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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttgtattttccaatgtagtattagtgacacttattagcgtatagttagtcatatctttttgttgctgtcttctaacagAGTTACGAGACCACTGAGAGCAGAATCAAAAGGGAGTTTGAGTCATATGGTCCAATCAAACGG

Basic information

species Glycine max
transcript GLYMA11G07200.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G07200.2 (Glycine max), 3'ss of exon 5
lower sequence: Vv04s0023g01580.t01 (Vitis vinifera), 3'ss of exon 5
---------gtaagttgtattttccaatgtagtattagtgac-acttattagcgtatagttagtcatatctt-tttgttgctgtcttctaacagAGTTACGAGACCACTGAGAGCAGAATCAAAAGGGAGTTTGAGTCATATGGTCCAATCAAACGG
              ||  | | |  |   |  |  || |  | |   ||||    |      |   ||| || ||| ||    | || | |||||  || ||||| |||||||||||||||||||||||||||||| | ||||| |||||||| |||
gtgagtattaatgattacactctttatcatttttctattttctatccattattaaactcactgatttattttattttttatattttttttacagAACTATGAGACAACTGAGAGCAGAATCAAAAGGGAGTTTGAGGCTTATGGGCCAATCAAGCGG

upper sequence: GLYMA11G07200.2 (Glycine max), 3'ss of exon 5
lower sequence: EFJ17734 (Selaginella moellendorffii), 3'ss of exon 5
gtaagttgtattttccaatgtagtattagtgacacttattagcgtatagttagtcatatctttttgttgctgtcttctaacagAGTTACGAGACCACTGAGAGCAGAATCAAAAGGGAGTTTGAGTCATATGGTCCAATCAAACGG------
|||||||   |||  |      ||  | |  |  |||          |  | ||| | | || || ||  | ||||   | ||||||||||||| || ||   || ||| ||||||||||||||| ||||||||||||| ||| ||      
gtaagtttcttttctcctctatgtcctggcaaggctt---------catcttgtcctttgttcttttttttttctttccatagAGTTACGAGACAACGGAACACAAAATTAAAAGGGAGTTTGAGGCATATGGTCCAATAAAAAGGGTAGGT
















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|209727268|gb|BW655253.1|BW655253
EST:     ACCCAAATGTGTCGGGAGATCCATACAAGACATTGTTTGTGGCTAAACTC                         AGTTACGAGACCACTGAGAGCAGAATCAAAAGGGAGTTTGAGTCATATGGT
genomic: ACCCAAATGTGTCGGGAGATCCATACAAGACATTGTTTGTGGCTAAACTCgtaagttgta ... cttctaacagAGTTACGAGACCACTGAGAGCAGAATCAAAAGGGAGTTTGAGTCATATGGT
EST: gi|209728976|gb|BW655019.1|BW655019
EST:     ACCCAAATGTGTCGGGAGATCCATACAAGACATTGTTTGTGGCTAAACTC                         AGTTACGAGACCACTGAGAGCAGAATCAAA-GGGAGTTTGAGTCATATGGT
genomic: ACCCAAATGTGTCGGGAGATCCATACAAGACATTGTTTGTGGCTAAACTCgtaagttgta ... cttctaacagAGTTACGAGACCACTGAGAGCAGAATCAAAAGGGAGTTTGAGTCATATGGT
EST: gi|209698445|gb|BW667242.1|BW667242
EST:     ACCCAAATGTGTCGGGAGATCCATACAAGACATTGTTTGTGGCTAAACTC                         AGTTACGAGACCACTGAGAGCAGAATCAAAAGGGAGTTTGAGTCATATGGT
genomic: ACCCAAATGTGTCGGGAGATCCATACAAGACATTGTTTGTGGCTAAACTCgtaagttgta ... cttctaacagAGTTACGAGACCACTGAGAGCAGAATCAAAAGGGAGTTTGAGTCATATGGT
EST: gi|11412754|gb|BF424765.1|BF424765
EST:     ACCCAGATGTGTCGGGAGATCCATACAAGACATTGTTTGTGGCTAAACTC                         AGTTACGAGACCACTGAGAGCAGAAATCAAAAGG-ATGTTTGAGTCATATG
genomic: ACCCAAATGTGTCGGGAGATCCATACAAGACATTGTTTGTGGCTAAACTCgtaagttgta ... cttctaacagAGTTACGAGACCACTGAGAGCAGAA-TCAAAAGGGA-GTTTGAGTCATATG
EST: gi|213603451|gb|DB970492.1|DB970492
EST:     ACCCAAATGTGTCGGGAGATCCATACAAGACATTGTTTGTGGCTAAACTC                         AGTTACGAGACCACTGAGAGCAGAATCAAAAGGGAGTTTGAGTCATATGGT
genomic: ACCCAAATGTGTCGGGAGATCCATACAAGACATTGTTTGTGGCTAAACTCgtaagttgta ... cttctaacagAGTTACGAGACCACTGAGAGCAGAATCAAAAGGGAGTTTGAGTCATATGGT
EST: gi|18039679|gb|BM307973.1|BM307973
EST:     ACCCAAATGTGTCGGGAGATCCATACAAGACATTGTTTGTGGCTAAACTC                         AGTTACGAGACCACTGAGAGCAGAATCAAAAGGGAG
genomic: ACCCAAATGTGTCGGGAGATCCATACAAGACATTGTTTGTGGCTAAACTCgtaagttgta ... cttctaacagAGTTACGAGACCACTGAGAGCAGAATCAAAAGGGAG
EST: gi|213618444|gb|DB963373.1|DB963373
EST:     ACCCAAATGTGTCGGGAGATCCATACAAGACATTGTTTGTGGCTAAACTC                         AGTTACGAGACCACTGAGAGCAGAATCAAAAGGGAGTTTGAGTCATATGGT
genomic: ACCCAAATGTGTCGGGAGATCCATACAAGACATTGTTTGTGGCTAAACTCgtaagttgta ... cttctaacagAGTTACGAGACCACTGAGAGCAGAATCAAAAGGGAGTTTGAGTCATATGGT
EST: gi|8826552|gb|BE210282.1|BE210282
EST:     ACCCAAATGTGTCGGGAGATCCATACAAGACATTGTTTGTGGCTAAACTC                         AGTTACGAGACCACTTAGAGCAGAATCAAAAAGGAGTTTTAGTCATATGGG
genomic: ACCCAAATGTGTCGGGAGATCCATACAAGACATTGTTTGTGGCTAAACTCgtaagttgta ... cttctaacagAGTTACGAGACCACTGAGAGCAGAATCAAAAGGGAGTTTGAGTCATATGGT
EST: gi|26058824|gb|CA801738.1|CA801738
EST:     ACCCAAATGTGTCGGGAGATCCATACAAGACATTGTTTGTGGCTAAACTC                         AGTTACGAGACCACTGAGAGCAGAATCAAAAGGGAGTTTGAGTCATATGGT
genomic: ACCCAAATGTGTCGGGAGATCCATACAAGACATTGTTTGTGGCTAAACTCgtaagttgta ... cttctaacagAGTTACGAGACCACTGAGAGCAGAATCAAAAGGGAGTTTGAGTCATATGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgacacttattagcgtatagttagtcatatctttttgttgctgtcttctaacagAGTTACGAGACCACTGAGAGCAGAATCAAAAGGGAGTTTGAGTCATATGGTCCAATCAAACGG
                                         ctgtcttct  CT-rich tract
                           atatcttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttgtattttccaatgtagtattagtgacacttattagcgtatagttagtcatatctttttgttgctgtcttctaacagAGTTACGAGACCACTGAGAGCAGAATCAAAAGGGAGTTTGAGTCATATGGTCCAATCAAACGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG