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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacaagatggatggacacagattttatgcttactattttcagtgctggtatatgagattgggtttgttttataaaatcacagGCCGTTGGGAAAGTTCTTCCTGAGCTAAATGGGAAACTCACTGGGATGGCATTCCGTGTACCGACTCCCAATGTTTCTGTGGTGGACTTGACTTGCCGGC

Basic information

species Glycine max
transcript GLYMA03G22790.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G22790.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os02g07490.1 (Oryza sativa), 3'ss of exon 10
gtacaagatggatggacacagattttatgcttactattttcagtgctggtatatgagattgggtttgttttataaaatcacagGCCGTTGGGAAAGTTCTTCCTGAGCTAAATGGGAAACTCACTGGGATGGCATTCCGTGTACCGACTCCCAATGTTTCTGTGGTGGACTTGACTTGCCGGC
      |   |||| ||  | | | ||   |   | | |  | | ||| | |    || ||  ||  ||   ||       |||| ||||||||||| || |||||||||||||| || |||||||| ||||| ||||| || || || || ||||| ||||| || |||||||| |||||| 
------gtacgatgaaccaaaaatctaccttgcttttctagatttctgttttggctgactgttttgattccttat-----tagGCTGTTGGGAAAGTCCTCCCTGAGCTAAATGGAAAGCTCACTGGTATGGCCTTCCGAGTTCCAACACCAAATGTGTCTGTTGTCGACTTGACCTGCCGGA

upper sequence: GLYMA03G22790.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G051004_T01 (Zea mays), 3'ss of exon 10
gtacaagatggatggacacagattttatgcttactattttcagtgctggtatatgagattgggtttgttttataaaatcacagGCCGTTGGGAAAGTTCTTCCTGAGCTAAATGGGAAACTCACTGGGATGGCATTCCGTGTACCGACTCCCAATGTTTCTGTGGTGGACTTGACTTGCCGGC
|||   ||  |    |  || |   |  |  |  ||   |||    | | |     || ||  ||   ||| |    |  ||||| ||||| |||||||| |||||||| ||||| || |||||||| ||||| ||||| || || || || ||||| ||||| ||||||||||| |||||| 
gtagctga-agccaaaggcacaccatgcgtattttagactcaaattttgcact---gactgatttcactttgt----tgtcagGCTGTTGGAAAAGTTCTGCCTGAGCTGAATGGAAAGCTCACTGGCATGGCCTTCCGAGTTCCAACACCAAATGTCTCTGTTGTGGACTTGACATGCCGGA

upper sequence: GLYMA03G22790.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G104632_T01 (Zea mays), 3'ss of exon 10
gtacaagatggatggacacagattttatgctta--ctattttcagtgctggtatatgagattgggtttgttttataaaatcacagGCCGTTGGGAAAGTTCTTCCTGAGCTAAATGGGAAACTCACTGGGATGGCATTCCGTGTACCGACTCCCAATGTTTCTGTGGTGGACTTGACTTGCCGGC
     || || |   | |   |    ||| |||   ||   |||    | | |  |   | ||| ||   |||||    |  ||||| ||||| ||||| || |||||||| ||||| ||||||||||| ||||| ||||| || || || || ||||| ||||| ||||| ||||| |||||| 
---gtagctgaagccaaaggcacaccatgtttagtttagactcaaattttgcactt---actggtttcactttat----tgtcagGCTGTTGGAAAAGTCCTGCCTGAGCTGAATGGAAAACTCACTGGTATGGCCTTCCGAGTTCCAACACCAAATGTCTCTGTTGTGGATTTGACATGCCGGA

upper sequence: GLYMA03G22790.1 (Glycine max), 3'ss of exon 10
lower sequence: AT1G79530.1 (Arabidopsis thaliana), 3'ss of exon 10
gtacaagatggatggacacag--attttatgcttactattttcagtgctggtatatgagattgggtttgt---tttataaaatcacagGCCGTTGGGAAAGTTCTTCCTGAGCTAAATGGGAAACTCACTGGGATGGCATTCCGTGTACCGACTCCCAATGTTTCTGTGGTGGACTTGACTTGCCGGC
|||||  |   |   |||  |  ||   | || |   ||| ||     | |   || | ||  |   |||   ||| | |      |||| || || ||||||||||| || || ||||||||||| || || ||||| ||||||||||| ||  | ||||||||||||||||| || ||||| || |
gtacacaa-aaactcacatggttatcgcaagcatgtaattatcctaaatcgggaatcatatctgagctgtggttttttgatcaagtagGCTGTAGGTAAAGTTCTTCCAGAACTGAATGGGAAACTTACGGGAATGGCCTTCCGTGTACCAACATCGAATGTTTCTGTGGTGGATTTAACTTGTCGAC

upper sequence: GLYMA03G22790.1 (Glycine max), 3'ss of exon 10
lower sequence: PP1S309_73V6.3 (Physcomitrella patens), 3'ss of exon 7
----------------------------gtacaagatggatggacacagattttatgctta-ctattttcagtgctggtatatgagattgggtttgttttataaaatc------------acagGCCGTTGGGAAAGTTCTTCCTGAGCTAAATGGGAAACTCACTGGGATGGCATTCCGTGTACCGACTCCCAATGTTTCTGTGGTGGACTTGACTTGCCGGC
                            |   |    |||  |    |  || |      |  | | |  |  |   | | ||  |  ||       |||     |               ||||| || || || || || || ||  | |||||||| |||||||| ||||| |||||||| || ||||||||||| |||||||| ||| ||||    || |
gtactgtgctcattatttggaccctggtggttagatgggactgctgtaagttgtgaatggagttgtctgtaaagtctgaacataggcctgatcccaattttcgtgactcgggattttcatgcagGCTGTGGGCAAGGTACTGCCAGAATTGAATGGGAAGCTCACTGGTATGGCTTTCCGTGTGCCAACTCCCAATGTGTCTGTGGTAGACCTGACCGTGCGAC

upper sequence: GLYMA03G22790.1 (Glycine max), 3'ss of exon 10
lower sequence: PP1S309_84V6.1 (Physcomitrella patens), 3'ss of exon 8
---------------------------------gtacaagatggatggacacagattttatgcttactattttcagtgctggt---atatgagattgg-----gtttgttttat--aaaatc-----acagGCCGTTGGGAAAGTTCTTCCTGAGCTAAATGGGAAACTCACTGGGATGGCATTCCGTGTACCGACTCCCAATGTTTCTGTGGTGGACTTGACTTGCCGGC
                                 | ||      |   |    |  || | ||      ||| || |  ||| |   | ||  |  ||      | ||   |  |     ||      ||||||||| || || || || || ||||| |||||||| ||||| || ||||| |||||||| |||||||||||||| |||||||||||  |||||   || |
gtactgtgcacgacagttgaatccttggcgagtgcactcatgaggctgctgtaagttatgtgagcggaattgtctgcactgattcaacattggcctgatcgtcgctttcctcgttcgggattttcaaacagGCCGTGGGCAAGGTGCTGCCAGAGCTGAATGGGAAGCTCACCGGTATGGCTTTCCGTGTCCCGACTCCCAATGTGTCTGTGGTGGATCTGACTGTGCGTC

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|151403747|gb|EV273557.1|EV273557
EST:     GAAGAGGGGCAGCTCAAAATATAATTCCAAGTTCAACTGGTGCTGCGAAG                         GCCGTTGGGAAAGTTCTTCCTGAGCTAAATGGGAAACTCACTGGGATGGCA
genomic: GAAGAGGGGCAGCTCAAAATATAATTCCAAGTTCAACTGGTGCTGCGAAGgtacaagatg ... aaaatcacagGCCGTTGGGAAAGTTCTTCCTGAGCTAAATGGGAAACTCACTGGGATGGCA
EST: gi|17022180|gb|BM093214.1|BM093214
EST:     CAAGTTCAACTGGTGCTGCGAAG                         GCCGTTGGGAAAGTTCTTCCTGAGCTAAATGGGAAACTCACTGGGATGGCA
genomic: CAAGTTCAACTGGTGCTGCGAAGgtacaagatg ... aaaatcacagGCCGTTGGGAAAGTTCTTCCTGAGCTAAATGGGAAACTCACTGGGATGGCA
EST: gi|193539491|gb|FK494751.1|FK494751
EST:     TCAAAATATAATTCCAAGTTCAACTGGTGCTGCGAAG                         GCCGTTGGGAAAGTTCTTCCTGAGCTAAATGGGAAACTCACTGGGATGGCA
genomic: TCAAAATATAATTCCAAGTTCAACTGGTGCTGCGAAGgtacaagatg ... aaaatcacagGCCGTTGGGAAAGTTCTTCCTGAGCTAAATGGGAAACTCACTGGGATGGCA
EST: gi|15589578|gb|BI674194.1|BI674194
EST:     GAAGAGGGGCAGCTCAAAATATAATTCCAAGTTCAACTGGTGCTGCGAAG                         GCCGTTGGGAAAGTTCTTCCTGAGCTAAATGGGAAACTCACTGGGATGGCA
genomic: GAAGAGGGGCAGCTCAAAATATAATTCCAAGTTCAACTGGTGCTGCGAAGgtacaagatg ... aaaatcacagGCCGTTGGGAAAGTTCTTCCTGAGCTAAATGGGAAACTCACTGGGATGGCA
EST: gi|51334832|gb|CO978698.1|CO978698
EST:     GAAGAGGGGCAGCTCAAAATATAATTCCAAGTTCAACTGGTGCTGCGAAG                         GCCGTTGGGAAAGTTCTTCCTGAGCTAAATGGGAAACTCACTGGGATGGCA
genomic: GAAGAGGGGCAGCTCAAAATATAATTCCAAGTTCAACTGGTGCTGCGAAGgtacaagatg ... aaaatcacagGCCGTTGGGAAAGTTCTTCCTGAGCTAAATGGGAAACTCACTGGGATGGCA
EST: gi|22927146|gb|BU544285.1|BU544285
EST:     GAAGAGGGGCAGCTCAAAATATAATTCCAAGTTCAACTGGTGCTGCGAAG                         GCCGTTGGGAAAGTTCTTCNNGAGCTAAATGGGAAACTCACTGGGATGGCA
genomic: GAAGAGGGGCAGCTCAAAATATAATTCCAAGTTCAACTGGTGCTGCGAAGgtacaagatg ... aaaatcacagGCCGTTGGGAAAGTTCTTCCTGAGCTAAATGGGAAACTCACTGGGATGGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcttactattttcagtgctggtatatgagattgggtttgttttataaaatcacagGCCGTTGGGAAAGTTCTTCCTGAGCTAAATGGGAAACTCACTGGGATGGCATTCCGTGTACCGACTCCCAATGTTTCTGTGGTGGACTTGACTTGCCGGC
 tgcttac  putative branch site (score: 2)
                                   tttgttttataaaatc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacaagatggatggacacagattttatgcttactattttcagtgctggtatatgagattgggtttgttttataaaatcacagGCCGTTGGGAAAGTTCTTCCTGAGCTAAATGGGAAACTCACTGGGATGGCATTCCGTGTACCGACTCCCAATGTTTCTGTGGTGGACTTGACTTGCCGGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA