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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agggagatgagaatatatgcaattgtttattacagtgttctcttcacattgattttggtacatgctaatagaggagaggttgtgtcccattttcctacagGGAGAGCCCCTGTGTGTGTTCTATTCACGTTACGGCATATGCAAATTTGGTCCAAGTTGCAAGTTTGATCACCCAATGGGAGTCTTCACCTATAACATAT

Basic information

species Glycine max
transcript GLYMA09G38650.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G38650.2 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G146514_T02 (Zea mays), 3'ss of exon 6
agggagatgagaatatatgcaattgtttattacagtgttctcttcacat-tgattttggtacatgctaatagaggagaggttgtgtcccatttt--cctacagGGAGAGCCCCTGTGTGTGTTCTATTCACGTTACGGCATATGCAAATTTGGTCCAAGTTGCAAGTTTGATCACCCAATGGGAGTCTTCACCTATAACATAT
|||  ||||  |    || |  |||    |    || |  |    ||||   |      ||| || |  |  |  |   ||| | |   ||||   |  ||||||||||||  | ||    |||||    || |||||||| ||||| || ||||||| |||||| || |||||||||||||||     ||  ||   |    
aggttgatgccatgcaatac--ttgacactggtggtataatgcaaacatgctacacacatacgtgttgcttaaccatctgtt-tattttatttccgctcacagGGAGAGCCAATATGCAGTTTCTACAATCGCTACGGCATGTGCAAGTTCGGTCCAAATTGCAAATTCGATCACCCAATGGGAAATGCCATGTACGGCCAGG

upper sequence: GLYMA09G38650.2 (Glycine max), 3'ss of exon 6
lower sequence: AT3G02830.1 (Arabidopsis thaliana), 3'ss of exon 6
agggagatgaga-atatatgcaattgtttattacagtgttctcttcacattgattttggtacatgctaatagaggagaggttgtgtcccattttcctacagGGAGAGCCCCTGTGTGTGTTCTATTCACGTTACGGCATATGCAAATTTGGTCCAAGTTGCAAGTTTGATCACCCAATGGGAGTCTTCACCTATAACATAT
 |  || | | | |  | ||||     | |||||   |||||||||   |  || |  | |     | ||          || | |  |        | ||||||| ||  |||||||||||||| |||| || || || ||||||||||||||||| || || ||||||||||||||| |||| ||||| ||  |||   
-gtaagctcaaagacttgtgca-----taattacttggttctcttcgattaaatctctgcattgtttgatttt-------ttttctttctcaaaatgatagGGAGAACCGTTGTGTGTGTTCTATACACGCTATGGAATCTGCAAATTTGGTCCAAGCTGTAAATTTGATCACCCAATGCGAGTATTCACATACGACAACA

upper sequence: GLYMA09G38650.2 (Glycine max), 3'ss of exon 6
lower sequence: AT5G16540.3 (Arabidopsis thaliana), 3'ss of exon 4
agggagatgagaatatatgc-aattgtttattacagtgttctcttcacattgattttggtacatgctaatagaggagaggttgtgtcccattttcctacagGGAGAGCCCCTGTGTGTGTTCTATTCACGTTACGGCATATGCAAATTTGGTCCAAGTTGCAAGTTTGATCACCCAATGGGAGTCTTCACCTATAACATAT
               || || |||     | | |||  |||| | |    |  | |   ||  || |  | |   |    |||| | |   |||   ||||||||| || ||||| ||||||||||| || || || || ||||| ||||||||||| || || ||||||||||| ||| |||||||||| || ||||   
--------------gtaagctaataaaagacttcag-attctttcctttatagtctcattatgtggt--ttggtaaattcttgt-tgctggtttgaaacagGGAGAACCACTGTGCGTGTTCTATTCTCGGTATGGGATCTGCAAGTTTGGTCCAAGCTGTAAATTTGATCACCCGATGCGAGTCTTCACTTACAACAACA

upper sequence: GLYMA09G38650.2 (Glycine max), 3'ss of exon 6
lower sequence: AT5G16540.2 (Arabidopsis thaliana), 3'ss of exon 5
agggagatgagaatatatgcaattgtttattacagtg-------ttctcttcacattgattttggtacatgctaatagaggagaggttgtgtcccattttcctacagGGAGAGCCCCTGTGTGTGTTCTATTCACGTTACGGCATATGCAAATTTGGTCCAAGTTGCAAGTTTGATCACCCAATGGGAGTCTTCACCTATAACATAT
   |   |     ||    |  |    || || |          |||| | |    |  | |   ||  || |  | |   |    |||| | |   |||   ||||||||| || ||||| ||||||||||| || || || || ||||| ||||||||||| || || ||||||||||| ||| |||||||||| || ||||   
gttggccttcctttacgcccggtaagctaataaaagacttcagattctttcctttatagtctcattatgtggt--ttggtaaattcttgt-tgctggtttgaaacagGGAGAACCACTGTGCGTGTTCTATTCTCGGTATGGGATCTGCAAGTTTGGTCCAAGCTGTAAATTTGATCACCCGATGCGAGTCTTCACTTACAACAACA

upper sequence: GLYMA09G38650.2 (Glycine max), 3'ss of exon 6
lower sequence: Vv04s0023g00370.t01 (Vitis vinifera), 3'ss of exon 6
--agggagatgagaatatatgcaattgtttattacagtgttctcttcacattgattttggtacatgctaatagaggagaggttgtgtcccattttcctacagGGAGAGCCCCTGTGTGTGTTCTATTCACGTTACGGCATATGCAAATTTGGTCCAAGTTGCAAGTTTGATCACCCAATGGGAGTCTTCACCTATAACATAT
      |      ||| ||    |   ||  || |  || | |     | ||| | | | ||  |   |||      ||  | || |   ||||| | ||||||||| ||  ||||  | || ||||| ||||| || || ||||||||||||||||||||||||||||| ||||| |||||| ||||| | || ||  | |
accataatgcataaatgtacttcaactttggttgctctgatatagagtccttg-tctagttatttataaatttgatggatctggt-ttttatttttcaacagGGAGAACCTTTGTGCATTTTTTATTCTCGTTATGGGATCTGCAAATTTGGTCCAAGTTGCAAGTTTGACCACCCTATGGGAATCTTCGCATACAATCTGT

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|4397329|gb|AI496326.1|AI496326
EST:     TTCCTGCTCCTGACTGTGTTTTGAGTCCTATAGGTCTTCCTTTACGTCCT                         GGAGAGCCCCTGTGTGTGTTCTATTCACGTTATGGCATATGCAAATTTGGT
genomic: TTCCTGCTCCTGACTGTGTTTTGAGTCCTATAGGTCTTCCTTTACGTCCTgtgagttgaa ... tttcctacagGGAGAGCCCCTGTGTGTGTTCTATTCACGTTACGGCATATGCAAATTTGGT
EST: gi|31307304|gb|CD392507.1|CD392507
EST:     TTCCTGCTCCTGACTGTGTTTTGAGTCCTATAGGTCTTCCTTTACGTCCT                         GGAGAGCCCCTGTGTGTGTTCTATTCACGTTACGGCATATGCAAATTTGGT
genomic: TTCCTGCTCCTGACTGTGTTTTGAGTCCTATAGGTCTTCCTTTACGTCCTgtgagttgaa ... tttcctacagGGAGAGCCCCTGTGTGTGTTCTATTCACGTTACGGCATATGCAAATTTGGT
EST: gi|11413083|gb|BF425094.1|BF425094
EST:     TTCCTGCTCCTGACTGTGTTTTGAGTCCTATAGGTCTTCCTTTACGTCCT                         GGAGAGCCCCTGTGTGTGTTCTATTCACGTTATGGCATATGCAAATTTGGT
genomic: TTCCTGCTCCTGACTGTGTTTTGAGTCCTATAGGTCTTCCTTTACGTCCTgtgagttgaa ... tttcctacagGGAGAGCCCCTGTGTGTGTTCTATTCACGTTACGGCATATGCAAATTTGGT
EST: gi|9204745|gb|BE330969.1|BE330969
EST:     TTCCTGCTCCTGACTGTGTTTTGAGTCCTATAGGTCTTCCTTTACGTCCT                         GGAGAGCCCCTGTGTGTGTTCTATTCACGTTACGGCATATGCAAATGTGGT
genomic: TTCCTGCTCCTGACTGTGTTTTGAGTCCTATAGGTCTTCCTTTACGTCCTgtgagttgaa ... tttcctacagGGAGAGCCCCTGTGTGTGTTCTATTCACGTTACGGCATATGCAAATTTGGT
EST: gi|5508891|gb|AI855449.1|AI855449
EST:     TTCCTGCTCCTGACTGTGTTTTGAGTCCTATAGGTCTTCCTTTACGTCCT                         GNAGAGCCCCTGTGTGTGTTCTATTCACGTTACGGCATATGCAAATTTGGT
genomic: TTCCTGCTCCTGACTGTGTTTTGAGTCCTATAGGTCTTCCTTTACGTCCTgtgagttgaa ... tttcctacagGGAGAGCCCCTGTGTGTGTTCTATTCACGTTACGGCATATGCAAATTTGGT
EST: gi|23728273|gb|BU762185.1|BU762185
EST:     TTCCTGCTCCTGACTGTGTTTTGAGTCCTATAGGTCTTCCTTTACGTCCT                         GGAGAGCCCCTGTGTGTGTTCTATTCACGTTACGGCATATGCAAATTTGAT
genomic: TTCCTGCTCCTGACTGTGTTTTGAGTCCTATAGGTCTTCCTTTACGTCCTgtgagttgaa ... tttcctacagGGAGAGCCCCTGTGTGTGTTCTATTCACGTTACGGCATATGCAAATTTGGT
EST: gi|14991679|gb|BI317352.1|BI317352
EST:     TTCCTGCTCCTGACTGTGTTTTGAGTCCTATAGGTCTTCCTTTACCTCCT                         GGAGACGCCC-TGTGAGTGTTCTATTCACGATACGGCATATGCCAATTTGG
genomic: TTCCTGCTCCTGACTGTGTTTTGAGTCCTATAGGTCTTCCTTTACGTCCTgtgagttgaa ... tttcctacagGGAGA-GCCCCTGTGTGTGTTCTATTCACGTTACGGCATATGCAAATTTGG
EST: gi|254332007|gb|GR846210.1|GR846210
EST:     TTCCTGCTCCTGACTGTGTTTTGAGTCCTATAGGTCTTCCTTTACGTCCT                         GGAGAGCCCCTGTGTGTGTTCTATTCACGTTACGGCATATGCAAATTTGGT
genomic: TTCCTGCTCCTGACTGTGTTTTGAGTCCTATAGGTCTTCCTTTACGTCCTgtgagttgaa ... tttcctacagGGAGAGCCCCTGTGTGTGTTCTATTCACGTTACGGCATATGCAAATTTGGT
EST: gi|15000058|gb|BI320872.1|BI320872
EST:     TTCCTGCTCCTGACTGTGTTTTGAGTCCTATAGGTCTTCCTTTACGTCCT                         GGAGAGCCCCTGTGTGTGTTCTATTCACGTTATGGCATATGCAAATTTGGT
genomic: TTCCTGCTCCTGACTGTGTTTTGAGTCCTATAGGTCTTCCTTTACGTCCTgtgagttgaa ... tttcctacagGGAGAGCCCCTGTGTGTGTTCTATTCACGTTACGGCATATGCAAATTTGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acattgattttggtacatgctaatagaggagaggttgtgtcccattttcctacagGGAGAGCCCCTGTGTGTGTTCTATTCACGTTACGGCATATGCAAATTTGGTCCAAGTTGCAAGTTTGATCACCCAATGGGAGTCTTCACCTATAACATAT
                 tgctaat  putative branch site (score: 2)
                                     tgtcccattttcct  putative PPT
                    taataga  TA-rich tract