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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgaagtttcatcttcctttgaatgatgttcaatgacttgtatgaatgtttgtactctcaaaaggcttgagcaagcacatctctgtgcatccttatgcaagataatatggaaccagtagtgggaagaaattttcttaatgcttacattttgtggtgaatgtcttctgcagTTGCTTGAGGCAGCTTGGTGTCTCACAAATATTGCTGCAGGGAATCCAGAAGAAACAAAAGCTTTGTTGCCTGCATTGCCCTTGCTTATTGCTCATCTTG

Basic information

species Glycine max
transcript GLYMA13G20090.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G20090.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g06470.1 (Oryza sativa), 3'ss of exon 3
gtctgaagtttcatcttcctttgaatgatgttcaatgacttgtatgaatgtttgtactctcaaaaggcttgagcaagcacatctctgtgcatccttatgcaagataatatggaaccagtagtgggaagaaattttcttaatgcttacattttgtggtgaatgtcttctgcagTTGCTTGAGGCAGCTTGGTGTCTCACAAATATTGCTGCAGGGAATCCAGAAGAAACAAAAGCTTTGTTGCCTGCATTGCCCTTGCTTATTGCTCATCTTG
                     |  || ||| |  |  | |||| |  | | |  ||   |||  |    | |  ||||  |  |   ||  | |    |||  |||||     | |  | ||     ||| |||   |  |      |   | |  ||| |   |  |||||||||| |||||||||||||| || ||||| || || || ||| | ||||||||||||||| | ||| |||||||  | || |||||||||||||| ||||
--------------------gttgatcatgctgcactaattgtttcgaagct-atatcttcattaaatattataaagctgagttgaatgtgttca---gcattataattctatatcttttgttatttgaagtttgtctcttatcaggaccat-tcatgatt--ttaatgcagTTGCTAGAGGCAGCTTGGTGCCTTACAAACATAGCAGCTGGGGAACCAGAAGAAACAAAATCCTTGCTGCCTGCTCTACCATTGCTTATTGCTCACCTTG

upper sequence: GLYMA13G20090.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G165692_T01 (Zea mays), 3'ss of exon 3
gtctgaagtttcatcttcctttgaatgatgttcaatgacttgtatgaatgtttgtactctcaaaaggcttgagcaa-gcacatctctgtgcatccttatgcaagataatatggaaccagtagtgggaagaaattttcttaatgcttacattttgtggtgaatgtcttctgcagTTGCTTGAGGCAGCTTGGTGTCTCACAAATATTGCTGCAGGGAATCCAGAAGAAACAAAAGCTTTGTTGCCTGCATTGCCCTTGCTTATTGCTCATCTTG
                    ||||      | |  | | |  |    || | |       |||      |||| || |      | |||  ||| ||   || ||||||       |  || |  |  ||  ||||||   |    | ||| |        | |    |||||||||| |||||||||||||| || ||||| || || |||||||| || || ||||| ||| | ||  | |||||  | || ||||| |||||||| ||||
-------------------gttgagcacactccgcttattgttccatatctctaccagtacaactaaactgagtaaagtttgggtgtgttgatcatt-cacatgataattgtatcactatactcagttgatcttttctct-tatcaagattcttcatgcttttttaattgcagTTGCTAGAGGCAGCTTGGTGCCTTACAAACATAGCGGCAGGGAAACCTGAGGAAACTAAATCCTTACTTCCTGCTCTACCATTGCTCATTGCTCACCTTG

upper sequence: GLYMA13G20090.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G03070.1 (Arabidopsis thaliana), 3'ss of exon 3
gtctgaagtttcatcttcctttgaatgatgttcaatg----acttgtatgaatgtttgtactctcaaaaggcttgagcaagcacatctctgtgcatccttatgcaagataatatggaaccagtagtgggaagaaattttcttaatgcttaca-ttttgtggtgaatgtctt------ctgcagTTGCTTGAGGCAGCTTGGTGTCTCACAAATATTGCTGCAGGGAATCCAGAAGAAACAAAAGCTTTGTTGCCTGCATTGCCCTTGCTTATTGCTCATCTTG
       ||| ||| || | ||  ||    || |||     || | | |   ||  | || |  |  |    ||   |  |||| |  ||||  ||  | |    |  |||      |    | |   ||||| || ||    |   ||  | | || || | |  ||  |      |||||||| |||||| ||||||||||||| || || |||||||| || || || ||||||||||||||| | || ||||||||||| || || |||||||| ||||
-------gttacat-ttgccttatatatgctttaatactatacctttgttcttgcatttatttgcttatatattcgtccggcactttactgtagattttgac---aagtaactc---atgcattgaaagaagatatattaaggagagttgtaatcttttgatcacagttctgtctaactgcagTTACTTGAGTCAGCTTGGTGTCTTACCAACATTGCTGCTGGAAAACCTGAAGAAACAAAAGCTCTATTACCTGCATTGCCGTTACTCATTGCTCACCTTG

upper sequence: GLYMA13G20090.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv08s0040g02290.t01 (Vitis vinifera), 3'ss of exon 3
gtctgaagtttcatcttcctttgaatgatgttcaatgacttgtatgaatgtttgtactctcaaaaggcttgagcaagcacatctctgtgcatccttatgcaagat-aatatggaaccagtagtgggaagaaattttcttaatgcttacattttg-tggtgaatgtctt-ctgcagTTGCTTGAGGCAGCTTGGTGTCTCACAAATATTGCTGCAGGGAATCCAGAAGAAACAAAAGCTTTGTTGCCTGCATTGCCCTTGCTTATTGCTCATCTTG
                                                                            | |   || | ||  |    ||  || ||    |||| |  | ||   | ||    | |  ||| |      ||| |  |    | |||  |  ||||||||||||||||||||||||| || ||||||||||| || || || ||||||||||||||||||||| |||||||||| ||  |||||||||||||| | |
---------------------------------------------------------------------------tggattactgtttgtcttaccatttaaaattggcatgggagaactaaaagaaaactttctgattattatcacaattataattacaattgttatattgcagTTGCTTGAGGCAGCTTGGTGCCTTACAAATATTGCAGCTGGAAAACCAGAAGAAACAAAAGCTTTGGTGCCTGCATTACCACTGCTTATTGCTCATTTGG

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|298194590|gb|HO043062.1|HO043062
EST:     CTGTACCCTTGCTTGTGCAGTGTCTTTCATTTGGTTCTCCAGATGAACAG                         TTGCTTGAGGCAGCTTGGTGTCTCACAAATATTGCTGCAGGGAATCCAGAA
genomic: CTGTACCCTTGCTTGTGCAGTGTCTTTCATTTGGTTCTCCAGATGAACAGgtctgaagtt ... tcttctgcagTTGCTTGAGGCAGCTTGGTGTCTCACAAATATTGCTGCAGGGAATCCAGAA
EST: gi|151397313|gb|EV267186.1|EV267186
EST:     CTGTACCCTTGCTTGTGCAGTGTCTTTCATTTGGTTCTCCAGATGAACAG                         TTGCTTGAGGCAGCTTGGTGTCTCACAAATATTGCTGCAGGGAATCCAGAA
genomic: CTGTACCCTTGCTTGTGCAGTGTCTTTCATTTGGTTCTCCAGATGAACAGgtctgaagtt ... tcttctgcagTTGCTTGAGGCAGCTTGGTGTCTCACAAATATTGCTGCAGGGAATCCAGAA
EST: gi|11413637|gb|BF425648.1|BF425648
EST:     CTGTACCCTTGCTTGTGCAGTGTCTTTCATGTGGTTCTGCAGATGAACAG                         TTGCTTGAGGCAGCTTGGTGTCTCACAAATATTGCTGCAGGGAATTCAGAA
genomic: CTGTACCCTTGCTTGTGCAGTGTCTTTCATTTGGTTCTCCAGATGAACAGgtctgaagtt ... tcttctgcagTTGCTTGAGGCAGCTTGGTGTCTCACAAATATTGCTGCAGGGAATCCAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtagtgggaagaaattttcttaatgcttacattttgtggtgaatgtcttctgcagTTGCTTGAGGCAGCTTGGTGTCTCACAAATATTGCTGCAGGGAATCCAGAAGAAACAAAAGCTTTGTTGCCTGCATTGCCCTTGCTTATTGCTCATCTTG
                       tgcttac  putative branch site (score: 2)
                                           tgtcttct  putative PPT
        aagaaattttcttaat  TA-rich tract