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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAAATCTGGTCAGTCTCCAAGGCTACTCTTTGTCAACGTACGGAAATCTTCTCTTTTATGACTACATGGAAAATGGCAGTCTATGGGATCTTCTGCATGgtaagttcaagccttggcttgaaagatgctgatgtactttgttgaaaacttttctgtacaatctactatgtacattcaaccttgcattgatttagcaata...

Basic information

species Glycine max
transcript GLYMA06G05900.1
intron # 26
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G05900.1 (Glycine max), 5'ss of exon 26
lower sequence: LOC_Os02g53720.1 (Oryza sativa), 5'ss of exon 4
AGAAATCTGGTCAGTCTCCAAGGCTACTCTTTGTCAACGTACGGAAATCTTCTCTTTTATGACTACATGGAAAATGGCAGTCTATGGGATCTTCTGCATGgtaagttcaagccttg-gcttgaaagatgctgatgtactttgttgaaaacttttctgtacaatctactatgtacattcaaccttgcattgat-ttagcaata
 | ||||| ||||| || ||||| || ||  | ||| |    || ||||||||||| || |||||| |||||||||||||||| |||||| || | ||||||||||  |        |    | | || |  | | ||| |    | ||   ||  |||      || ||     |||    ||| || |   ||  |  | 
CGGAATCTTGTCAGCCTTCAAGGGTATTCCCTATCACCTGCTGGGAATCTTCTCTTCTACGACTACTTGGAAAATGGCAGTCTCTGGGATGTTTTACATGgtaagtgaattttacatggcaaacaaatacataggaactgtaagcagaatagttg-gtatttagaacgattgttcttctggtttgtatagccgttgcctgt-

upper sequence: GLYMA06G05900.1 (Glycine max), 5'ss of exon 26
lower sequence: LOC_Os06g10230.1 (Oryza sativa), 5'ss of exon 25
AGAAATCTGGTCAGTCTCCAAGGCTACTCTTTGTCAACGTACGGAAATCTTCTCTTTTATGACTACATGGAAAATGGCAGTCTATGGGATCTTCTGCATGgtaagt--------tcaagccttggcttgaa--agatgctgatgtactttgttgaaaa-----------cttttctgtacaatctactatgt---acattcaaccttgcattgattta--gcaata----------------------------------------------------------
 | ||||| |||||||| ||||| || ||  | ||  |    |||||||||||||| || || |||||||||||||| || || |||||| || ||||||||||||         |||  | | ||          ||    || | ||||   | ||           |  ||||  | |   |  ||| |   ||||| |   |||| |   || |  ||||||                                                          
CGGAATCTAGTCAGTCTTCAAGGATATTCCCTATCTCCTGTTGGAAATCTTCTCTTCTACGATTACATGGAAAATGGAAGCCTCTGGGATGTTTTGCATGgtaagtgccgactgccaactcattgcacagtttgattgtcattgcaatttgcacagaagcaccaacatgccattctcaaaagcatgatatttgacacattgatatttgcttctgttgattgcaataccaaattgttacatgacatcttgttaccatgttaaaatcttttttttcattattctag

upper sequence: GLYMA06G05900.1 (Glycine max), 5'ss of exon 26
lower sequence: AT2G26330.1 (Arabidopsis thaliana), 5'ss of exon 25
AGAAATCTGGTCAGTCTCCAAGGCTACTCTTTGTCAACGTACGGAAATCTTCTCTTTTATGACTACATGGAAAATGGCAGTCTATGGGATCTTCTGCATGgtaagttcaa--gccttggcttgaaagatgctgatgtactttgt----tgaaaacttttctgtacaatctactatgtacattcaaccttgcattgatttagcaata
|||||||| || || || ||||  || ||  | ||    |  || | |||||| || ||||||||  |||||||||| || || ||||||||||| ||||||||||   |  |||     | ||||  |  |    |  | |||    | | |||||   |||    | |   | |                              
AGAAATCTTGTGAGCCTACAAGCTTATTCCCTCTCTCACTTGGGGAGTCTTCTGTTCTATGACTATTTGGAAAATGGTAGCCTCTGGGATCTTCTTCATGgtaagtctcatcgccaaacatagaaaattatttgaatcttctgtgacataacaacttgcttgtgtgttttgtaaag------------------------------

upper sequence: GLYMA06G05900.1 (Glycine max), 5'ss of exon 26
lower sequence: Vv04s0008g01970.t01 (Vitis vinifera), 5'ss of exon 25
AGAAATCTGGTCAGTCTCCAAGGCTACTCTTTGTCAACGTACGGAAATCTTCTCTTTTATGACTACATGGAAAATGGCAGTCTATGGGATCTTCTGCATGgtaagttcaagccttggcttgaaagatgctgatgtactttgttgaaaacttttctgtacaa---tctactatgtacattcaaccttgcattg-atttagcaata---
|| ||||||||| |||| ||||| || ||  ||||  | |  || || || ||||| |||||||||||||||||||||||||| |||||||| || ||||||||||| || | ||  | ||||  ||   |   | || ||   ||  ||  |||| | ||   | ||  |  || ||     ||     ||  |  || | |    
AGGAATCTGGTCTGTCTACAAGGATATTCCCTGTCCCCTTCTGGGAACCTACTCTTCTATGACTACATGGAAAATGGCAGTCTCTGGGATCTACTTCATGgtaagtttaaacttt--cctgaacaatatgg---tgctctgc--aagtctgatctgaaaaaatatttatcacttaaatgggtgctaaatgtgtgtcaagaagtgtga

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|207785662|gb|GD755731.1|GD755731
EST:     TCTCTTTTATGACTACATGGAAAATGGCAGTCTATGGGATCTTCTGCATG                         GACCTACCAAGAAGAAAAAGCTTGATTGGGATCTTCGTCTAAAAATAGCAC
genomic: TCTCTTTTATGACTACATGGAAAATGGCAGTCTATGGGATCTTCTGCATGgtaagttcaa ... ttttttgcagGACCTACCAAGAAGAAAAAGCTTGATTGGGATCTTCGTCTAAAAATAGCAC
EST: gi|207777724|gb|GD749687.1|GD749687
EST:     TCTCTTTTATGACTACATGGAAAATGGCAGTCTATGGGATCTTCTGCATG                         GACCTACCAAGAAGAAAAAGCTTGATTGGGATCTTCGTCTAAAAATAGCAC
genomic: TCTCTTTTATGACTACATGGAAAATGGCAGTCTATGGGATCTTCTGCATGgtaagttcaa ... ttttttgcagGACCTACCAAGAAGAAAAAGCTTGATTGGGATCTTCGTCTAAAAATAGCAC
EST: gi|193490625|gb|FK456408.1|FK456408
EST:     TCTCTTTTATGACTACATGGAAAATGGCAGTCTATGGGATCTTCTGCATG                         GACCTACCAAGAAGAAAAAGCTTGATTGGGATCTTCGTCTAAAAA
genomic: TCTCTTTTATGACTACATGGAAAATGGCAGTCTATGGGATCTTCTGCATGgtaagttcaa ... ttttttgcagGACCTACCAAGAAGAAAAAGCTTGATTGGGATCTTCGTCTAAAAA
EST: gi|193337606|gb|FK304624.1|FK304624
EST:     TCTTTTATTGACTACATGGAAAATAGGCAGTCTATGGGATCTTCTGCATG                         GACCTACCAAGAAGAAAAAGACTTGATTGGGATCTTCGTCTAAAAATAGCA
genomic: TCTTTTA-TGACTACATGGAAAAT-GGCAGTCTATGGGATCTTCTGCATGgtaagttcaa ... ttttttgcagGACCTACCAAGAAGAAAAAG-CTTGATTGGGATCTTCGTCTAAAAATAGCA
EST: gi|193696097|gb|FK637565.1|FK637565
EST:     TCTCTTTTATGACTACATGGAAAATGGCAGTCTATGGGATCTTCTGCATG                         GACCTACCAAGAAGAAAAAGCTTGATTGGGATCTTCGTCTAAAAA
genomic: TCTCTTTTATGACTACATGGAAAATGGCAGTCTATGGGATCTTCTGCATGgtaagttcaa ... ttttttgcagGACCTACCAAGAAGAAAAAGCTTGATTGGGATCTTCGTCTAAAAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAAATCTGGTCAGTCTCCAAGGCTACTCTTTGTCAACGTACGGAAATCTTCTCTTTTATGACTACATGGAAAATGGCAGTCTATGGGATCTTCTGCATGgtaagttcaagccttggcttgaaagatgctgatgtactttgttgaaaacttttctgtacaatctactatgtacattcaaccttgcattgatttagcaata

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA