

species Glycine max
transcript GLYMA20G31490.2
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G31490.2 (Glycine max), 3'ss of exon 20
lower sequence: Vv18s0072g00720.t01 (Vitis vinifera), 3'ss of exon 20
---atgctggttttctat-gttgtgaagtcggttctgatactagtcagtgtgttgaattctg-ttgctaaatttactatctaaagctatattttgggtatttcagTCTCTTGCACAGCAGTACAGCTCCGAGTTCCTTCAATCAGAGCTTGAGAGGACACGCATTAACACAGCATGCTTTGCAGAATCTATTCCTTTGGACTCTT
   |     |||    || | | | |       | |  |  | ||   ||  || | || || ||    ||||| |||| |   ||| ||  |   || |   || ||||||||||||| | ||| || ||| | |||||  |||||||||| ||||| || || ||||||||||||||||  || || ||||| || |||    
gcaaaagcagttacaaatagctcttataggacatatatttgttgtttatgctttaagttgtggttttctaatttgctattt--cgctgtacat---gtttgcaagGCTCTTGCACAGCAATTCAGTTCTGAGCTACTTCAGGCAGAGCTTGAAAGGACTCGGATCAACACAGCATGCTTTGTGGAGTCAATTCCATTAGACATGG
















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|193552263|gb|FK509412.1|FK509412
EST:     TTGCAGATGATAAGCAACAAGGAACAACTGTATCACCTGATGAGCTCATT                         TCTCTTGCACAGCAGTACAGCTCCGAGTTCCTTCAATCAGAGCTTGAGAGG
genomic: TTGCAGATGATAAGCAACAAGGAACAACTGTATCACCTGATGAGCTCATTgtaagcaact ... ggtatttcagTCTCTTGCACAGCAGTACAGCTCCGAGTTCCTTCAATCAGAGCTTGAGAGG
EST: gi|208245912|gb|GE044784.1|GE044784
EST:     TTGCAGATGATAAGCAACAAGGAACAACTGTATCACCTGATGAGCTCATT                         TCTCTTGCACAGCAGTACAGCTCCGAGTTCCTTCAATCAGAGCTTGAGAGG
genomic: TTGCAGATGATAAGCAACAAGGAACAACTGTATCACCTGATGAGCTCATTgtaagcaact ... ggtatttcagTCTCTTGCACAGCAGTACAGCTCCGAGTTCCTTCAATCAGAGCTTGAGAGG
EST: gi|193562656|gb|FK519131.1|FK519131
EST:     TTGCAGATGATAAGCAACAAGGAACAACTGTATCACCTGATGAGCTCATT                         TCTCTTGCAACAGCAGTACAGCTCCGAGTTCCTTCAATCAGAGCTTGAGAG
genomic: TTGCAGATGATAAGCAACAAGGAACAACTGTATCACCTGATGAGCTCATTgtaagcaact ... ggtatttcagTCTCTTGCA-CAGCAGTACAGCTCCGAGTTCCTTCAATCAGAGCTTGAGAG
EST: gi|207802579|gb|GD772112.1|GD772112
EST:     TTGCAGATGATAAGCAACAAGGAACAACTGTATCACCTGATGAGCTCATT                         TCTCTTGCACAGCAGTACAGCTCCG
genomic: TTGCAGATGATAAGCAACAAGGAACAACTGTATCACCTGATGAGCTCATTgtaagcaact ... ggtatttcagTCTCTTGCACAGCAGTACAGCTCCG
EST: gi|254315381|gb|GR825190.1|GR825190
EST:     TTGCAGATGATAAGCAACAAGGAACAACTGTATCA-CTGATGAGCTCATT                         TCTCTTGCACAGCAGTACAGCTCCGAGTTCCTTCAATCAGAGCTTGAGAGG
genomic: TTGCAGATGATAAGCAACAAGGAACAACTGTATCACCTGATGAGCTCATTgtaagcaact ... ggtatttcagTCTCTTGCACAGCAGTACAGCTCCGAGTTCCTTCAATCAGAGCTTGAGAGG
EST: gi|254315380|gb|GR825189.1|GR825189
EST:     TTGCAGATGATAAGCAACAAGGAACAACTGTATCACCTGATGAGCTCATT                         TCTCTTGCACAGCAGTACAGCTCCGAGTTCCTTCAATCAGAGCTTGAGAGG
genomic: TTGCAGATGATAAGCAACAAGGAACAACTGTATCACCTGATGAGCTCATTgtaagcaact ... ggtatttcagTCTCTTGCACAGCAGTACAGCTCCGAGTTCCTTCAATCAGAGCTTGAGAGG
EST: gi|192303414|gb|FG995666.1|FG995666
EST:     TTGCAGATGATAAGCAACAAGGAACAACTGTATCACCTGATGAGCTCATT                         TCTCTTGCACAGCAGTACAGCTCCGAGTTCCTTCAATCAGAGCTTGAGAGG
genomic: TTGCAGATGATAAGCAACAAGGAACAACTGTATCACCTGATGAGCTCATTgtaagcaact ... ggtatttcagTCTCTTGCACAGCAGTACAGCTCCGAGTTCCTTCAATCAGAGCTTGAGAGG
EST: gi|193528704|gb|FK483534.1|FK483534
EST:     TTGCAGATGATAAGCAACAAGGAACAACTGTATCACCTGATGAGCTCATT                         TCTCTTGCACAGCAGTACAGCTCCGAGTTCCTTCAATCAGAGCTTGAGAGG
genomic: TTGCAGATGATAAGCAACAAGGAACAACTGTATCACCTGATGAGCTCATTgtaagcaact ... ggtatttcagTCTCTTGCACAGCAGTACAGCTCCGAGTTCCTTCAATCAGAGCTTGAGAGG
EST: gi|207796510|gb|GD767914.1|GD767914
EST:     TTGCAGATGATAAGCAACAAGGAACAACTGTATCACCTGATGAGCTCATT                         TCTCTTGCACAGCAGTACAGCTCCG
genomic: TTGCAGATGATAAGCAACAAGGAACAACTGTATCACCTGATGAGCTCATTgtaagcaact ... ggtatttcagTCTCTTGCACAGCAGTACAGCTCCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgttgaattctgttgctaaatttactatctaaagctatattttgggtatttcagTCTCTTGCACAGCAGTACAGCTCCGAGTTCCTTCAATCAGAGCTTGAGAGGACACGCATTAACACAGCATGCTTTGCAGAATCTATTCCTTTGGACTCTT
                 taaatttactatctaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgctggttttctatgttgtgaagtcggttctgatactagtcagtgtgttgaattctgttgctaaatttactatctaaagctatattttgggtatttcagTCTCTTGCACAGCAGTACAGCTCCGAGTTCCTTCAATCAGAGCTTGAGAGGACACGCATTAACACAGCATGCTTTGCAGAATCTATTCCTTTGGACTCTT

-tgctggt
- - - - - - - tgttgtg
- - - - - - - - - - - - - ggttctg
- - - - - - - - - - - - - - - - - - - - - -gtgtgtt