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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattctgttataatgttcaataatgagtcagttcagtttgtcactactttggaaaattccttttgatttcatttactaaacagctcattgagagttttgttgcattgccttgtttggcagAGTGAGAGGTTGCACAAGGTTCTTGAATTTGTGAGTACTGTGCATGATCTATGTGCTGTCCTTGGTATGGACTTCTTCAGTACTGCAACTGAGGTTCATC

Basic information

species Glycine max
transcript GLYMA14G02180.4
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G02180.3 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os06g40840.1 (Oryza sativa), 3'ss of exon 4
gtaattctgttataatgttcaataatgagtcagttcagtttgtcactactttggaaaattccttttgatttcatttactaaacagctcattgagagttttgttgcattgccttgtttggcagAGTGAGAGGTTGCACAAGGTTCTTGAATTTGTGAGTACTGTGCATGATCTATGTGCTGTCCTTGGTATGGACTTCTTCAGTACTGCAACTGAGGTTCATC
          |   ||     || || | ||  | || | |      | ||| ||  |||    |  | || ||| |||  | | |  |||       |  || ||||  ||||  | ||||||  | ||  |||||||| ||||||| || |||||| | ||||||||||| ||| |||||||||| ||||| ||| | || ||||  ||||| |||||||
----------tgatatagctgatgataa-tctttgcattatacacacattttcgactatt----taaaatttattgacttgaaatcgtatt-------tctttccattttcttgcattgcagAGCAATAGACTGCACAAGATTCTTGACTTCGTGAGTTCAGTGCATGATCTCTGTTCTGTCCTTGGGATGGATTTCCTGAGCACTGTTACTGAAGTTCATC

upper sequence: GLYMA14G02180.3 (Glycine max), 3'ss of exon 4
lower sequence: AT4G26760.1 (Arabidopsis thaliana), 3'ss of exon 4
gtaattctgttataatgttcaataatgagtcagttcagtttgtcactactttggaaaattccttttgatttcatttactaaacagctcattgagagttttgttgcattgccttgtttggcagAGTGAGAGGTTGCACAAGGTTCTTGAATTTGTGAGTACTGTGCATGATCTATGTGCTGTCCTTGGTATGGACTTCTTCAGTACTGCAACTGAGGTTCATC
                                     ||     | || || || | ||   | |   |  | | |  | ||      |     | |     ||| |||  |  ||  ||||||||| ||||| || ||||| || || |||||||| || ||||||||||||||||| |||||| || | || ||||| || ||||  || || |||||||
-------------------------------------gtaaaatattagtt-gggatatggttatgtgtggcctatgttcaa------accagaactaaaactgctttgtgt--ttgagcagAGTGATAGGTTACAGAAGGTGCTCGAGTTTGTGAGCACGGTGCATGATCTATGTGCCGTCCTTCGTTTAGATTTCTTAAGCACTGTCACCGAAGTTCATC

upper sequence: GLYMA14G02180.3 (Glycine max), 3'ss of exon 4
lower sequence: AT5G55230.1 (Arabidopsis thaliana), 3'ss of exon 4
gtaattctgttataatgttcaataatgagtcagttcagtttgtcactactttggaaaattccttttgatttcatttactaaacagctcattgagagttttgttgc--attgccttgttt-ggcagAGTGAGAGGTTGCACAAGGTTCTTGAATTTGTGAGTACTGTGCATGATCTATGTGCTGTCCTTGGTATGGACTTCTTCAGTACTGCAACTGAGGTTCATC
                                       |   || |   || ||||  ||| |        || |  ||    ||| ||      |||  || |  | |||  ||||| |||||||||| ||| ||| ||||||  | || |||||||||||||| ||||||||||||||||| |||||| |||| ||||| || || |  || || |||||||
--------------------------------------gtaaacattgagttagaaatctccgt--------atatgatatgttgcttat----gttttccttaccaactgctctgttttggcagAGTGACAGGCTGCGCAAGGTGTTAGAGTTTGTGAGTACTGTTCATGATCTATGTGCTGTTCTTGGTTTGGATTTCTTAAGCACCGTCACCGAAGTTCATC

upper sequence: GLYMA14G02180.3 (Glycine max), 3'ss of exon 4
lower sequence: Vv19s0090g01230.t01 (Vitis vinifera), 3'ss of exon 3
gtaattctgttataatgttcaataatgagtcagttcagtttgtcactactttggaaaattccttttgatttcatttactaaacagctcattgagagttttgttgcattgccttgtttggcagAGTGAGAGGTTGCACAAGGTTCTTGAATTTGTGAGTACTGTGCATGATCTATGTGCTGTCCTTGGTATGGACTTCTTCAGTACTGCAACTGAGGTTCATC
                ||  ||| ||   ||||||||   | | | || ||  | |  ||  |  |     ||| |        | |||     | ||       |||   |  | || |||||||| |||||||||||||| ||||| |||||||| ||||| ||||||||||||||||||||||| ||||||||||| | |||||  ||||| |||||||
----------------gtaaaattatagatcagttcacactat-attagttatggacttttatgctagcc-catatgtcttcaggatcaccaccaatt------aattatttgatctgccagAGTGACAGGTTGCACAAGGTCCTTGAGTTTGTGAGCACTGTTCATGATCTATGTGCTGTCCTTGGGATGGACTTCTTTAATACTGTTACTGAAGTTCATC

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|7147025|gb|AW508947.1|AW508947
EST:     AGAAGTTGGATGAATATCAATCTGAGCTCCAAGAACTTCAAAAGGAAAAG                         AGTGAGAGGTTGCACAAGGTTCTTGAATTTGTGAGTACTGTGCATGATCTA
genomic: AGAAGTTGGATGAATATCAATCTGAGCTCCAAGAACTTCAAAAGGAAAAGgtaattctgt ... tgtttggcagAGTGAGAGGTTGCACAAGGTTCTTGAATTTGTGAGTACTGTGCATGATCTA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttcatttactaaacagctcattgagagttttgttgcattgccttgtttggcagAGTGAGAGGTTGCACAAGGTTCTTGAATTTGTGAGTACTGTGCATGATCTATGTGCTGTCCTTGGTATGGACTTCTTCAGTACTGCAACTGAGGTTCATC
        tactaaa  putative branch site (score: 1)
                                          ccttgttt  putative PPT
     atttactaaa  TA-rich tract