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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgtatgcagtaattgtgttcaaatggcataagccttttgttactatgcattaatttttctttttttatttttcattcagACATTAAGACGGCTTGCTCAAAATCGTGAGGCTGCCAGGAAAAGCCGACTGAGGAAAAAG

Basic information

species Glycine max
transcript GLYMA03G28320.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G28320.2 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os07g48820.2 (Oryza sativa), 3'ss of exon 4
-----gttgtatgcagtaattgtgttcaaatggcataagccttttgttactatgcattaatttttctttttttatttttcattca---gACATTAAGACGGCTTGCTCAAAATCGTGAGGCTGCCAGGAAAAGCCGACTGAGGAAAAAG
      || || |      || | |||  ||   ||  | |  ||  |  | ||   | | |||  | || |  |||  ||| ||   |||| |  | ||||||||||||||||||||||| || || ||||| || ||||||||||||
gtgacatttta-gttccgtttcttttcgtatacaat--gtcacttaatcttgtgtgattaatttcatattgtattttggcatgcaatagACAATTCGGCGGCTTGCTCAAAATCGTGAGGCAGCAAGAAAAAGTCGGCTGAGGAAAAAG

upper sequence: GLYMA03G28320.2 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os03g20310.2 (Oryza sativa), 3'ss of exon 4
-----gttgtatgcagtaattgtgttcaaatggca-taagccttttgttactatgcattaatttttctttttttatttttcattcagACATTAAGACGGCTTGCTCAAAATCGTGAGGCTGCCAGGAAAAGCCGACTGAGGAAAAAG
       | |||    || || |  |  | ||  | | | |||||  | |  |||   |        | | ||| || ||| |  ||   ||| | |||||||||||||||||||||||||| || ||||| || ||||| ||||||
gtgttaatttatctcctatttcttgtgcagtgctacttatcctttcttaatgatggtatttaggaagtatgtttgttattc-tgtagGTGTTACGCCGGCTTGCTCAAAATCGTGAGGCTGCAAGAAAAAGTCGGCTGAGAAAAAAG

upper sequence: GLYMA03G28320.2 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G056099_T02 (Zea mays), 3'ss of exon 3
--gttgtatgcagtaattgtgttcaaatggcataagccttttgttactat---gcattaat----ttttctttttttatttttcattc---agACATTAAGACGGCTTGCTCAAAATCGTGAGGCTGCCAGGAAAAGCCGACTGAGGAAAAAG
   ||   |        | | |     |    |      |||||||| ||    || | ||    | |   |  |  ||||   ||||   ||   ||| |||||||||| |||||||||||||| || || |||||||| ||||||||||||
gtattaattttgtctcctatctctctgtactctttagtgtttgttaccatttcacaatgatggtatctagatgatgcatttggtattctttagGTTTTACGACGGCTTGCCCAAAATCGTGAGGCAGCAAGAAAAAGCCGGCTGAGGAAAAAG

upper sequence: GLYMA03G28320.2 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G174284_T01 (Zea mays), 3'ss of exon 4
----------gttgtatgcagtaattgtgttcaaatggc-ataagccttttgttactatgcattaatttttctttttttatttttcattcagACATTAAGACGGCTTGCTCAAAATCGTGAGGCTGCCAGGAAAAGCCGACTGAGGAAAAAG
           |  ||||   |   |    |  | ||    | | | |||    |  ||| | |     |  |   |||  | ||| || ||   ||| |||||||||| |||||||||||||| || |||||||| || ||||||||||||
gtttttttatctcatatgtcttctgtactctttagtgtttgttaccatttcacaatgatggaatctagataatgcatttgatattc-tttagGTTTTACGACGGCTTGCCCAAAATCGTGAGGCAGCAAGGAAAAGTCGGCTGAGGAAAAAG

upper sequence: GLYMA03G28320.2 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G030280_T02 (Zea mays), 3'ss of exon 3
gttgtatgcagtaattgtgttcaaatggcataagccttttgttactatgcattaatttttcttttt--ttatttttcatt---cagACATTAAGACGGCTTGCTCAAAATCGTGAGGCTGCCAGGAAAAGCCGACTGAGGAAAAAG
          ||    || || |||| ||||     || |  | | |||  |    | ||  ||||  |||| ||| |||   ||||||||  | || ||||||||||||||||||||||| ||||| |||||||| ||||| |||
----------gtgcaggt-ttgaaatagcattcttgttctcattccatgtttctgctgtttcttttacttatatttgattttgcagACATTGCGTCGCCTTGCTCAAAATCGTGAGGCTGCAAGGAAGAGCCGACTAAGGAAGAAG

upper sequence: GLYMA03G28320.2 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G361847_T04 (Zea mays), 3'ss of exon 3
gttgtat-gcagtaattgtgttcaaatggcata---agccttttgttactatgcattaatttttctttttttatttttcat---tcagACATTAAGACGGCTTGCTCAAAATCGTGAGGCTGCCAGGAAAAGCCGACTGAGGAAAAAG
||  ||| |  ||   | | |   ||   | ||   | |||| | || ||    |||||||   | ||||| | |||||||   | ||||| |  |||||||||| |||||||||||||| || || ||||| || ||||||||||||
gtaatatcgtggttcctttttctcaagttcttatttaaccttgtattgcttgttattaattg--catttttgaattttcatatcttagACAATGCGACGGCTTGCCCAAAATCGTGAGGCAGCAAGAAAAAGTCGGCTGAGGAAAAAG

upper sequence: GLYMA03G28320.2 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G125243_T02 (Zea mays), 3'ss of exon 6
-----------gttgtatgcagtaattgtgttcaaatggcataagccttttgttactatgcattaatttttctttttttatttttcattcagACATTAAGACGGCTTGCTCAAAATCGTGAGGCTGCCAGGAAAAGCCGACTGAGGAAAAAG----------------------------------------
             | |||   |  |   || |||  ||   ||| ||  |  ||| | |  ||    |||   | | || ||||| |  |||||| |  | || ||||| ||||||||||| |||||||||||||||||| |  | ||||||                                        
gtactcttatcactatatcatgatacattgatcatgtgt--taatccactgcttaatgtaaatattatttatatatattttttttaaaacagACACTTCGGCGTCTTGCCCAAAATCGTGAAGCTGCCAGGAAAAGCCGATTACGAAAAAAGGTAATTTGGAAGTTGGAAGATTACTGAATCTTTGCTTCTT

upper sequence: GLYMA03G28320.2 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G125243_T01 (Zea mays), 3'ss of exon 5
-----------gttgtatgcagtaattgtgttcaaatggcataagccttttgttactatgcattaatttttctttttttatttttcattcagACATTAAGACGGCTTGCTCAAAATCGTGAGGCTGCCAGGAAAAGCCGACTGAGGAAAAAG
             | |||   |  |   || |||  ||   ||| ||  |  ||| | |  ||    |||   | | || ||||| |  |||||| |  | || ||||| ||||||||||| |||||||||||||||||| |  | ||||||
gtactcttatcactatatcatgatacattgatcatgtgt--taatccactgcttaatgtaaatattatttatatatattttttttaaaacagACACTTCGGCGTCTTGCCCAAAATCGTGAAGCTGCCAGGAAAAGCCGATTACGAAAAAAG

upper sequence: GLYMA03G28320.2 (Glycine max), 3'ss of exon 6
lower sequence: Vv08s0007g05170.t01 (Vitis vinifera), 3'ss of exon 5
---gttgtatgcagtaattgtgttcaaatggcataagccttttgttactatgcattaatttttctttttttatt--tttcattcagACATTAAGACGGCTTGCTCAAAATCGTGAGGCTGCCAGGAAAAGCCGACTGAGGAAAAAG
       | |  | || || | || | |||  | | || |    | |  |||   | | |||  |  ||| ||   | |  ||||||||||| | |||||||||||||||||||| |||||||| ||||||||| | |||||||||
gttaaaatttaaattagttatatttagatgataca-gcttagcataataatgttcttaatttgttcctttgatcaatcttcttcagACATTACGCCGGCTTGCTCAAAATCGTGAAGCTGCCAGAAAAAGCCGATTAAGGAAAAAG

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|120530210|gb|EH258344.1|EH258344
EST:     CCTGAAAGGGATGAATCCAGTGGATCAAAAGATAAATCAGATCAAAAG                         ACATTAAGACGGCTTGCTCAAAATCGTGAGGCTGCCAGGAAAAGCCGACTG
genomic: CCTGAAAGGGATGAATCCAGTGGATCAAAAGATAAATCAGATCAAAAGgttgtatgca ... tttcattcagACATTAAGACGGCTTGCTCAAAATCGTGAGGCTGCCAGGAAAAGCCGACTG
EST: gi|193450264|gb|FK414358.1|FK414358
EST:     ATCAAAAGATAAATCAGATCAAAAG                         ACATTAAGACGGCTTGCTCAAAATCGTGAGGCTGCCGGGAAAAGCCGACTG
genomic: ATCAAAAGATAAATCAGATCAAAAGgttgtatgca ... tttcattcagACATTAAGACGGCTTGCTCAAAATCGTGAGGCTGCCAGGAAAAGCCGACTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggcataagccttttgttactatgcattaatttttctttttttatttttcattcagACATTAAGACGGCTTGCTCAAAATCGTGAGGCTGCCAGGAAAAGCCGACTGAGGAAAAAG
                       cattaat  putative branch site (score: 3)
                         ttaatttttctttttt  CT-rich tract
          ttttgttactatgcat  TA-rich tract