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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagctttgtgcttaattttgccccatttgtatttgttacaggtgtttatgattgttcttttattattttgtgattttagcttatggggtttgctgtgtttttttttctaatgaagGCAAACTGGTAACATGTACAAGAATGTGAAGAGGAAGATTGAGAGAGGTGTTGCCTTCCCGACATGTGTGTCTGTGAACAACACTGTCTGTCACTTCTCT

Basic information

species Glycine max
transcript GLYMA01G29420.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G29420.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv06s0004g06870.t01 (Vitis vinifera), 3'ss of exon 3
-------------------------------------gtaagctttgtgcttaattttgccccatt-tgtatttgttacaggtgtttatgattgttcttttattattttgtgattttagcttatggggtttgctg---------tgtttttttttctaatgaagGCAAACTGGTAACATGTACAAGAATGTGAAGAGGAAGATTGAGAGAGGTGTTGCCTTCCCGACATGTGTGTCTGTGAACAACACTGTCTGTCACTTCTCT
                                      |||  |||||  || | ||      ||  ||||| |  |     |||||   |||  | | |  |||||| |||   || | | ||||| |||| ||         || |||  ||     || ||||||||||| ||  ||||||| ||||| |||| |||||| ||||| |||||||| || ||||| ||  | || || ||||||||||| ||||||||||| 
gtatgatatgatatgataaattttgtttttctgaagcataatttttgtttttgagttaaagagataatgtatcttcttt---tgtttggcattagtttgtgtttatttggtgggatttgat-atgggttttgatgctacttaagtgatttggttgtggctgtagGCAAACTGGGAATGTGTACAAAAATGTCAAGAAGAAGATCGAGAGGGGTGTTGCATTTCCGACTTGCATTTCAGTAAACAACACTGTTTGTCACTTCTCA

upper sequence: GLYMA01G29420.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv08s0217g00020.t01 (Vitis vinifera), 3'ss of exon 2
------------------------------------------------------------gtaagctttgtgcttaattttgcc--------ccatttgtatttgttacaggtgtttatgattgttcttttattattttgtgattttagcttatggggtttgc---tgtgtttttttttcta---atgaagGCAAACTGGTAACATGTACAAGAATGTGAAGAGGAAGATTGAGAGAGGTGTTGCCTTCCCGACATGTGTGTCTGTGAACAACACTGTCTGTCACTTCTCT
                                                             || | |   |  || | | ||||          ||||  |||| ||   | | | |  | ||| | |||    |      |  |||| | ||| |   |      |  ||||| || | ||   ||| ||||||||||| || ||||||||||| || |||| |||||||||||| ||||||||||| || || ||  | ||||| ||||||||||||||||| || |||
gtgagccttctttttttacatagacattatattatgttgaatatttttttgataggcataatatgttcaatatttgagtatgccgatgtattttatttagatttcttgt-gttttgttgggttgatttttgcaaagaaaaaggctttatcatattgttataatctataggttttgttgtttatgtatgcagGCAAACTGGCAATATGTACAAGAACGTTAAGAAGAAGATTGAGAGGGGTGTTGCCTTTCCAACTTGCATTTCTGTTAACAACACTGTCTGTCATTTTTCT

upper sequence: GLYMA01G29420.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S119_137V6.1 (Physcomitrella patens), 3'ss of exon 2
gtaagctttgtgcttaattttgccccatttgtatttgttacaggtgtttatgattgttcttttattattttgtgattttagcttatggggtttgctgtgtttttttttctaatgaagGCAAACTGGTAACATGTACAAGAATGTGAAGAGGAAGATTGAGAGAGGTGTTGCCTTCCCGACATGTGTGTCTGTGAACAACACTGTCTGTCACTTCTCT
         ||  ||| || |   | ||         | | |||||||     ||| | |  | | | |||  |  || |  || |      ||||       |||| ||   | || | ||| |     |||||||||||  | || | ||| ||||| ||||| ||||| || || || || || ||||||||||||||||| ||||||||||||
---------gta-ttagttatattc-atcaactcaattgataggtgtt----gttgctgtcgtctgaatttacgtgttgaaattcttactgctgctaacggaattttact--cgcagTCTAACAGCAGGTATGTACAAGAACTTTAAAAAGAAAATTGACAGAGGAGTTGCATTTCCCACTTGCGTATCTGTGAACAACACTGTATGTCACTTCTCT

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|209710685|gb|BW676559.1|BW676559
EST:     AAGACAAAGATTGTTGACCTTTGCGAGAAAGGGGATTCGTATATTAGAGA                         GCAAACTGGTAACATGTACAAGAATGTGAAGAGGAAGATTGAGAGAGGTGT
genomic: AAGACAAAGATTGTTGACCTTTGCGAGAAAGGGGATTCGTATATTAGAGAgtaagctttg ... tctaatgaagGCAAACTGGTAACATGTACAAGAATGTGAAGAGGAAGATTGAGAGAGGTGT
EST: gi|192326702|gb|FK017329.1|FK017329
EST:     AAGACAAAGATTGTTGACCTTTGCGAGAAAGGGGATTCGTATATTAGAGA                         GCAAACTGGTAACATGTACAAGAATGTGAAGAGGTAGATTGAGAGAGGTGT
genomic: AAGACAAAGATTGTTGACCTTTGCGAGAAAGGGGATTCGTATATTAGAGAgtaagctttg ... tctaatgaagGCAAACTGGTAACATGTACAAGAATGTGAAGAGGAAGATTGAGAGAGGTGT
EST: gi|298195396|gb|HO039227.1|HO039227
EST:     AAGACAAAGATTGTTGACCTTTGCGAGAAAGGGGATTCGTATATTAGAGA                         GCAAACTGGTAACATGTACAAGAATGTGAAGAGGAAGATTGAGAGAGGTGT
genomic: AAGACAAAGATTGTTGACCTTTGCGAGAAAGGGGATTCGTATATTAGAGAgtaagctttg ... tctaatgaagGCAAACTGGTAACATGTACAAGAATGTGAAGAGGAAGATTGAGAGAGGTGT
EST: gi|13478014|gb|BG507662.1|BG507662
EST:     AAGACAAAGATTGTTGACCTTTGCGAGAAAGGGGATTCGTATATTAGAGA                         GCAAACTGGTAACATGTACAAGAATGTGAAGAGGAAGATTGAGAGAGGTGT
genomic: AAGACAAAGATTGTTGACCTTTGCGAGAAAGGGGATTCGTATATTAGAGAgtaagctttg ... tctaatgaagGCAAACTGGTAACATGTACAAGAATGTGAAGAGGAAGATTGAGAGAGGTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattattttgtgattttagcttatggggtttgctgtgtttttttttctaatgaagGCAAACTGGTAACATGTACAAGAATGTGAAGAGGAAGATTGAGAGAGGTGTTGCCTTCCCGACATGTGTGTCTGTGAACAACACTGTCTGTCACTTCTCT
                                            ttctaat  putative branch site (score: 2)
                                ctgtgtttttttttct  CT-rich tract
                                     tttttttttctaatga  TA-rich tract