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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTCTTACGGGGTCTGAATGTGTCACTTTCTACTGATGATCCTCTCCAAATTCACTTAACAAAGGAACCATTGGTTGAAGAATATAGCATAGCTGCTTCTgtgagctctctctctctctctctctctctgtgcatgtgatataaacaagcaatgctcacagccaggatataaatcttactttacag

Basic information

species Glycine max
transcript GLYMA03G07460.1
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G07460.1 (Glycine max), 5'ss of exon 16
lower sequence: GRMZM2G416667_T03 (Zea mays), 5'ss of exon 17
CTTCTTACGGGGTCTGAATGTGTCACTTTCTACTGATGATCCTCTCCAAATTCACTTAACAAAGGAACCATTGGTTGAAGAATATAGCATAGCTGCTTCTgtgagctctctctctctctctctct----ctctgtgcatgtgatat-aaacaagcaatgctcaca------gccaggatataaatcttac---tttacag-----------------------------------------------------------------------
||||  ||| ||||||||||| ||| | ||||| ||||| ||| | ||||||||| | ||||| ||||||||||| |||||||| ||||| |||||||| ||   | ||   || ||| || | |    |  | ||  |||  | | | ||| |||   |   |       ||  |  |||  | |  ||   |||||                                                                         
CTTCCAACGAGGTCTGAATGTCTCATTATCTACGGATGACCCTTTGCAAATTCACCTGACAAAAGAACCATTGGTGGAAGAATACAGCATTGCTGCTTCGgtactcgctacttccctcgcttttttgcgccttttgattgttctttcacacatgcagcacgagctttgtgtgcacgtgtatgcagcacacacctttacgcatagatactattgtacccacgccaaaagggacgagtgactaatgtccattactccattttgattgtttcag

upper sequence: GLYMA03G07460.1 (Glycine max), 5'ss of exon 16
lower sequence: AT2G38280.1 (Arabidopsis thaliana), 5'ss of exon 16
CTTCTTACGGGGTCTGAATGTGTCACTTTCTACTGATGATCCTCTCCAAATTCACTTAACAAAGGAACCATTGGTTGAAGAATATAGCATAGCTGCTTCTgtgagctctc-tctctctctctctctctctgtgcatgtgatataaacaa-gcaatgctcacagccaggatataaatcttact--ttacag----------
 |||||| | ||||| ||||| || || ||||||||||| || || || ||||||||||| || |||||  | || ||||| |||||||||||||| || || ||   |  ||| ||  |    |  |||   ||      |||  |   | || | | |         || || ||||| |  |||             
TTTCTTAAGAGGTCTCAATGTTTCTCTGTCTACTGATGACCCCCTTCAGATTCACTTAACTAAAGAACCTCTCGTGGAAGAGTATAGCATAGCTGCATCAgtaagtcataatctttccattatgcagtcttgccacacatcataggccttgaaaagttgattatatttttaaaagtcttattagttattacctttaaatg

upper sequence: GLYMA03G07460.1 (Glycine max), 5'ss of exon 16
lower sequence: Vv08s0105g00570.t01 (Vitis vinifera), 5'ss of exon 16
CTTCTTACGGGGTCTGAATGTGTCACTTTCTACTGATGATCCTCTCCAAATTCACTTAACAAAGGAACCATTGGTTGAAGAATATAGCATAGCTGCTTCTgtgagctctctctctctctctctctctctgtgca--tgtgatataaacaagcaatgctcacagccaggatataaa----tcttactttacag
 ||| | ||||| || ||||| || || ||||| |||||||| || ||||| ||| ||||||| ||||| ||||| |||||||| ||||||||||||||||| |||||||||||||||||||||||||| | |      | ||| |   |   || ||   |    |  ||| |      || |  || |||
TTTCCTTCGGGGCCTCAATGTTTCCCTCTCTACAGATGATCCACTACAAATCCACCTAACAAAAGAACCCTTGGTGGAAGAATACAGCATAGCTGCTTCTgtaagctctctctctctctctctctctctcttccatcagggtattagggattgat-ctggtactttgtttatgataattcctcatcttgcag

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|58017264|gb|CX704006.1|CX704006
EST:     TTCACTTAACAAAGGAACCATTGGTTGAAGAATATAGCATAGCTGCTTCT                         GTGTGGAAGTTGAGCTCATGTGATTTATGTGAGATTGCCCGTAATTCAGTT
genomic: TTCACTTAACAAAGGAACCATTGGTTGAAGAATATAGCATAGCTGCTTCTgtgagctctc ... tactttacagGTGTGGAAGTTGAGCTCATGTGATTTATGTGAGATTGCCCGTAATTCAGTT
EST: gi|151401309|gb|EV271123.1|EV271123
EST:     TTCACTTAACAAAGGAACCATTGGTTGAAGAATATAGCATAGCTGCTTCT                         GTGTGGAAGTTGAGCTCATGTGATTTATGTGAGATTGCCCGTAATTCAGTT
genomic: TTCACTTAACAAAGGAACCATTGGTTGAAGAATATAGCATAGCTGCTTCTgtgagctctc ... tactttacagGTGTGGAAGTTGAGCTCATGTGATTTATGTGAGATTGCCCGTAATTCAGTT
EST: gi|58019743|gb|CX706485.1|CX706485
EST:     TTCACTTAACAAAGGAACCATTGGTTGAAGAATATAGCATAGCTGCTTCT                         GTGTGGAAGTTGAGCTCATGTGATTTATGTGAGATTGCCCGTAATTCAGTT
genomic: TTCACTTAACAAAGGAACCATTGGTTGAAGAATATAGCATAGCTGCTTCTgtgagctctc ... tactttacagGTGTGGAAGTTGAGCTCATGTGATTTATGTGAGATTGCCCGTAATTCAGTT
EST: gi|14126159|gb|BG790597.1|BG790597
EST:     TTCACTTAACAAAGGAACCATTGGTTGAAGAATATAGCATAGCTGCTTCT                         GTGTGGAAGTTGAGCTCATGTGATTTATGTGAGATTGCCCGTAATTCAGTT
genomic: TTCACTTAACAAAGGAACCATTGGTTGAAGAATATAGCATAGCTGCTTCTgtgagctctc ... tactttacagGTGTGGAAGTTGAGCTCATGTGATTTATGTGAGATTGCCCGTAATTCAGTT
EST: gi|57574541|gb|CX547516.1|CX547516
EST:     TTCACTTAACAAAGGAACCATTGGTTGAAGAATATAGCATAGCTGCTTCT                         GTGTGGAAGTTGAGCTCATGTGATTTATGTGAGATTGCCCGTAATTCAGTT
genomic: TTCACTTAACAAAGGAACCATTGGTTGAAGAATATAGCATAGCTGCTTCTgtgagctctc ... tactttacagGTGTGGAAGTTGAGCTCATGTGATTTATGTGAGATTGCCCGTAATTCAGTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTCTTACGGGGTCTGAATGTGTCACTTTCTACTGATGATCCTCTCCAAATTCACTTAACAAAGGAACCATTGGTTGAAGAATATAGCATAGCTGCTTCTgtgagctctctctctctctctctctctctgtgcatgtgatataaacaagcaatgctcacagccaggatataaatcttactttacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT