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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCGAGCAGCAGAGATTCTTTGGCATAAGCGGGGTGGGAAGTTAGTGCACCCAAATGACCATGTCAATAGATCACAGTCTTCAAATGATACATTCCCAACTgtaagcctcttgtaattatatatattcccgtttttttttgttgttgatatgtctcgccatctgtgtagtgcaactcttgatagactttcttaaactttgtttatccactgtacagctcttgtttaaagtattgatttctttttaatctatatttgtttacttctttccag

Basic information

species Glycine max
transcript GLYMA02G01920.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G01920.1 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os03g21950.1 (Oryza sativa), 5'ss of exon 4
CCGAGCAGCAGAGATTCTTTGGCATAAGCGGGGTGGGAAGTTAGTGCACCCAAATGACCATGTCAATAGATCACAGTCTTCAAATGATACATTCCCAACTgtaagcctcttgtaattatatatattcccgtttttttttgttgttgatatgtctcgccatctgtgtagtgcaactcttgatagactttcttaaactttgtttatccactgtacagctcttgtttaaagtattgatttctttttaatctatatttgtttacttctttccag
  | || || ||||||||| | |||||||| || | |||||| || ||||| ||||| ||||| || ||||||||||| |||||||||||||| || ||||||||  |      | ||| | | |  ||||  ||||    |||  || |  ||         |||  ||       |    ||| || | |                                                                              
TAGGGCCGCTGAGATTCTTGGACATAAGCGTGGCGAGAAGTTTGTACACCCTAATGATCATGTGAACAGATCACAGTCCTCAAATGATACATTTCCCACTgtaagatttc----actatttttttggccgtcatttt--aatgtgcatttacctt--tgctgatgttatgatttatgttgctgacattttcag-----------------------------------------------------------------------------

upper sequence: GLYMA02G01920.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G010823_T01 (Zea mays), 5'ss of exon 4
CCGAGCAGCAGAGATTCTTTGGCATAAGCGGGGTGGGAAGTTAGTGCACCCAAATGACCATGTCAATAGATCACAGTCTTCAAATGATACATTCCCAACTgtaagcctcttgtaattatatatattcccgttttttt-ttgttgttg-atatgtctcgccatctgtgtagtgcaactcttgatagactttcttaaactttgtttatccactgtacagctcttgtttaaagtattgatttctttttaatctatatttgtttacttctttccag
  | ||| | ||||| ||| | || ||||| |||| |||||| |||||||||||||||||||| ||||| ||||| ||||||||||||||||| || |||||||||||    ||| ||| | |||| | || ||  | ||  || || | |||| |    ||   ||   |  |  | |  |                                                                                          
TAGGGCATCTGAGATCCTTGGACACAAGCGCGGTGAGAAGTTTGTGCACCCAAATGACCATGTGAATAGGTCACAATCTTCAAATGATACATTTCCCACTgtaagcct----taactatttttatttcagtattactattactgctgcagatgttt-attattcatggcattgacgtttccag-----------------------------------------------------------------------------------------

upper sequence: GLYMA02G01920.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G348729_T01 (Zea mays), 5'ss of exon 7
CCGAGCAGCAGAGATTCTTTGGCATAAGCGGGGTGGGAAGTTAGTGCACCCAAATGACCATGTCAATAGATCACAGTCTTCAAATGATACATTCCCAACTgtaagcctcttgtaattatatatattcccgtttttttttgttgttgatatgtctcgccatctgtgtagtgcaactcttgatagactttcttaaactttgtttatccactgtacagctcttgtttaaagtattgatttctttttaatctatatttgtttacttctttccag
  | ||| | ||||| ||| | || ||| | |||  |||||| |||||||||||||||||||| ||||| ||||| ||||||||||||||||| || ||||||||| |    ||| ||| | |||| |    | ||  | ||  |  | |                                                                                                                        
TAGGGCATCTGAGATCCTTGGACACAAGGGCGGTCAGAAGTTTGTGCACCCAAATGACCATGTGAATAGGTCACAATCTTCAAATGATACATTTCCCACTgtaagctt----taactatttttatttca--ctattactattactactgtag----------------------------------------------------------------------------------------------------------------------

upper sequence: GLYMA02G01920.1 (Glycine max), 5'ss of exon 4
lower sequence: AT5G50950.3 (Arabidopsis thaliana), 5'ss of exon 3
CCGAGCAGCAGAGATTCTTTGGCATAAGCGGGGTGGGAAGTTAGTGCACCCAAATGACCATGTCAATAGATCACAGTCTTCAAATGATACATTCCCAACTgtaagcctcttgtaattatatatattcccgtttttttttgttgttgatatgtctcgccatctgtgtagtgcaactcttgatagactttcttaaact--ttg--tttatccactgtacagctcttgtttaaagtattgatttctttttaat--ctatatttgtttacttctttccag
  ||||||| ||||||||| | || || || ||||  ||  | |||||||||||||||||||| || |||||||| ||||| ||||| || || |||||||||||| |    || ||   |  |||| | ||  |  ||     | || |  |  ||     || |  | ||| |  | |  |  ||  |  |||   |||  |||||   || ||    |  |   |    | |  | | ||  || |      |||   |||  || | |  ||
TAGAGCAGCTGAGATTCTTGGTCACAAACGTGGTGAAAAAATTGTGCACCCAAATGACCATGTGAACAGATCACAATCTTCTAATGACACTTTTCCAACTgtaagctt----tagtt---tgcattctcattagtcattaccaataattttgcatgcttaacgt-tcattcaattgcttacggtgttcgtgtaaccgattgcttttatttcctatatgtatgctcactgctctgtcaagtactacttgacggtcgtataattttggttttgtatag

upper sequence: GLYMA02G01920.1 (Glycine max), 5'ss of exon 4
lower sequence: AT2G47510.2 (Arabidopsis thaliana), 5'ss of exon 5
CCGAGCAGCAGAGATTCTTTGGCATAAGCGGGGTGGGAAGTTAGTGCACCCAAATGACCATGTCAATAGATCACAGTCTTCAAATGATACATTCCCAACTgtaagcctcttgtaattatatatattcccgtttttttttgttgttgatatgtctcgccatctgtgtagtgcaactcttgatagactttcttaaactttg-tttatccactgtacagctcttgtttaaagtattgatttctttttaatctatatttgtttacttctttccag
  ||||||| ||||||||| | |  || || |||| ||| |  |||||||||||||||||||| || |||||||| ||||| || || || || || || |||||| |       | || |  ||||| | |     |   | || | |||  |     | |      |  || | ||      |||||||| |  |||  | |    |  | || ||  |  || | |   |  ||| |||||  |     ||||| ||           
TAGAGCAGCTGAGATTCTTGGTCGCAAACGTGGTGAGAAATGTGTGCACCCAAATGACCATGTGAACAGATCACAATCTTCTAACGACACTTTTCCTACCgtaagctt-------tcatttgcattccagctaccaat-actttttacatgctttaagtttt------taaaattttt------ctttcttatatgttggctcacttccctttcaacttctaattgacggtct--tttttttttttttggcttttgtctag----------

upper sequence: GLYMA02G01920.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv07s0005g00880.t01 (Vitis vinifera), 5'ss of exon 5
CCGAGCAGCAGAGATTCTTTGGCATAAGCGGGGTGGGAAGTTAGTGCACCCAAATGACCATGTCAATAGATCACAGTCTTCAAATGATACATTCCCAACTgtaagcctcttgtaattatatatattcccgtttttttttgttgttgatatgtctcgccatctgtgtagtgcaactcttgatagactttcttaaactttgtttatccactgtacagctcttgtttaaagtattgatttctttttaatctatatttgtttacttctttccag
  ||||||| ||||||||| | ||| |||| ||||  || |  ||||| |||||||||||||| || |||||||| ||||| |||||||||||||| ||||||||||| ||| |   |   |||  |  | |||||          | ||  ||  | |  |   | |    || | |   |   ||  | |||   || || |  ||||    | | || ||  || | |   ||| || ||  || |                     
TAGAGCAGCTGAGATTCTTGGCCATCAGCGTGGTGAAAAATATGTGCATCCAAATGACCATGTTAACAGATCACAATCTTCTAATGATACATTCCCTACTgtaagccttttgaa--caagaatagccatgattttt---------aagataactatctacttaaatggcttgacccatttca---ttgttgaaatgatgattttttactg----gtttttatt-gaattctatgtttgttgtttgtccag--------------------

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|16279870|gb|BI943659.1|BI943659
EST:     CAAATGACCATGTCAATAGATCACAGTCTTCAAATGATACATTCCCAACT                         GTAATGCACATTGCAGCCGCAATGGAAATAAACTCAAGACTAATTCCCAGC
genomic: CAAATGACCATGTCAATAGATCACAGTCTTCAAATGATACATTCCCAACTgtaagcctct ... ttctttccagGTAATGCACATTGCAGCCGCAATGGAAATAAACTCAAGACTAATTCCCAGC
EST: gi|151409155|gb|EV278963.1|EV278963
EST:     CAAATGACCATGTCAATAGATCACAGTCTTCAAATGATACATTCCCAACT                         GTAATGCACATTGCAGCCGCAATGGAAATAAACTCAAGACTAATTCCCAGC
genomic: CAAATGACCATGTCAATAGATCACAGTCTTCAAATGATACATTCCCAACTgtaagcctct ... ttctttccagGTAATGCACATTGCAGCCGCAATGGAAATAAACTCAAGACTAATTCCCAGC
EST: gi|192310921|gb|FG998897.1|FG998897
EST:     CAAATGACCATGTCAATAGATCACAGTCTTCAAATGATACATTCCCAACT                         GTAATGCACAT
genomic: CAAATGACCATGTCAATAGATCACAGTCTTCAAATGATACATTCCCAACTgtaagcctct ... ttctttccagGTAATGCACAT
EST: gi|298178427|gb|HO024162.1|HO024162
EST:     CAAATGACCATGTCAATAGATCACAGTCTTCAAATGATACATTCCCAACT                         GTAATGCACATTGCAGCCGCAATGGAA
genomic: CAAATGACCATGTCAATAGATCACAGTCTTCAAATGATACATTCCCAACTgtaagcctct ... ttctttccagGTAATGCACATTGCAGCCGCAATGGAA
EST: gi|192322683|gb|FK015020.1|FK015020
EST:     CAAATGACCATGTCAATAGATCACAGTCTTCAAATGATACATTCCCAACT                         GTAATGCACATTGCAGCCGCAATGGAAATAAACTCAAGACTAATTCCCAGC
genomic: CAAATGACCATGTCAATAGATCACAGTCTTCAAATGATACATTCCCAACTgtaagcctct ... ttctttccagGTAATGCACATTGCAGCCGCAATGGAAATAAACTCAAGACTAATTCCCAGC
EST: gi|192310776|gb|FK000290.1|FK000290
EST:     CAAATGACCATGTCAATAGATCACAGTCTTCAAATGATACATTCCCAACT                         GTAATGCACATTGCAGCCGCAATGGAAATAAACTCAAGACTAATTCCCAGC
genomic: CAAATGACCATGTCAATAGATCACAGTCTTCAAATGATACATTCCCAACTgtaagcctct ... ttctttccagGTAATGCACATTGCAGCCGCAATGGAAATAAACTCAAGACTAATTCCCAGC
EST: gi|209714881|gb|BW682046.1|BW682046
EST:     CAAATGACCATGTCAATAGATCACAGTCTTCAAATGATACATTCCCAACT                         GTAATGCACATTGCAG
genomic: CAAATGACCATGTCAATAGATCACAGTCTTCAAATGATACATTCCCAACTgtaagcctct ... ttctttccagGTAATGCACATTGCAG
EST: gi|209717303|gb|BW659018.1|BW659018
EST:     CAAATGACCATGTCAATAGATCACAGTCTTCAAATGATACATTCCCAACT                         GTAATGCACATTGCAGCCGCAATGGAAATAAACTCAAGACTAATTCCCAGC
genomic: CAAATGACCATGTCAATAGATCACAGTCTTCAAATGATACATTCCCAACTgtaagcctct ... ttctttccagGTAATGCACATTGCAGCCGCAATGGAAATAAACTCAAGACTAATTCCCAGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCGAGCAGCAGAGATTCTTTGGCATAAGCGGGGTGGGAAGTTAGTGCACCCAAATGACCATGTCAATAGATCACAGTCTTCAAATGATACATTCCCAACTgtaagcctcttgtaattatatatattcccgtttttttttgttgttgatatgtctcgccatctgtgtagtgcaactcttgatagactttcttaaactttgtttatccactgtacagctcttgtttaaagtattgatttctttttaatctatatttgtttacttctttccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA