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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgcactgttcagctagatttgcattcacttgattcagttttgaataacttttcagctgatggttggatgaatctggttgcctgcagCTTGACTTCCAGCTTCCTGATCGTTTTAAGTTGGAATTCTCAGCTGAGGATGAAGCCAAAATTGAGAGACCTGTAATGATACACAGAGCCATTCTAGGAT

Basic information

species Glycine max
transcript GLYMA02G03750.1
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G03750.1 (Glycine max), 3'ss of exon 15
lower sequence: LOC_Os08g19850.1 (Oryza sativa), 3'ss of exon 16
gtttgcactgttcagctagatttgcattcacttgattcagttttgaataacttttcagctgatggttggatgaatctggttgcctg---cagCTTGACTTCCAGCTTCCTGATCGTTTTAAGTTGGAATTCTCAGCTGAGGATGAAGCCAAAATTGAGAGACCTGTAATGATACACAGAGCCATTCTAGGAT
         |||    |  || | ||||   ||  || | || |  | |   |   || | ||  ||   | ||  |  || ||||   ||||| || || ||||| ||    || || ||| ||   | ||| || ||||||||||||||| ||||||| ||||| ||||| ||||| || || ||||| |
---------gttatattgaatgt-cattttgtt--tttaattgtagacagaatagaaggttat--ttatctaaacttcatttcctgttacagCTCGATTTTCAGCTGCCCCTACGCTTCAAGCTGACTTACTCTGCAGAGGATGAAGCCAAACTTGAGAGGCCTGTGATGATTCACAGGGCAATCCTAGGTT

upper sequence: GLYMA02G03750.1 (Glycine max), 3'ss of exon 15
lower sequence: GRMZM2G553314_T01 (Zea mays), 3'ss of exon 16
gtttgcactgttcagctagatttgcattcacttgattcagttttgaataacttttcagctgatggttggatgaatctggttgcctgcagCTTGACTTCCAGCTTCCTGATCGTTTTAAGTTGGAATTCTCAGCTGAGGATGAAGCCAAAATTGAGAGACCTGTAATGATACACAGAGCCATTCTAGGAT
         ||||   |  || |  ||||  |      |   |||||  | |  | | || |   ||  || | |    |    | ||||| || || ||||| ||   ||| || ||| |||  |  || ||||||||||||||||||||||| || ||||| ||||||||||| || || ||||| |
---------gttcccttgaatgt-tattctgtcatcaaatgattgaaatagtaattatctaacc-ttacattatt---atctgttacagCTGGATTTTCAGCTGCCCATTCGGTTCAAGCTGGCTTATTCTGCTGAGGATGAAGCCAAAATTGAAAGGCCTGTGATGATACACAGGGCAATCCTAGGTT

upper sequence: GLYMA02G03750.1 (Glycine max), 3'ss of exon 15
lower sequence: GRMZM2G137615_T01 (Zea mays), 3'ss of exon 5
gtttgcactgttcagctagatttgcattcacttgattcagt-tttgaataacttttcagctgatggttggatgaatctggttgcctgcagCTTGACTTCCAGCTTCCTGATCGTTTTAAGTTGGAATTCTCAGCTGAGGATGAAGCCAAAATTGAGAGACCTGTAATGATACACAGAGCCATTCTAGGAT
         ||||   |  || |  ||||  |   | |||  || ||||||   || | || |   |    |  |||||      | ||||| || || ||||| ||   ||| || ||| ||   |  || |||||||||||||| |||||||| || ||||| ||||||||||| || || ||||| |
---------gttcgcttgaatgt-tattctatcattacagaattagaataatcatttatctaaccatgtatt--atctg-----ttacagCTGGATTTTCAGCTGCCCATTCGGTTCAAGCTGACTTATTCTGCTGAGGATGAAGCAAAAATTGAAAGGCCTGTGATGATACACAGGGCAATCCTAGGTT

upper sequence: GLYMA02G03750.1 (Glycine max), 3'ss of exon 15
lower sequence: AT5G26830.1 (Arabidopsis thaliana), 3'ss of exon 16
-----gtttgcactgttcagctagatttgc--attcacttgattcagttttgaataacttttcagctgatggttggatgaatctggttgcctg----cagCTTGACTTCCAGCTTCCTGATCGTTTTAAGTTGGAATTCTCAGCTGAGGATGAAGCCAAAATTGAGAGACCTGTAATGATACACAGAGCCATTCTAGGAT
       |  ||   |     ||| ||| |   |  |     |||  ||     || |  | |||  | || ||  |||  ||| || ||||     |||||||| || || |||||   ||| || || ||||||| | |||||||||||||||| ||||     ||||||||||||||||| |||||| |  | ||||
gttatactcccaaattctttttagtttttcttgtctatgcatttctcttgctgttatcagtgcaggagttgattttatgtttcttgtggcctcaaatcagCTTGATTTTCAACTTCCGATTCGCTTCAACTTGGAATACGCAGCTGAGGATGAAGCGAAAAAGAGTAGACCTGTAATGATACATAGAGCCGTGTTGGGAT

upper sequence: GLYMA02G03750.1 (Glycine max), 3'ss of exon 15
lower sequence: Vv19s0015g00470.t01 (Vitis vinifera), 3'ss of exon 16
--------------------gtttgcactgttcagctagat-ttgcattcacttgattcagttttgaataacttttcagctgatggttggatgaatctggttgcctgcagCTTGACTTCCAGCTTCCTGATCGTTTTAAGTTGGAATTCTCAGCTGAGGATGAAGCCAAAATTGAGAGACCTGTAATGATACACAGAGCCATTCTAGGAT
                     |||  | | || ||   | |  | | ||       ||  ||   |||| |  ||| |  |  ||| |     ||| |||||||    |||| ||||| |||||||||  ||||||| | |||   | |||||| ||||||||||| || |  ||||||||||| ||||||||| ||||||| ||||| |
gtttatcatgttaacttgctttttttattctttagtgtgctgctacttttgtactttttggtgcggaattaggttttaattagtggat-----aatgtggttgc----agCTGGACTTTCAGCTTCCTTCTCGTTTTGACTTGTCTTACTCAGCAGAGGATGAAGCTAAGAGGGAGAGACCTGTCATGATACACCGAGCCATCCTAGGGT

upper sequence: GLYMA02G03750.1 (Glycine max), 3'ss of exon 15
lower sequence: Vv01s0026g00340.t01 (Vitis vinifera), 3'ss of exon 16
gtttgcactgttcagctagatttg--cattcacttgatt-------cagttttgaataacttttcagctgatggttggatgaatctggt----tgcctgcagCTTGACTTCCAGCTTCCTGATCGTTTTAAGTTGGAATTCTCAGCTGAGGATGAAGCCAAAATTGAGAGACCTGTAATGATACACAGAGCCATTCTAGGAT
||||    ||||||  |    |||  |||||  | |  |       || || ||  |   | | |||     ||||  |    |  | |    ||| ||||||| ||||| |||||||||  ||||||| | |||   | |||||||||||||||||| || |  ||||||||||| ||||||||| ||||||| ||||| |
gtttatcatgttcacttgctcttgttcattctttcgtgtgctgcaacacttgtgctttcttgtgcagaattaggttttaattgttggataatgtgcttgcagCTGGACTTTCAGCTTCCTTCTCGTTTTGATTTGTCTTACTCAGCTGAGGATGAAGCTAAGAGGGAGAGACCTGTCATGATACACCGAGCCATCCTAGGGT

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|9900873|gb|BE609841.1|BE609841
EST:     TCAGTGTATCTGATGCATTGGGTAGGAAATTCCAGTGTGCAACTTTGCAG                         CTTGACTTCCAGCTTCCTGATCGTTTTAAGTTGGAATTCTCAGCTGAGGAT
genomic: TCAGTGTATCTGATGCATTGGGTAGGAAATTCCAGTGTGCAACTTTGCAGgtttgcactg ... ttgcctgcagCTTGACTTCCAGCTTCCTGATCGTTTTAAGTTGGAATTCTCAGCTGAGGAT
EST: gi|6341579|gb|AW164403.1|AW164403
EST:     TCAGGGTATCTGATGCATTGGGTAGGAAATTCCAGTGTGCAACTTTGCAG                         CTTGACTTCCAGCTTCCTGATCGTTTTAAGTTGGAATTCTCAGCTGAGGAT
genomic: TCAGTGTATCTGATGCATTGGGTAGGAAATTCCAGTGTGCAACTTTGCAGgtttgcactg ... ttgcctgcagCTTGACTTCCAGCTTCCTGATCGTTTTAAGTTGGAATTCTCAGCTGAGGAT
EST: gi|13478764|gb|BG508107.1|BG508107
EST:     TCAGTGTATCTGATGCATTGGGTAGGAAATTCCAGTGTGCAACTTTGCAG                         CTTGACTTCCAGCTTCCTGATCGTTTTAAGTTGGAATTCTCAGCTGAGGAT
genomic: TCAGTGTATCTGATGCATTGGGTAGGAAATTCCAGTGTGCAACTTTGCAGgtttgcactg ... ttgcctgcagCTTGACTTCCAGCTTCCTGATCGTTTTAAGTTGGAATTCTCAGCTGAGGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attcagttttgaataacttttcagctgatggttggatgaatctggttgcctgcagCTTGACTTCCAGCTTCCTGATCGTTTTAAGTTGGAATTCTCAGCTGAGGATGAAGCCAAAATTGAGAGACCTGTAATGATACACAGAGCCATTCTAGGAT
      ttttgaataactttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgcactgttcagctagatttgcattcacttgattcagttttgaataacttttcagctgatggttggatgaatctggttgcctgcagCTTGACTTCCAGCTTCCTGATCGTTTTAAGTTGGAATTCTCAGCTGAGGATGAAGCCAAAATTGAGAGACCTGTAATGATACACAGAGCCATTCTAGGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC