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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattctgttataatgttcaataatgtgtcagtttgtcattaatttggaaaattccatttgatttcattcacaaaacagctcattgagagttttgttgcattgccttgtttggcagAGCGAGAGGTTGCACAAGGTTCTTGAATTTGTGAGTACGGTGCATGATCTATGTGCTGTCCTTGGTATAGACTTCTTCACTACTGTAACTGAGGTTCATC

Basic information

species Glycine max
transcript GLYMA02G46450.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G46450.3 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os06g40840.1 (Oryza sativa), 3'ss of exon 4
gtaattctgttataatgttcaataatgtgtcagtttgtcattaatttggaaaattccatttgat-ttcattcacaaaacagctcattgagagttttgttgcattgccttgtttggcagAGCGAGAGGTTGCACAAGGTTCTTGAATTTGTGAGTACGGTGCATGATCTATGTGCTGTCCTTGGTATAGACTTCTTCACTACTGTAACTGAGGTTCATC
       || ||||       ||||| | |   ||   ||   ||||   |    | |||| |  || ||| ||   | | |  |||       |  || ||||  ||||  | ||||||| | ||  |||||||| ||||||| || |||||| | ||||||||||| ||| |||||||||| || || ||| | |  ||||| ||||| |||||||
-------tgatatagctgatgataatctttgcattatacacacattttcga----ctatttaaaatttattgacttgaaatcgtatt-------tctttccattttcttgcattgcagAGCAATAGACTGCACAAGATTCTTGACTTCGTGAGTTCAGTGCATGATCTCTGTTCTGTCCTTGGGATGGATTTCCTGAGCACTGTTACTGAAGTTCATC

upper sequence: GLYMA02G46450.3 (Glycine max), 3'ss of exon 4
lower sequence: AT4G26760.1 (Arabidopsis thaliana), 3'ss of exon 4
gtaattctgttataatgttcaataatgtgtcagtttgtcattaatttggaaaattccatttg-atttcattcacaaaacagctcattgagagttttgttgcattgccttgtttggcagAGCGAGAGGTTGCACAAGGTTCTTGAATTTGTGAGTACGGTGCATGATCTATGTGCTGTCCTTGGTATAGACTTCTTCACTACTGTAACTGAGGTTCATC
                                ||     |||| || ||| |     || ||      ||   |||| |||   | | | |       ||| |||  ||  |  |||||| || ||||| || ||||| || || |||||||| |||||||||||||||||||| |||||| || |||| ||||| |  ||||| || || |||||||
--------------------------------gtaaaatattagttgggatatggttatgtgtggcctatgttcaaaccaga--actaaaa------ctgctttgtgtt--tgagcagAGTGATAGGTTACAGAAGGTGCTCGAGTTTGTGAGCACGGTGCATGATCTATGTGCCGTCCTTCGTTTAGATTTCTTAAGCACTGTCACCGAAGTTCATC

upper sequence: GLYMA02G46450.3 (Glycine max), 3'ss of exon 4
lower sequence: AT5G55230.1 (Arabidopsis thaliana), 3'ss of exon 4
gtaattctgttataatgttcaataatgtgtcagtttgtcattaatttggaaaattccatttgatttcattcacaaaacagctcattgagagttttgttgc--attgccttgttt-ggcagAGCGAGAGGTTGCACAAGGTTCTTGAATTTGTGAGTACGGTGCATGATCTATGTGCTGTCCTTGGTATAGACTTCTTCACTACTGTAACTGAGGTTCATC
                                  |   |||| | || ||||  ||| |            | |  | |  |   | |   |||  || |  | |||  ||||| ||||||| || ||| ||| ||||||  | || ||||||||||| || ||||||||||||||||| |||||| | || ||||| |  || || || || |||||||
---------------------------------gtaaacattgagttagaaatctccgt------------atatgatatgttgcttatgttttccttaccaactgctctgttttggcagAGTGACAGGCTGCGCAAGGTGTTAGAGTTTGTGAGTACTGTTCATGATCTATGTGCTGTTCTTGGTTTGGATTTCTTAAGCACCGTCACCGAAGTTCATC

upper sequence: GLYMA02G46450.3 (Glycine max), 3'ss of exon 4
lower sequence: Vv19s0090g01230.t01 (Vitis vinifera), 3'ss of exon 3
gtaattctgttataatgttcaataatgtgtcagtttgtcattaatttggaaaattccatttgatttcattcacaaaacagctcattgagagttttgttgcattgccttgtttggcagAGCGAGAGGTTGCACAAGGTTCTTGAATTTGTGAGTACGGTGCATGATCTATGTGCTGTCCTTGGTATAGACTTCTTCACTACTGTAACTGAGGTTCATC
                ||  ||| ||   ||||||   || ||  || |  |    | |||    |    || |   |   |||     |       |  |||   |  | || ||||| || |||||||||||||| ||||| |||||||| || || ||||||||||||||||||||||| || |||||||| | |||||| ||||| |||||||
----------------gtaaaattatagatcagttca-cactatattagttatggacttttatgctagcccatatgtc--ttcaggatcaccaccaattaattatttgatctgccagAGTGACAGGTTGCACAAGGTCCTTGAGTTTGTGAGCACTGTTCATGATCTATGTGCTGTCCTTGGGATGGACTTCTTTAATACTGTTACTGAAGTTCATC

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|17022059|gb|BM093093.1|BM093093
EST:     AGAAGTTGGATGAATATCAATCCGAGCTCCAAGAACTTCAAAAGGAAAAG                         AGCGAGAGGTTGCACAAGGTTCTTGAATTTGTGAGTACGGTGCATGATCTA
genomic: AGAAGTTGGATGAATATCAATCCGAGCTCCAAGAACTTCAAAAGGAAAAGgtaattctgt ... tgtttggcagAGCGAGAGGTTGCACAAGGTTCTTGAATTTGTGAGTACGGTGCATGATCTA
EST: gi|151397195|gb|EV267068.1|EV267068
EST:     TGGATGAATATCAATCCGAGCTCCAAGAACTTCAAAAGGAAAAG                         AGCGAGAGGTTGCACAAGGTTCTTGAATTTGTGAGTACGGTGCATGATCTA
genomic: TGGATGAATATCAATCCGAGCTCCAAGAACTTCAAAAGGAAAAGgtaattctgt ... tgtttggcagAGCGAGAGGTTGCACAAGGTTCTTGAATTTGTGAGTACGGTGCATGATCTA
EST: gi|208301779|gb|GE099009.1|GE099009
EST:     AGAAGTTGGATGAATATCAATCCGAGCTCCAAGAACTTCAAAAGGAAAAG                         AGCGAGAGGTTGCACAAGGTTCCTGAATTTGTGAGTACGGTGCATGATCTA
genomic: AGAAGTTGGATGAATATCAATCCGAGCTCCAAGAACTTCAAAAGGAAAAGgtaattctgt ... tgtttggcagAGCGAGAGGTTGCACAAGGTTCTTGAATTTGTGAGTACGGTGCATGATCTA
EST: gi|193712473|gb|FK649636.1|FK649636
EST:     AGAAGTTGGATGAATATCAATCCGAGCTCCAAGAACTTCAAAAGGAAAAG                         AGCGAGAGGTTGCACAAGGTTCTTGAATTTGTGAGTACGGTGCATGATCTA
genomic: AGAAGTTGGATGAATATCAATCCGAGCTCCAAGAACTTCAAAAGGAAAAGgtaattctgt ... tgtttggcagAGCGAGAGGTTGCACAAGGTTCTTGAATTTGTGAGTACGGTGCATGATCTA
EST: gi|193607364|gb|FK558251.1|FK558251
EST:     AGAAGTTGGATGAATATCAATCCGAGCTCCAAGAACTTCAAAAGGAAAAG                         AGCGAGAGGTTGCACAAGGTTCTTGAATTTGTGAGTACGGTGCATGATCTA
genomic: AGAAGTTGGATGAATATCAATCCGAGCTCCAAGAACTTCAAAAGGAAAAGgtaattctgt ... tgtttggcagAGCGAGAGGTTGCACAAGGTTCTTGAATTTGTGAGTACGGTGCATGATCTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttcattcacaaaacagctcattgagagttttgttgcattgccttgtttggcagAGCGAGAGGTTGCACAAGGTTCTTGAATTTGTGAGTACGGTGCATGATCTATGTGCTGTCCTTGGTATAGACTTCTTCACTACTGTAACTGAGGTTCATC
 atttgat  putative branch site (score: 5)
                                          ccttgttt  putative PPT
                             ttttgtt  TA-rich tract