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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttacacaatctactacttcaatgcaatgcttgagcttaccaatgcagtagtattttcttatctctggttttgactaattgtgtattttctcgatgcagGTTGATGCATTCCCTATCACTGTTATGTTTGGCATGTGCTCAATTTTCCTTTTGGTGGCTTGTATCTTGCAAAGGCGACTGATGGTGATTTCCGATAAGC

Basic information

species Glycine max
transcript GLYMA06G13760.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G13760.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os03g02380.1 (Oryza sativa), 3'ss of exon 6
gtatgttacacaatctactacttcaatgcaa-tgcttgagcttaccaatgcagtagtattttcttatctctggttttgactaattgtgtattttctcga---tgcagGTTGATGCATTCCCTATCACTGTTATGTTTGGCATGTGCTCAATTTTCCTTTTGGTGGCTTGTATCTTGCAAAGGCGACTGATGGTGATTTCCGATAAGC
                      | | || || || |    || |         |  || | | ||   |    |    | |||   | | || | |  |   |||||||  ||||||||||||||||||| |||||||||||||| || || ||||| ||  ||||    ||| |||| || || || |||||  |||| ||    |
---------------------gtaagtgaaagtgttcttactgaatctcatgattctaatctgttgatttccttcaaaaataacatttttttctgtgaattttgcagGTGAATGCATTCCCTATCACTGTCATGTTTGGCATGTGTTCTATCTTCCTCTTCATGGCGGCAATCCTGCAGAGACGGCTAATGGTTGTTTCTGACCTAC

upper sequence: GLYMA06G13760.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os10g37520.1 (Oryza sativa), 3'ss of exon 6
---------------------gtatgttacacaatctactacttcaatgcaatg-cttgagcttaccaatgcagtagtatttt-cttatctctggttttgactaattgtgtattttct-cgatgcagGTTGATGCATTCCCTATCACTGTTATGTTTGGCATGTGCTCAATTTTCCTTTTGGTGGCTTGTATCTTGCAAAGGCGACTGATGGTGATTTCCGATAAGC
                      | | ||      | ||  |    ||  ||    |  |    | | ||||||  |  |     | | | ||    |   | ||||  |  |  |  |    |||||||  |||||||||| |||||||| ||||||||||||||  | |||||||||||  ||||    |||||||| ||||| ||||||||  | || |||   |
gtaagtagctaaatccaacttctgtttttttttctttatgaaaataacacaccaacaagcaaatgcaaatgcaaaaaaaaaagacatttgtcccagtaacattaatcatacaaatgatgttctgcagGTGAATGCATTCCCCATCACTGTCATGTTTGGCATGTGTGCTATTTTCCTTTTCATGGCAGCAATCTTGCAGAGGCGGCTGATGGTTGTCTCTGATCTCC

upper sequence: GLYMA06G13760.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G067638_T01 (Zea mays), 3'ss of exon 6
gtatgttacacaatctactacttcaatgcaatgcttgagcttaccaatgcagtagta----ttttcttatctctggttttgactaattgtgtattttctcgatgcagGTTGATGCATTCCCTATCACTGTTATGTTTGGCATGTGCTCAATTTTCCTTTTGGTGGCTTGTATCTTGCAAAGGCGACTGATGGTGATTTCCGATAAGC
       | |||      ||  |  | |     ||  | ||     ||  | ||| |    |  | |||  | |  || |   |  || |  || || ||| |||||||  |||||||||| || ||||| ||||| ||||||||||| ||||||||| |  ||||     ||||||| |||||  | ||||   | || |||   |
------gaaacatgtggataaatagaagttcctctaaatctggtatatatattaggacatctcattttaattattattgttctttcttataaatgttgtcg-tgcagGTGAATGCATTCCCAATAACTGTCATGTTCGGCATGTGCTCCATTTTCCTTCTCATGGCAGCAGTCTTGCAGAGGCGCTTAATGGCTGTCTCTGATCTTC

upper sequence: GLYMA06G13760.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G051189_T01 (Zea mays), 3'ss of exon 1
-------gtatgttacacaatctactacttcaatg-caatgcttgagcttacca--atgcagtagtattttcttatctctggttttgact-aattgtgtattttctcgatgcagGTTGATGCATTCCCTATCACTGTTATGTTTGGCATGTGCTCAATTTTCCTTTTGGTGGCTTGTATCTTGCAAAGGCGACTGATGGTGATTTCCGATAAGC
       |    |  | |   | ||||||    |  |  |  ||| |||  | |  ||    ||| | | ||    | |  ||   |  |   ||||| |  |  ||  |||||||  ||||||||||||||||||| |||||||| ||||| || || ||||| ||  ||||    |||||||| || ||  |||||||              
gtaaggagccattccctctcccaactactatgttctctttagttgtgctggcaagaattatatagaaatatcagcacacaagtaacggtttgcttgtggacatggtctttgcagGTGAATGCATTCCCTATCACTGTCATGTTTGGGATGTGTTCTATCTTCCTCTTCATGGCAGCCATCTTGCAGAGACGGTTGATGGTT-------------

upper sequence: GLYMA06G13760.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G064563_T03 (Zea mays), 3'ss of exon 6
----------gtatgttacacaatctactac-ttcaatgcaatgct--tgagcttaccaatgcagtagtattttcttatctctggttttgactaattgtgtattttctcgatgcagGTTGATGCATTCCCTATCACTGTTATGTTTGGCATGTGCTCAATTTTCCTTTTGGTGGCTTGTATCTTGCAAAGGCGACTGATGGTGATTTCCGATAAGC
           |    |   | | ||||||  |||  |  | |  |  ||     |   || ||| | |||   |  |    |     |   |   |||| |  |  ||  |||||||  ||||||||||||||||||| |||||||| ||||| || || ||||| ||  ||||    |||||||| || || ||||||||  | || ||| |  
gcaaggagccattccctctcccaactactatgttctctttagttgtgctggcaagaattatacagaaatatcagcacacaagtaacgct--ttgcctgtggacatggtctttgcagGTGAATGCATTCCCTATCACTGTCATGTTTGGGATGTGTTCTATCTTCCTCTTCATGGCAGCAATCTTGCAGAGACGGCTGATGGTTGTCTCTGATCAAG

upper sequence: GLYMA06G13760.1 (Glycine max), 3'ss of exon 6
lower sequence: AT4G27720.1 (Arabidopsis thaliana), 3'ss of exon 6
gtatgttac----acaatctactacttcaatgcaatgcttgagcttaccaatgcagtagtattttcttatctctggttttgactaattgtgtattttctcgatgcagGTTGATGCATTCCCTATCACTGTTATGTTTGGCATGTGCTCAATTTTCCTTTTGGTGGCTTGTATCTTGCAAAGGCGACTGATGGTGATTTCCGATAAGC
||| ||  |    ||| |||  | || ||    | |   |||| || |   | |  |     | |||    | ||||  |||||| || | | |  |||    | ||||  |||||||||||||||| || |||||||| |||||||| || ||||| || || ||  || || | |||||||| || ||| |||||   || || |
gtaagtccccccaacattctttttctgcaccatagtagctgagatttcgtgtcccatg----tctctgtgttgtggtactgactagttttatgtgctct----gaagGTAAATGCATTCCCTATCACGGTCATGTTTGGAATGTGCTCGATCTTCCTCTTTGTTGCAAGTCTCCTACAAAGGCGGCTCATGATGATTGTTGACAAAC

upper sequence: GLYMA06G13760.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv02s0025g02420.t01 (Vitis vinifera), 3'ss of exon 6
gtatgttacacaatctactacttcaatgcaatgcttgagcttaccaatgcagtagtattttcttatctctggttttgactaattgtgtatttt---ctcgatgcagGTTGATGCATTCCCTATCACTGTTATGTTTGGCATGTGCTCAATTTTCCTTTTGGTGGCTTGTATCTTGCAAAGGCGACTGATGGTGATTTCCGATAAGC
 | |  |     |     | ||||  |  ||   | | | |    |||  |    | | | ||  |||||     | | || | || | || |   ||   || ||||| ||||||| || |||||||| ||||||||||||||||| |||||||| || |||||     | ||||||||| | || ||| ||||||| || |  |
-tgtactgttttaatggtttcttctct-taaccatagggat----aatttatctctctctgctcctctctaacactaaatattggtttgttcttccctttttgaagGTTAATGCATTTCCAATCACTGTCATGTTTGGCATGTGCTCGATTTTCCTCTTTGTGGCAACACTGTTGCAAAGGAGGCTCATGATGATTTCAGAGAGCC

upper sequence: GLYMA06G13760.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv16s0098g01290.t01 (Vitis vinifera), 3'ss of exon 6
--gtatgttacacaatctactacttcaatgcaatgcttgagcttaccaatgcagtagtattttcttatctctggttttgactaattgtg-tattttctcgatgcagGTTGATGCATTCCCTATCACTGTTATGTTTGGCATGTGCTCAATTTTCCTTTTGGTGGCTTGTATCTTGCAAAGGCGACTGATGGTGATTTCCGATAAGC
   ||| ||  | | |  || |  | ||  |  |   || |||  |   |   ||  |  || ||| | | |  |  |   |  || || ||| || | ||   ||||| |||||||||| |||||||| ||||||||||||||||| |||||||| || ||||| | ||||||||||||||| || ||||||||| | || ||| 
ccttattttggata-tagaccatgtgaagact-tctatgtgctc-cttctctggtgatcgttccttctgtttcttaatagttgtttttggtatgtttttga---agGTTAATGCATTCCCCATCACTGTCATGTTTGGCATGTGCTCGATTTTCCTCTTTGTGGCATCTATCTTGCAAAGGCGGCTCATGGTGATTGCTGACAAGT

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|58024668|gb|CX711409.1|CX711409
EST:     ACTTTTTCCGCATTCCTCTCAACATTTTTGTGTGTGTTGTGCTGTACAAT                         GTTGATGCATTCCCTATCACTGTTATGTTTGGCATGTGCTCAATTTTCCTT
genomic: ACTTTTTCCGCATTCCTCTCAACATTTTTGTGTGTGTTGTGCTGTACAATgtatgttaca ... ctcgatgcagGTTGATGCATTCCCTATCACTGTTATGTTTGGCATGTGCTCAATTTTCCTT
EST: gi|13787504|gb|BG650096.1|BG650096
EST:     ACTTTTTCCGCATTCCTCTCAACATTTTTGTGTGTGTTGTGCTGTACAAT                         GTTGATGCATTCCCTATCACTGTTATGTTTGGCATGTGCTCAATTTTCCTT
genomic: ACTTTTTCCGCATTCCTCTCAACATTTTTGTGTGTGTTGTGCTGTACAATgtatgttaca ... ctcgatgcagGTTGATGCATTCCCTATCACTGTTATGTTTGGCATGTGCTCAATTTTCCTT
EST: gi|57575204|gb|CX548179.1|CX548179
EST:     ACTTTTTCCGCATTCCTCTCAACATTTTTGTGTGTGTTGTGCTGTACAAT                         GTTGATGCATTCCCTATCACTGTTATGTTTGGCATGTGCTCAATTTTCCTT
genomic: ACTTTTTCCGCATTCCTCTCAACATTTTTGTGTGTGTTGTGCTGTACAATgtatgttaca ... ctcgatgcagGTTGATGCATTCCCTATCACTGTTATGTTTGGCATGTGCTCAATTTTCCTT
EST: gi|207725952|gb|GD701408.1|GD701408
EST:     ACTTTTTCCGCATTCCTCTGAACATTTTTGTGTGTGTTGTGCTGTACAAT                         GTTGATGCATTCCCTATCACTGTT
genomic: ACTTTTTCCGCATTCCTCTCAACATTTTTGTGTGTGTTGTGCTGTACAATgtatgttaca ... ctcgatgcagGTTGATGCATTCCCTATCACTGTT
EST: gi|193366501|gb|FK332867.1|FK332867
EST:     ACTTTTTCCGCATTCCTCTCAACATTTTTGTGTGTGTTGTGCTGTACAAT                         GTTGATGCATTCCCTATCACTGTTATGTTTGGCATGTGCTCAATTTTCCTT
genomic: ACTTTTTCCGCATTCCTCTCAACATTTTTGTGTGTGTTGTGCTGTACAATgtatgttaca ... ctcgatgcagGTTGATGCATTCCCTATCACTGTTATGTTTGGCATGTGCTCAATTTTCCTT
EST: gi|208254628|gb|GE057334.1|GE057334
EST:     ACTTTTTCCGCATTCCTCTCAACATTTTTGTGTGTGTTGTGCTGTACAAT                         GTTGATGCATTCCCTATCACTGTTATGTTTGGCATGTGCTCAATTTTCCTT
genomic: ACTTTTTCCGCATTCCTCTCAACATTTTTGTGTGTGTTGTGCTGTACAATgtatgttaca ... ctcgatgcagGTTGATGCATTCCCTATCACTGTTATGTTTGGCATGTGCTCAATTTTCCTT
EST: gi|58018126|gb|CX704868.1|CX704868
EST:     ACTTTTTCCGCATTCCTCTCAACATTTTTGTGTGTGTTGTGCTGTACAAT                         GTTGATGCATTCCCTATCACTGTTATGTTTGGCATGTGCTCAATTTTCCTT
genomic: ACTTTTTCCGCATTCCTCTCAACATTTTTGTGTGTGTTGTGCTGTACAATgtatgttaca ... ctcgatgcagGTTGATGCATTCCCTATCACTGTTATGTTTGGCATGTGCTCAATTTTCCTT
EST: gi|193667243|gb|FK613485.1|FK613485
EST:     ACTTTTTCCGCATTCCTCTCAACATTTTTGTGTGTGTTGTGCTGTACAAT                         GTTGATGCATTCCCTATCACTGTTATGTTTGGCATGTGCTCAATTTTCCTT
genomic: ACTTTTTCCGCATTCCTCTCAACATTTTTGTGTGTGTTGTGCTGTACAATgtatgttaca ... ctcgatgcagGTTGATGCATTCCCTATCACTGTTATGTTTGGCATGTGCTCAATTTTCCTT
EST: gi|18690866|gb|BM519722.1|BM519722
EST:     ACTTTTTCCGCATTCCTCTCAACATTTTTGTGTGTGTTGTGCTGTACAAT                         GTTGATGCATTCCCTATCACTGTTATGTTTGGCATGTGCTCAATTTTCCTT
genomic: ACTTTTTCCGCATTCCTCTCAACATTTTTGTGTGTGTTGTGCTGTACAATgtatgttaca ... ctcgatgcagGTTGATGCATTCCCTATCACTGTTATGTTTGGCATGTGCTCAATTTTCCTT
EST: gi|12773026|gb|BG237953.1|BG237953
EST:     ACTTTTTCCGCATTCCTCTCAACATTTTTGTGTGTGTTGTGCTGTACAAT                         GTTGATGCATTCCCTATCACTGTTATGTTTGGCATGTGCTCAATTTTCCTT
genomic: ACTTTTTCCGCATTCCTCTCAACATTTTTGTGTGTGTTGTGCTGTACAATgtatgttaca ... ctcgatgcagGTTGATGCATTCCCTATCACTGTTATGTTTGGCATGTGCTCAATTTTCCTT
EST: gi|23728732|gb|BU762426.1|BU762426
EST:     ACTTTTTCCGCATTCCTCTCAACATTTTTGTGTGTGTTGTGCTGTACAAT                         GTTGATGCTTTCCCTATCACTGTTATGTTTGGCATGTGCTCAATTTTCCTT
genomic: ACTTTTTCCGCATTCCTCTCAACATTTTTGTGTGTGTTGTGCTGTACAATgtatgttaca ... ctcgatgcagGTTGATGCATTCCCTATCACTGTTATGTTTGGCATGTGCTCAATTTTCCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcagtagtattttcttatctctggttttgactaattgtgtattttctcgatgcagGTTGATGCATTCCCTATCACTGTTATGTTTGGCATGTGCTCAATTTTCCTTTTGGTGGCTTGTATCTTGCAAAGGCGACTGATGGTGATTTCCGATAAGC
                            gactaat  putative branch site (score: 2)
                                       tattttctc  putative PPT
                               taattgtgtatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgttacacaatctactacttcaatgcaatgcttgagcttaccaatgcagtagtattttcttatctctggttttgactaattgtgtattttctcgatgcagGTTGATGCATTCCCTATCACTGTTATGTTTGGCATGTGCTCAATTTTCCTTTTGGTGGCTTGTATCTTGCAAAGGCGACTGATGGTGATTTCCGATAAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG