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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggattatgagagaagcttctttctttttatgattctgatttgagtatgacagaagttatttcaatattattaaaagagatttatatgtcggtgaatatgttctctttgtacatcattagccttgcaactttttctcacctcctttttcttttcttgcagATTCGATGCTGTCATACATTTTGCTGGACTGAAAGCAGTAGGAGAAAGTGTGCAAAAACCTTTACTATACTATAACAACAACTTGACTGGGACAATCACT

Basic information

species Glycine max
transcript GLYMA01G43540.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G43540.2 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os09g15420.1 (Oryza sativa), 3'ss of exon 2
gtaaggattatgagagaagcttctttctttttatgattctgatttgagtatgacagaagttatttcaatattattaaaagagatttatatgtcggtgaatatgttctctttgtacatcattagccttgcaactttttctcacctcctttttcttttcttgcagATTCGATGCTGTCATACATTTTGCTGGACTGAAAGCAGTAGGAGAAAGTGTGCAAAAACCTTTACTATACTATAACAACAACTTGACTGGGACAATCACT
||||     | |  | ||  |  | |  | || | ||||   |||               |  ||  ||| | || |||   |   || |||     || ||     || |||| |  |  ||  |   || ||  |   |  |   ||||||        ||||| ||||||||| | ||||||||||| |||||||| || || ||||||||||| || || || || || ||| || | ||  |  |||||||||| | |
gtaaaa--cacgctataaaatagtattatctttttattccttttta-------------cttcttttatacttttcaaaagcagcaatttgt-----aacat-----ctctgtaaagtaaaagtatc-taaattcctaaaatatgtcttttct--------agATTTGATGCTGTCGTTCATTTTGCTGGTCTGAAAGCTGTGGGTGAAAGTGTGCAGAAGCCATTGCTTTATTATGACCATAATGTTGCTGGGACAATAATT

upper sequence: GLYMA01G43540.2 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G138410_T01 (Zea mays), 3'ss of exon 2
gtaaggattatgagagaagcttctttctttttatgattctgatttgagtat-gacagaagttatttcaatattattaaaagagatttatatgtcggtgaatatgttctctttgtacat-cattagc-cttgcaactttttctcacctcctttttcttttcttgcagATTCGATGCTGTCATACATTTTGCTGGACTGAAAGCAGTAGGAGAAAGTGTGCAAAAACCTTTACTATACTATAACAACAACTTGACTGGGACAATCACT
                                 | |  ||   | ||  || | ||  |  ||| |    || |||||   |   ||  ||||   |     |||  ||| |||| || |||  || | ||  |||| ||   |       |    | |  | |||||| |||||||| || |||||||||||||||||||| || ||||||||||| ||||| ||||| || || ||| || | ||  |   ||| ||||| | |
--------------------------------gtaaagcttgctggaagattggcaatatatatctgttcataattaattaactattcaatgtt--tagccttgtcttctatgtaaatgcatctgcacctggtacttatttatatgcatgctacgctgttctccagATTTGATGCTGTTATTCATTTTGCTGGACTGAAAGCTGTTGGAGAAAGTGTACAAAAGCCTTTGCTTTATTATGACCATAATGTTGTTGGCACAATAAAT

upper sequence: GLYMA01G43540.2 (Glycine max), 3'ss of exon 2
lower sequence: Vv02s0025g01560.t01 (Vitis vinifera), 3'ss of exon 2
gtaaggattatgagagaagcttctttctttttatgattctgatttgagtatgacagaagttatttcaatattattaaaagagatttatatgtcggtgaatatgttctctttgtacatcatta-gccttgcaactttttctcacctcctttttcttttcttgcagATTCGATGCTGTCATACATTTTGCTGGACTGAAAGCAGTAGGAGAAAGTGTGCAAAAACCTTTACTATACTATAACAACAACTTGACTGGGACAATCACT
                                                                | || | ||   |       ||| | || |   ||| ||| |   |||  || | ||| |  ||  |||||  | |  || |||| ||  |    ||||| || ||||||||||| || ||||||||  |||| ||||| || ||||||||||||||||| || || |||| | | |||||| | | ||| ||||| |||
----------------------------------------------------------acagactgaagaata--gatttgatgttacacgtaga--aatttgtgcatcttgctcaactttatgttttataacttactttgtccaccttgtt--tccactgcagTTTTGATGCTGTCATTCACTTTGCTGGGTTGAAGGCAGTTGGTGAAAGTGTGCAAAAACCCTTGCTTTACTTTGATAACAACCTTATTGGCACAATTACT

upper sequence: GLYMA01G43540.2 (Glycine max), 3'ss of exon 2
lower sequence: Vv02s0025g01580.t01 (Vitis vinifera), 3'ss of exon 2
gtaaggattatgagagaagcttctttctttttatgattctgatttgagtatgacagaagttatttcaatattattaaaagagat-ttatatgtcggtgaatatgttctctttgtacatcatta-gccttgcaactttttctcacctcctttttcttttct----tgcagATTCGATGCTGTCATACATTTTGCTGGACTGAAAGCAGTAGGAGAAAGTGTGCAAAAACCTTTACTATACTATAACAACAACTTGACTGGGACAATCACT
                                                                     |  | || |   ||| ||| |||| |   ||| | | ||  |||  || | ||| |  ||  |||| ||||| || |  |    ||| | |    ||||| || ||||||||||| || ||||||||  |||| ||||| || ||||||||||||||||| || || |||||| | |||||| | | ||| ||||| |||
-------------------------------------------------------------------tgaagaatagatttgatgttacatgtaga--aatttatgcttcttgctcaactttatgttttataactctttcttactttgtccaccttgtttccactgcagTTTTGATGCTGTCATTCACTTTGCTGGGTTGAAGGCAGTTGGTGAAAGTGTGCAAAAACCATTGCTTTACTATGATAACAACCTTATTGGCACAATTACT

upper sequence: GLYMA01G43540.2 (Glycine max), 3'ss of exon 2
lower sequence: PP1S101_67V6.2 (Physcomitrella patens), 3'ss of exon 2
gtaaggattatgagagaagcttctttctttttatgattctgatttgagtatgacagaagttatttcaatattattaaaagagatttatatgtcggtgaatatgttctctttgtacatcattagccttgcaactttttctcacctcctttttcttttcttgcagATTCGATGCTGTCATACATTTTGCTGGACTGAAAGCAGTAGGAGAAAGTGTGCAAAAACCTTTACTATACTATAACAACAACTTGACTGGGACAATCACT
                                                         | |  |   | | ||  | |       | || |   | | || ||  |   || ||   | || |  | ||  |  | |||| ||       |||       |||| |||||||||||||| || ||||| || ||||| || |||||||||||||||   || ||||| |  ||||| | ||||||  | |   | || || | |
---------------------------------------------------------aatgttgctagtgtttgtcattacacctaattttgtgcttaagataatag-ttcgtggtttatcacacctgtgaaatattcttac-----aattcaaaatcggcagGTTCGATGCTGTCATTCACTTTGCAGGCCTGAAGGCTGTAGGAGAAAGTGTGTCGAAGCCTTTGCGTTACTACAGCAACAATCTAATAAGCACCATTAAT

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|209713128|gb|BW653837.1|BW653837
EST:     GTGGACCTACGGGACAGAGCTGCTCTAGACCAAATATTTTCTTCCACACA                         ATTCGATGCTGTCATACATTTTGCTCGACTGAAAGCAGTAGGAGAAAGTGT
genomic: GTGGACCTACGGGACAGAGCTGCTCTAGACCAAATATTTTCTTCCACACAgtaaggatta ... tttcttgcagATTCGATGCTGTCATACATTTTGCTGGACTGAAAGCAGTAGGAGAAAGTGT
EST: gi|192333229|gb|FK026110.1|FK026110
EST:     GTGGACCTACGGGACAGAGCTGCTCTAGACCAAATATTTTCTTCCACACA                         ATTCGATGCTGTCATACATTTTGCTGGACTGAAAGCAGTAGGAGAAAGTGT
genomic: GTGGACCTACGGGACAGAGCTGCTCTAGACCAAATATTTTCTTCCACACAgtaaggatta ... tttcttgcagATTCGATGCTGTCATACATTTTGCTGGACTGAAAGCAGTAGGAGAAAGTGT
EST: gi|15000492|gb|BI321306.1|BI321306
EST:     GTGGACCTACGGGACAGAGCTGCTCTAGACCAAATATTTTCTTCCACACA                         ATTCGATGCTGTCATACATTTTGCTGGACTGAAAGCAGTAGGAGAAAGTGT
genomic: GTGGACCTACGGGACAGAGCTGCTCTAGACCAAATATTTTCTTCCACACAgtaaggatta ... tttcttgcagATTCGATGCTGTCATACATTTTGCTGGACTGAAAGCAGTAGGAGAAAGTGT
EST: gi|15813402|gb|BI785677.1|BI785677
EST:     GTGGACCTACGGGACAGAGCTGCTCTAGACCAAATATTTTCTTCCACACA                         ATTCGATGCTGTCATACATTTTGCTGGACTGAAAGCAGTANGAGAAAGTGT
genomic: GTGGACCTACGGGACAGAGCTGCTCTAGACCAAATATTTTCTTCCACACAgtaaggatta ... tttcttgcagATTCGATGCTGTCATACATTTTGCTGGACTGAAAGCAGTAGGAGAAAGTGT
EST: gi|151398432|gb|EV268303.1|EV268303
EST:     GTGGACCTACGGGACAGAGCTGCTCTAGACCAAATATTTTCTTCCACACA                         ATTCGATGCTGTCATACATTTTGCTGGACTGAAAGCAGTAGGAGAAAGTGT
genomic: GTGGACCTACGGGACAGAGCTGCTCTAGACCAAATATTTTCTTCCACACAgtaaggatta ... tttcttgcagATTCGATGCTGTCATACATTTTGCTGGACTGAAAGCAGTAGGAGAAAGTGT
EST: gi|14991639|gb|BI317312.1|BI317312
EST:     GTGGACCTACGGGACAGAGCTGCTCTAGACCAAATATTTTCTTCCACACA                         ATTCGATGCTGTCATACATTTTGCTGGACTGAAAGCAGTAGGAGAAAGTGT
genomic: GTGGACCTACGGGACAGAGCTGCTCTAGACCAAATATTTTCTTCCACACAgtaaggatta ... tttcttgcagATTCGATGCTGTCATACATTTTGCTGGACTGAAAGCAGTAGGAGAAAGTGT
EST: gi|209699775|gb|BW652120.1|BW652120
EST:     GTGGACCTACGGGACAGAGCTGCTCTAGACCAAATATTTTCTTCCACACA                         ATTCGATGCTGTCATACATTTTGCTGGACTGAAAGCAGTAGGAGAAAGTGT
genomic: GTGGACCTACGGGACAGAGCTGCTCTAGACCAAATATTTTCTTCCACACAgtaaggatta ... tttcttgcagATTCGATGCTGTCATACATTTTGCTGGACTGAAAGCAGTAGGAGAAAGTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgtacatcattagccttgcaactttttctcacctcctttttcttttcttgcagATTCGATGCTGTCATACATTTTGCTGGACTGAAAGCAGTAGGAGAAAGTGTGCAAAAACCTTTACTATACTATAACAACAACTTGACTGGGACAATCACT
                           ttctcac  putative branch site (score: 2)
               ccttgcaactttttct  CT-rich tract
                                      tttttctttt  TA-rich tract