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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacttactttttcccagatacgatttatttattaccaatcaacgcggtatgccatgccttaattgacggttcatgtgcctgcagGCTTCAGAAATTTGGAGCATGATATCTCAAGGAGCTTACATTTATGTGTGTGGTGATGCCAAGGGCATGGCCAGGGATGTACACCGTGCCCTGCACACAA

Basic information

species Glycine max
transcript GLYMA13G00990.1
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G00990.1 (Glycine max), 3'ss of exon 16
lower sequence: LOC_Os08g14570.1 (Oryza sativa), 3'ss of exon 15
---------gtacttactttttcccagatacgatttatttat-taccaatcaacgc----ggtatgccatgccttaattgacggttcatgtgcctgcagGCTTCAGAAATTTGGAGCATGATATCTCAAGGAGCTTACATTTATGTGTGTGGTGATGCCAAGGGCATGGCCAGGGATGTACACCGTGCCCTGCACACAA
          |||||    ||| | | | | | ||| || || | | |||  | |     | |  ||  |||    |||  |      |||   | |||||||| ||||| |||  |||||| || || || | ||||||||| || |||||||||||||| ||||||||||| ||||||||  | |  || ||||| |
gtaattgaactacttgacattttc-atacatg-tttgttgatctgcaaattcatgtttttgttcagcgttgctcatatttcctacctttgtctgtccagGCTTCCGAAATCTGGGACATGATCTCCCAGGGTGGTTACATTTACGTCTGTGGTGATGCCAAAGGCATGGCCAGAGATGTACATAGAGTTCTCCACACCA

upper sequence: GLYMA13G00990.1 (Glycine max), 3'ss of exon 16
lower sequence: GRMZM2G144407_T01 (Zea mays), 3'ss of exon 16
-----gtacttactttttcccagatacgatttatttattaccaatcaa-cgcggtatgccatgccttaattgacggttcatgtgcctgcagGCTTCAGAAATTTGGAGCATGATATCTCAAGGAGCTTACATTTATGTGTGTGGTGATGCCAAGGGCATGGCCAGGGATGTACACCGTGCCCTGCACACAA
       |  | ||  ||  | ||| | | ||   |  | ||   ||| | | ||    ||   ||         |||||| |   | ||||| || ||||| |||  |||||| || ||||| |||||||| ||||| |||||||||||||| ||||||||||| ||||||||  | |  || ||||| |
gtaacacagctgctcgttttctgat-caactt--ctgctgccctccaaacccagtggctcactgctcttgcctttgttcattt-tttccagGCATCTGAAATCTGGGACATGATCTCCCAAGGTGCTTACATCTATGTCTGTGGTGATGCCAAAGGCATGGCCAGAGATGTACATAGAGTTCTCCACACCA

upper sequence: GLYMA13G00990.1 (Glycine max), 3'ss of exon 16
lower sequence: AC217947.4_FGT002 (Zea mays), 3'ss of exon 15
gtactta--ctttttcccagatacgatttatttattaccaatcaacgcggtatgccatgcctt--aattgacgg-ttcatgtgcctgcagGCTTCAGAAATTTGGAGCATGATATCTCAAGGAGCTTACATTTATGTGTGTGGTGATGCCAAGGGCATGGCCAGGGATGTACACCGTGCCCTGCACACAA
||| | |  ||  |   |   |   |    | | |||||   |||| ||  |  |  || ||   | ||   |  ||  |     | ||||| || ||||| |||  |||||| || ||||| |||||||| ||||| |||||||| ||||| ||||||||||| || |||||  | |  || || || |
gtaatcaagctgctcatcttgtgacaaacttctgttaccctccaacccgtaacccagtggctcacagttcttgcctttgtccatttccagGCATCTGAAATCTGGGACATGATCTCCCAAGGTGCTTACATCTATGTCTGTGGTGACGCCAAAGGCATGGCCAGAGACGTACATAGAGTTCTCCATACCA

upper sequence: GLYMA13G00990.1 (Glycine max), 3'ss of exon 16
lower sequence: AT4G30210.1 (Arabidopsis thaliana), 3'ss of exon 15
gtacttactttttcccagatacgatttatttattaccaatcaacgcggtatgccatgccttaattgacggttcatgtgcc-tgcagGCTTCAGAAATTTGGAGCATGATATCTCAAGGAGCTTACATTTATGTGTGTGGTGATGCCAAGGGCATGGCCAGGGATGTACACCGTGCCCTGCACACAA
|||    ||| |    |   |  | | |  | || |  ||  |  |    |   || | | |  ||||  |   | |||  |||||||||| || || ||||  ||||| ||||||||||||||  | ||||| |||||||| ||||| |||||||| || ||||| ||| |  | || |||||||
gtatgagcttatagaaacccaaaactcagatctt-catatagattcaaattcagattcttgagctgacaatctttctgcaatgcagGCTTCTGATATCTGGAATATGATCTCTCAAGGAGCTTATTTATATGTTTGTGGTGACGCCAAAGGCATGGCAAGAGATGTTCACAGATCTCTCCACACAA

upper sequence: GLYMA13G00990.1 (Glycine max), 3'ss of exon 16
lower sequence: Vv11s0052g00880.t01 (Vitis vinifera), 3'ss of exon 16
-------------------------------------gtacttactttttcccagatacg---atttatttattaccaatcaacgcggtatgccatgccttaattgacggttcatgtgcctgcagGCTTCAGAAATTTGGAGCATGATATCTCAAGGAGCTTACATTTATGTGTGTGGTGATGCCAAGGGCATGGCCAGGGATGTACACCGTGCCCTGCACACAA
                                     | | ||  | |||   | |||     || ||| |||||     ||     || ||  |||| | | |  | | ||  | |   |  |||| || || |||||||   | || ||||| ||||  ||||||||||| |||||||||||||| |||||||| |||||||| ||| |  | || || || |
gtacgggactctcatttctcagaagggccattcatctgaagtttttgtttttgatatatatatatatatgtattattgtccatt--tgtttgagatgc-taagtgcatgtttgctttatatctagGCGTCGGATATTTGGAATGTAATTTCTCAGGGAGGCTACATTTATGTCTGTGGTGATGCCAAAGGCATGGCAAGGGATGTCCACAGAACTCTTCATACCA

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|209728345|gb|BW659982.1|BW659982
EST:     CTCGAGAGGGACCCACCAAGGAGTATGTACAACATAAAATGATGGAGAAG                         GCTTCAGAAATTTGGAGCATGATATCTCAAGGAGCTTACATTTATGTGTGT
genomic: CTCGAGAGGGACCCACCAAGGAGTATGTACAACATAAAATGATGGAGAAGgtacttactt ... gtgcctgcagGCTTCAGAAATTTGGAGCATGATATCTCAAGGAGCTTACATTTATGTGTGT
EST: gi|209722908|gb|BW669454.1|BW669454
EST:     ACAACATAAAATGATGGAGAAG                         GCTTCAGNAAA-TTGGAGCATGATATCTCAAGGAGCTTACATTTATGTGTG
genomic: ACAACATAAAATGATGGAGAAGgtacttactt ... gtgcctgcagGCTTCAG-AAATTTGGAGCATGATATCTCAAGGAGCTTACATTTATGTGTG
EST: gi|254318721|gb|GR828665.1|GR828665
EST:     CTCGAGAGGGACCCACCAAGGAGTATGTACAACATAAAATGATGGAGAAG                         GCTTCAGAAATTTGGAGCATGATATCTCAAGGAGCTTACATTTATGTGTGT
genomic: CTCGAGAGGGACCCACCAAGGAGTATGTACAACATAAAATGATGGAGAAGgtacttactt ... gtgcctgcagGCTTCAGAAATTTGGAGCATGATATCTCAAGGAGCTTACATTTATGTGTGT
EST: gi|209729002|gb|BW655032.1|BW655032
EST:     CTCGAGAGGGACCCACCAAGGAGTATGTACAACATAAAATGATGGAGAAG                         GCTTCAGAAATTTGGAGCATGATATCTCAAGGAGCTTACATTTATGTGTGT
genomic: CTCGAGAGGGACCCACCAAGGAGTATGTACAACATAAAATGATGGAGAAGgtacttactt ... gtgcctgcagGCTTCAGAAATTTGGAGCATGATATCTCAAGGAGCTTACATTTATGTGTGT
EST: gi|6914702|gb|AW396232.1|AW396232
EST:     CTCGAGAGGGACCCACCAAGGAGTATGTACAACATAAAATGATGGAGAAG                         GCTTCAGAAATTTGGAGCATGATATCTCAAGGAGCTTACATTTATGTGTGT
genomic: CTCGAGAGGGACCCACCAAGGAGTATGTACAACATAAAATGATGGAGAAGgtacttactt ... gtgcctgcagGCTTCAGAAATTTGGAGCATGATATCTCAAGGAGCTTACATTTATGTGTGT
EST: gi|209699334|gb|BW664053.1|BW664053
EST:     CATAAAATGATGGAGAAG                         GCTTCAGAAATCTGGAGCCTGATATCTCAAGGAGCTTACATTTATGTGTGT
genomic: CATAAAATGATGGAGAAGgtacttactt ... gtgcctgcagGCTTCAGAAATTTGGAGCATGATATCTCAAGGAGCTTACATTTATGTGTGT
EST: gi|209727361|gb|BW663346.1|BW663346
EST:     CATAAAATGATGGAGAAG                         GCTTCAGAAATTTGGAGCATGATATCTCAAGGAGCTTACATTTATGTGTGT
genomic: CATAAAATGATGGAGAAGgtacttactt ... gtgcctgcagGCTTCAGAAATTTGGAGCATGATATCTCAAGGAGCTTACATTTATGTGTGT
EST: gi|4313809|gb|AI460928.1|AI460928
EST:     CTCGAGAGGGACCCACCAAGGAGTATGTACC-CATAAAATGATGGAGAAG                         GCTTCAGAAATTTGNAGCATGATATCTCAAGGAGCT
genomic: CTCGAGAGGGACCCACCAAGGAGTATGTACAACATAAAATGATGGAGAAGgtacttactt ... gtgcctgcagGCTTCAGAAATTTGGAGCATGATATCTCAAGGAGCT
EST: gi|209710559|gb|BW670983.1|BW670983
EST:     CATAAAATGATGGAGAAG                         GCTTCAGAAATTTGGAGCATGATATCTCAAGGAGCTTACATTTATGTGTGT
genomic: CATAAAATGATGGAGAAGgtacttactt ... gtgcctgcagGCTTCAGAAATTTGGAGCATGATATCTCAAGGAGCTTACATTTATGTGTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattaccaatcaacgcggtatgccatgccttaattgacggttcatgtgcctgcagGCTTCAGAAATTTGGAGCATGATATCTCAAGGAGCTTACATTTATGTGTGTGGTGATGCCAAGGGCATGGCCAGGGATGTACACCGTGCCCTGCACACAA
                               aattgac  putative branch site (score: 3)
                             ttaattga  TA-rich tract