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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactattgaattaagtcaaattcctaactaggggggcttctgtttcataacaaggccaactttaaactattttagtttaccactactttataaaatgctaaactgtgtgtgattatgatttatgtttccagGGATGAGTTGAAAGTCTTTTCTGATGAGGTAATTCGTTTTGGAAATCGTTCAAAGGATCCTCAGTGGCACAACTTGGACCGATACTTTGAGAA

Basic information

species Glycine max
transcript GLYMA08G00670.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G00670.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os05g35530.1 (Oryza sativa), 3'ss of exon 3
gtaactattgaattaag---tcaaattcctaactaggggggcttctgtt-------tcataacaaggccaactttaaactattttagtttaccactactttataaaatgctaaactgtgt---gtgattatgatttatgtttc-cagGGATGAGTTGAAAGTCTTTTCTGATGAGGTAATTCGTTTTGGAAATCGTTCAAAGGATCCTCAGTGGCACAACTTGGACCGATACTTTGAGAA
|||| || ||  ||       |  | || |  |||    | |   | |        || || ||        |  |   || | || | || |  | |||| |||  |  |||  ||| |   ||| | ||  |||   | |  |||||| |||||  || |||||||  | || ||  |||| |||||||||||||  ||| ||||||| ||||||| ||||||||| |||||||| ||
gtaaataatggttttgtgctccccagtcttttctatcatgcccattataaatattatcctaccagatatgtatccaggttactgtactataacctttcttt-taatgttgtaagttgtatcaagtgctaattgtttggttctaacagGGAAGAGTTAGAAATCTTTTCAAAAGAAGTTGTTCGATTTGGAAATCGTTGCAAGAATCCTCAATGGCACAGCTTGGACCGCTACTTTGAAAA

upper sequence: GLYMA08G00670.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os01g65330.2 (Oryza sativa), 3'ss of exon 2
gtaactattgaattaagt-------caaattcctaac-taggggggc---ttctgttt-cataacaaggccaactttaaactattttagtttaccactactttat--------aaaatgctaaactgtgtgtgattatgattta---tgtttc---cagGGATGAGTTGAAAGTCTTTTCTGATGAGGTAATTCGTTTTGGAAATCGTTCAAAGGATCCTCAGTGGCACAACTTGGACCGATACTTTGAGAA
|| |  |||||  | | |       ||||||   ||| |  |   ||   |||| ||    |   |     |  | || |  ||  ||  | | || ||   |||        || |||    | | | |   |||    |||    | ||||   |||||| ||||||||||| ||||||   || ||  |||| |||||||| || |  ||||||||||||||||| |||||||| || |||||||| ||
gttagcattgatctcactgcttctgcaaattataaacatgtgactgcacattctattcatttgctagaaatatgtatacatgatggtatatcaacaatatcgtattgtgcttaaagatgtactattttcttctattgaagttttggttatttctgacagGGAAGAGTTGAAAGTGTTTTCTACAGAAGTTGTTCGCTTTGGAAACCGCTGCAAGGATCCTCAGTGGCATAACTTGGATCGCTACTTTGACAA

upper sequence: GLYMA08G00670.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G046846_T01 (Zea mays), 3'ss of exon 3
----------------------------gtaactattgaattaagtcaaattcctaactaggggggcttctgtttcataacaaggccaactttaaactattttagtttaccactactttataaaatgctaaactgtgtgtgattatgatttatgtttccagGGATGAGTTGAAAGTCTTTTCTGATGAGGTAATTCGTTTTGGAAATCGTTCAAAGGATCCTCAGTGGCACAACTTGGACCGATACTTTGAGAA
                              ||||||   | |      ||    |   |        || | |  ||| |    |   |  |  ||  | | || || | |     ||||||   |  ||   |   ||   || | ||||       |||||| ||||||||||| || |||   || ||  |||| |||||||||||||  ||||||||||||||||||||||||||||| |||||||| ||
gttagtgaataatctctgattctttttataaactataacaattgtctgaaccatttgtttattttatttatctagcatcaacctggttatatagaagaaatgtacttcaacttgtttttatatgcttgtag-ttacctgaagtttttatttggtccaacagGGAAGAGTTGAAAGTGTTCTCTACAGAAGTTGTTCGCTTTGGAAATCGTTGCAAGGATCCTCAGTGGCACAACTTGGACCGCTACTTTGATAA

upper sequence: GLYMA08G00670.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G320615_T01 (Zea mays), 3'ss of exon 2
----------------------------gtaactattgaattaagtcaaattcctaactaggggggcttctgtttcataacaaggccaactttaaactattttagtttaccactactttataaaatgctaaactgtgtgtgattatgatttatgtttccagGGATGAGTTGAAAGTCTTTTCTGATGAGGTAATTCGTTTTGGAAATCGTTCAAAGGATCCTCAGTGGCACAACTTGGACCGATACTTTGAGAA
                            |||| ||| |  |  | |  ||||    | |   |  |    |||| |   |       |  | |  |  | | |||| | ||  |  ||| || | ||  ||||  |   | | | |  || ||     ||||||  ||||  |||| ||| |  | ||||| ||||| |||||||||||||  ||||||||||||||||| ||||||||| | |||||||| ||
gtttgtgcttgtgttcacttcttatcatgtaattatggcct--aatttaattatccattcttgtcgtgcgtgttaccctattcaat-atgtatggaaaactgtagtgtgccttttatttttatattga-aaacaataccttaat-tagttaattccatcagGGAAAAGTTAGAAGTATTTACAAAAGAGGTCATTCGCTTTGGAAATCGTTGCAAGGATCCTCAGTGGCATAACTTGGACTGCTACTTTGAAAA

upper sequence: GLYMA08G00670.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G077621_T01 (Zea mays), 3'ss of exon 2
--------------------gtaactattgaatta-agtcaaatt---cctaactaggggggcttctgtttcataacaaggccaactttaaactattttagtttaccactactttataaaatgctaaactgtgtgtgattatgatttatgtttccagGGATGAGTTGAAAGTCTTTTCTGATGAGGTAATTCGTTTTGGAAATCGTTCAAAGGATCCTCAGTGGCACAACTTGGACCGATACTTTGAGAA
                     | |  ||  |||||  | | ||||   ||   || |  | || | |    |    |||     |    ||||| | ||    | ||  |  ||| || | ||  ||||  |   | | | |  || ||     |||||| |||||  |||| ||  |  | ||||| ||||| |||||||| ||||  ||||||||||||||||| ||||||||||| |||||||| ||
gtttgtgcttgtgttcacttcttatcatgtaattatggcctaatttatccatgcttgtcgtgcgtgttaccctattcaatatgtatggaaaactgtattg---tgccttttatttttatattga-aaacaataccttaat-tagttaattccatcagGGAAGAGTTAGAAGTATTCACAAAAGAGGTCATTCGCTTTGGAAACCGTTGCAAGGATCCTCAGTGGCATAACTTGGACCGCTACTTTGAAAA

upper sequence: GLYMA08G00670.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G148773_T02 (Zea mays), 3'ss of exon 2
gtaactattgaattaagtcaaattcctaactaggggggcttctgtttcataacaaggccaactttaaactatttta-gtttaccactactttataaaatgctaaactgtgtgtgattatgatttatgtttccagGGATGAGTTGAAAGTCTTTTCTGATGAGGTAATTCGTTTTGGAAATCGTTCAAAGGATCCTCAGTGGCACAACTTGGACCGATACTTTGAGAA
                        | |  || |      | || |  || |||  |||  |  |  ||   |   | | |      | |||| |    | || || | | |||     || |  |      |||||| ||||||||||| ||||||   || ||  |||| ||||||||| |||  |||||||||||||||||||| ||| |||| |||||||| ||
------------------------cttgcctcgatttattcctttccca-aacccggctcatgtggaatcctccaacgctgggtcttccttttttggttactgaagtttttgtt----tggtccaa-----cagGGAAGAGTTGAAAGTGTTTTCTACAGAAGTTGTTCGCTTTGGAAATTGTTGCAAGGATCCTCAGTGGCACAATTTGAACCGCTACTTTGATAA

upper sequence: GLYMA08G00670.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G097502_T02 (Zea mays), 3'ss of exon 2
----------------------------gtaactattgaat--taagtcaaattcctaactaggggggcttctgtttcataacaaggccaactttaaactattttagtttaccactactttataaaatgctaaactgtgtgtgattatgatttatgtttccagGGATGAGTTGAAAGTCTTTTCTGATGAGGTAATTCGTTTTGGAAATCGTTCAAAGGATCCTCAGTGGCACAACTTGGACCGATACTTTGAGAA
                            ||||||  | | |  |||   ||  |    |     |  |  | |||| |      ||     | || ||  | |  ||| | ||  |  ||| ||    |  ||    |   | | | |  || ||     |||||| |||||  |||| ||  |    |||||  |||| |||||||| ||||  ||||||||||| ||||| ||||||||||| |||||||| ||
gtttgtgcttgtgttcacgtgatatcatgtaacttgtaagttgtaacctaatctatccatgcttgttgtgtgtgttaccctgttagatatgcattgaaa-actgcagtgtgccttttatttttatctcga-aattaataccttaat-tagttaattccaacagGGAAGAGTTAGAAGTATTCACAAGAGAGGTTGTTCGCTTTGGAAACCGTTGCAAGGATCCTCAATGGCATAACTTGGACCGCTACTTTGAAAA

upper sequence: GLYMA08G00670.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv07s0031g02970.t01 (Vitis vinifera), 3'ss of exon 2
gta-actattgaattaagtcaaattcctaactaggggggcttctgtttcataacaaggccaactttaaactattttagtttaccactactttataaaatgctaaactgtgtgtgattatgat-ttatgtttccagGGATGAGTTGAAAGTCTTTTCTGATGAGGTAATTCGTTTTGGAAATCGTTCAAAGGATCCTCAGTGGCACAACTTGGACCGATACTTTGAGAA
||  |||| || ||   | | || |  | | ||  |       |||  | | |  ||      |    |||||| | || ||    |  ||| |  | || ||| || ||     ||| | | |||||||| |||||| ||||||||| | |||   |  || ||  ||||||||||||||| ||  |  |||||||||||||||||||||||||  || ||||||||
gtggactaatggatactggctaaatagttaatattgccatcaatgtg-cttgatcagaatggtt----actattgt-gtctat--ttcatttctgcagtggtaacct-tgctgatttacggtattatgttttcagGGAAGAGTTGAAAATTTTTGTGGGAGAAGTGGTTCGTTTTGGAAATCATTGTAGAGATCCTCAGTGGCACAACTTGGACCTTTATTTTGAGAA

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|41146182|gb|CK606393.1|CK606393
EST:     GTATCAAAGGATACGGATGAACTTCTAAAGATTGTTGGTGCAGACAAAAG                         GGATGAGTTGAAAGTCTTTTCTGATGAGGTAATTCGTTTTGGAAATCGTTC
genomic: GTATCAAAGGATACGGATGAACTTCTAAAGATTGTTGGTGCAGACAAAAGgtaactattg ... atgtttccagGGATGAGTTGAAAGTCTTTTCTGATGAGGTAATTCGTTTTGGAAATCGTTC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaccactactttataaaatgctaaactgtgtgtgattatgatttatgtttccagGGATGAGTTGAAAGTCTTTTCTGATGAGGTAATTCGTTTTGGAAATCGTTCAAAGGATCCTCAGTGGCACAACTTGGACCGATACTTTGAGAA
                   tgctaaa  putative branch site (score: 2)
                                              tgtttcc  putative PPT
          tttataaaatgctaaa  TA-rich tract