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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agggagatgagaatatatgcaattgtttattacagtgttctcttcacattgattttggtacatgctaatagaggagaggttgtgtcccattttcctacagGGAGAGCCCCTGTGTGTGTTCTATTCACGTTACGGCATATGCAAATTTGGTCCAAGTTGCAAGTTTGATCACCCAATGGGAGTCTTCACCTATAACATAT

Basic information

species Glycine max
transcript GLYMA09G38650.1
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
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agggagatgagaatatatgcaattgtttattacagtgttctcttcacattgattttggtacatgctaatagaggagaggttgtgtcccattttcctacagGGAGAGCCCCTGTGTGTGTTCTATTCACGTTACGGCATATGCAAATTTGGTCCAAGTTGCAAGTTTGATCACCCAATGGGAGTCTTCACCTATAACATAT

- - - - - - - -tatgcaa
- - - - - - - - - - - - - - - tacagtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggttgtg