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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTGACACATCCTGAACTGTATGAAGACATTGGTATCAAGCCTCCTAAGGGAGTTATTTTATATGGGGAACCAGGAACTGGGAAGACATTGCTTGCAAAGgtgtgcattttttggggtttcttatatggtgttgaaatatattatcaacatattttctatttctcattttctatgtttaatacgaagtttgaatttcttt...

Basic information

species Glycine max
transcript GLYMA03G32800.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G32800.1 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os07g49150.1 (Oryza sativa), 5'ss of exon 2
CCTGACACATCCTGAACTGTATGAAGACATTGGTATCAAGCCTCCTAAGGGAGTTATTTTATATGGGGAACCAGGAACTGGGAAGACATTGCTTGCAAAGgtgtgcattttttggggtttcttatatggtgttgaaatatattat-----caacata--------ttttctatttctcattttctatgtttaatacgaagtttgaatttcttt------------------------------------------------------
  |||| |||||||| || |||||||||||||| |||| ||| || |||||||| || ||||| || ||||| ||||| ||||||||| | ||||| |||||  |  || |   || || | |||  || ||  | |||  ||||      ||   |           || |||| |   ||   ||  ||||    |   ||| | |  ||                                                       
TTTGACCCATCCTGAGCTATATGAAGACATTGGCATCAGGCCACCCAAGGGAGTCATATTATACGGAGAACCTGGAACAGGGAAGACACTACTTGCCAAGgttagtgttct---ggtttgcgtattgggagtcaatatagcttatggcagtaatgcaggcttcagccctccatttatggcttgtaataattaagcaaagcattgcactatttgtcattctgtacctctcagttctctgaccactgattacttgcattgttgttgcag

upper sequence: GLYMA03G32800.1 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os03g18690.1 (Oryza sativa), 5'ss of exon 2
CCTGACACATCCTGAACTGTATGAAGACATTGGTATCAAGCCTCCTAAGGGAGTTATTTTATATGGGGAACCAGGAACTGGGAAGACATTGCTTGCAAAGgtgtgcattttttggggtttcttatatggtgttgaaatatattatcaacatattttctatttctcattttctatgtttaatacgaagtttgaatttcttt----------
| |||| |||||||| || ||||| |||||||| || | |||||| |||||||| || |||||||||||||| || || || || ||  | ||||||||||| ||  | ||||        |  || |   ||||| | |   ||   ||| ||| ||   | |||  ||| ||  | | ||  ||  | | |  |   |          
CTTGACTCATCCTGAGCTATATGAGGACATTGGAATAAGGCCTCCCAAGGGAGTAATATTATATGGGGAACCTGGCACAGGCAAAACTCTACTTGCAAAGgtttgtctctttt--------tcttaggacattgaagtcttgaattcccatgtttactccatttcaaattcaat--tcattaataaactagtaacttaataaatgctagt

upper sequence: GLYMA03G32800.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G104373_T01 (Zea mays), 5'ss of exon 2
CCTGACACATCCTGAACTGTATGAAGACATTGGTATCAAGCCTCCTAAGGGAGTTATTTTATATGGGGAACCAGGAACTGGGAAGACATTGCTTGCAAAGgtgtgcattttttggggtttcttatatggtgttgaaatatattatcaacatatttt--ctatttctcattttctatgtt-taatacgaagtttgaatttcttt------------------------------------------------------------------------------------------
| | ||||||||||| || ||||| |||||||| |||| |||||| |||||||||||  ||||||||||||| ||||| ||||| ||  | || |||||||| ||   |      | || |||       |||  ||  | ||||   |||   ||   | ||| |  |  |  ||     | |        ||||    |||                                                                                          
CTTAACACATCCTGAGCTATATGAGGACATTGGGATCAGGCCTCCGAAGGGAGTTATACTATATGGGGAACCTGGAACAGGGAAAACTCTACTCGCAAAGgtttgtgct------gattccttgaggacagttccaagtttttatttccatgccttagttgtttttgttcattgataaagcagtgaaggaactgaacgcttttcattcttcttttcttcctgacataagatattctctatgcctttattcctaaaatcatattttaattacttaaaacttttgaacgctgtag

upper sequence: GLYMA03G32800.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G056569_T01 (Zea mays), 5'ss of exon 2
CCTGACACATCCTGAACTGTATGAAGACATTGGTATCAAGCCTCCTAAGGGAGTTATTTTATATGGGGAACCAGGAACTGGGAAGACATTGCTTGCAAAGgtgtgcattttttggggtttct-tatatggtgttgaaatat--------attatcaacata---ttttctatttctcattttctatgtttaatacgaagtttgaatttcttt------------------------------------------------------------
| |||| || ||||| |||||||||||||||||||| | |||||| |||||||| || |||||||| ||||| ||||| || || ||  | ||||| |||||  | ||| | |   |    | || | | |||  | ||||        |||        |   |||  ||| |  | || ||||||||||   | || ||  | | | |||                                                            
CTTGACTCACCCTGAGCTGTATGAAGACATTGGTATTAGGCCTCCCAAGGGAGTCATATTATATGGAGAACCTGGAACAGGAAAAACTCTTCTTGCCAAGgtcagtattctgtcttgcaagtatacaagatgtcaatatattgcttagtattgcaggggcaggctttgatatctgcctttgtctatgtttat--ccaaattacactctttttctacttttcagttttcaaatagcatgtacttgggtagtgattacttgaaactgtctgcag

upper sequence: GLYMA03G32800.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G095593_T01 (Zea mays), 5'ss of exon 2
CCTGACACATCCTGAACTGTATGAAGACATTGGTATCAAGCCTCCTAAGGGAGTTATTTTATATGGGGAACCAGGAACTGGGAAGACATTGCTTGCAAAGgtgtgcattt-------------tttggggtttcttatatggtgttgaaatatatta--tcaacat---attttc-----tatttctcattttctatgtttaatacgaagtttgaatttcttt-----------------------------------------------------------------
| |||| ||||||||  |||||||||||||||| |||| ||| || |||||||| || |||||||| ||||| |||||||| || ||  | || || |||||  |   |              |    | | |||   ||  || | |    ||||   |||   |   ||  ||     |||||  | || |||||||||| |  ||| | || |||  |||                                                                 
CTTGACTCATCCTGAGTTGTATGAAGACATTGGGATCAGGCCACCCAAGGGAGTCATATTATATGGCGAACCTGGAACTGGAAAAACTCTACTCGCCAAGgtcagtgctcaggcttgcaagcatacaagatatctgtaatattgcttagtgttattgggtcaggcttcgatcctcaatgatatttgcctttgtctatgttta-tctgaattatgcattatttttttctactctccagttttcaaatagcatgtacttgggcagtgactacttgaaactgtttctgcag

upper sequence: GLYMA03G32800.1 (Glycine max), 5'ss of exon 2
lower sequence: AT2G20140.1 (Arabidopsis thaliana), 5'ss of exon 2
CCTGACACATCCTGAACTGTATGAAGACATTGGTATCAAGCCTCCTAAGGGAGTTATTTTATATGGGGAACCAGGAACTGGGAAGACATTGCTTGCAAAGgtgtgcattttttggggtttcttatatg-gtgttgaaatatattatcaacatattttctatttctcattttctatgtt--taatacgaagtttgaatttcttt
  | |||||||| || ||||||||||| ||||| || ||||| || || || || || || ||||| || ||||| |||||||||||||||||||| |||||   | | |||| |  | |  | |||   |  |  ||||   | || |  | ||   |  ||   |      ||  |  || | |  |  |   |||  || 
TTTAACACATCCCGAGCTGTATGAAGATATTGGAATTAAGCCACCAAAAGGTGTGATCTTGTATGGTGAGCCAGGCACTGGGAAGACATTGCTTGCTAAGgtt--cgtcttttagcctatagtgtatccattatataataagctttctagttgttaattgcttaatacagcacataatggtacttcccaagtatgattggtt-

upper sequence: GLYMA03G32800.1 (Glycine max), 5'ss of exon 2
lower sequence: AT4G29040.1 (Arabidopsis thaliana), 5'ss of exon 2
CCTGACACATCCTGAACTGTATGAAGACATTGGTATCAAGCCTCCTAAGGGAGTTATTTTATATGGGGAACCAGGAACTGGGAAGACATTGCTTGCAAAGgtgtgcattttt-tggggtttcttatatggtgttgaaatatattatcaacatattttctatttctcattttctatgtttaatacgaagtttgaatttcttt-
  |||| ||||||||  |||||||||| |||||||| || || || ||||| || ||||| ||||| || || ||||||||||||||||||||||| ||||| ||  ||| |     |  ||| ||   || ||    | | ||  ||  |||  ||   |||   | ||    |||  | |||      | |||   ||  
TTTGACTCATCCTGAGTTGTATGAAGATATTGGTATTAAACCACCAAAGGGTGTAATTTTGTATGGTGAGCCTGGAACTGGGAAGACATTGCTTGCTAAGgtttgtctttgtacctagaatctaatg-agtattagtgtttgtttgcagtatagctta-gtttactacttaacttgtcaattacattcagttaatcgtttgt

upper sequence: GLYMA03G32800.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv07s0005g05160.t01 (Vitis vinifera), 5'ss of exon 2
CCTGACACATCCTGAACTGTATGAAGACATTGGTATCAAGCCTCCTAAGGGAGTTATTTTATATGGGGAACCAGGAACTGGGAAGACATTGCTTGCAAAGgtgtgcattttttggggtttcttat-atggtgttgaaatata--ttatcaacatattttctatttctcattttctatgtttaatacgaagtttgaatttcttt
 || |||||||||||||||||||| |||||||||||||||||||||||||| || ||  ||||||| || || ||||| || ||||| ||||||||||||||||| |||  |    | ||| ||| |   || || | || |  |||||  |  ||||| ||| ||| ||| |     |    |      ||| | |||  | 
TCTAACACATCCTGAACTGTATGAGGACATTGGTATCAAGCCTCCTAAGGGGGTCATACTATATGGAGAGCCTGGAACAGGAAAGACCTTGCTTGCAAAGgtgtgtattcatatttgcttcctatcaaactggtgcattacaatttatctgc-cattttatatctctgattgtgc-catcctctttttcctttcattttggt-

upper sequence: GLYMA03G32800.1 (Glycine max), 5'ss of exon 2
lower sequence: PP1S4_277V6.1 (Physcomitrella patens), 5'ss of exon 2
CCTGACACATCCTGAACTGTATGAAGACATTGGTATCAAGCCTCCTAAGGGAGTTATTTTATATGGGGAACCAGGAACTGGGAAGACATTGCTTGCAAAGgtgtgcattttttggggtttcttatatggtgttgaaatatattatcaacatattttctatttctcattttctatgtttaatacgaagtttgaatttcttt
  |||||||||| || |||||||||||||||||||||||||| || |||||||||||||| ||||| ||||| || |||||||| ||  | ||||| |||||    |  ||| |       | | ||  |||     |  | |  | || |  | ||| |         |     |||  ||  ||| |    ||| || 
GTTGACACATCCGGAGCTGTATGAAGACATTGGTATCAAGCCCCCCAAGGGAGTTATTTTGTATGGTGAACCCGGCACTGGGAAAACTCTTCTTGCTAAGgtaaatacgtttggcaaagggtgagatcatgtaattcttgacttgctaccttgtctctgtacagagaagttctgctttgctaacaaggtgacctttgttg

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|13789045|gb|BG651636.1|BG651636
EST:     GAGTTATTTTATATGGGGAACCAGGAACTGGGAAGACATTGCTTGCAAAG                         GCTGTGGCAAACTCAACATCAGCAACCTTTTTGCGTGTTGTTGGTAGTGAA
genomic: GAGTTATTTTATATGGGGAACCAGGAACTGGGAAGACATTGCTTGCAAAGgtgtgcattt ... ttactttcagGCTGTGGCAAACTCAACATCAGCAACCTTTTTGCGTGTTGTTGGTAGTGAA
EST: gi|6725713|gb|AW310112.1|AW310112
EST:     GAGTTATTTTATATGGGGAACCAGGAACTGGGAAGACATTGCTTGCAAAG                         GCTGTGGCAAACTCAACATCAGCAACCTTTTTGCGTGTTGTTGGTAGTGAA
genomic: GAGTTATTTTATATGGGGAACCAGGAACTGGGAAGACATTGCTTGCAAAGgtgtgcattt ... ttactttcagGCTGTGGCAAACTCAACATCAGCAACCTTTTTGCGTGTTGTTGGTAGTGAA
EST: gi|58019738|gb|CX706480.1|CX706480
EST:     AGTTATTTTATATGGGGAACCAGGAACTGGGAAGACA-TGCTTTGCAAAG                         GCTGTGGCAAACTCAACATCAGCAACCTTTTTGCGTGTTGTTGGTAGTGA
genomic: AGTTATTTTATATGGGGAACCAGGAACTGGGAAGACATTGC-TTGCAAAGgtgtgcattt ... ttactttcagGCTGTGGCAAACTCAACATCAGCAACCTTTTTGCGTGTTGTTGGTAGTGA
EST: gi|207825455|gb|GD800554.1|GD800554
EST:     GAGTTATTTTATATGGGGAACCAGGAACTGGGAAGACATTGCTTGCAAAG                         GCTGTGGCAAACTCAACATCAGCAACCTTTTTGCGTGTTGTTGGTAGTGAA
genomic: GAGTTATTTTATATGGGGAACCAGGAACTGGGAAGACATTGCTTGCAAAGgtgtgcattt ... ttactttcagGCTGTGGCAAACTCAACATCAGCAACCTTTTTGCGTGTTGTTGGTAGTGAA
EST: gi|16996954|gb|BM086326.1|BM086326
EST:     GAGTTA-TTTATATGGGGAACCAGGAACTGGGAAGACATTGCTTGCAAAG                         GCTGTGGCAAACTCAACATCAGCAACCTTTTTGCGTGTTGTTGGTAGTGAA
genomic: GAGTTATTTTATATGGGGAACCAGGAACTGGGAAGACATTGCTTGCAAAGgtgtgcattt ... ttactttcagGCTGTGGCAAACTCAACATCAGCAACCTTTTTGCGTGTTGTTGGTAGTGAA
EST: gi|151412684|gb|EV282496.1|EV282496
EST:     GAGTTATTTTATATGGGGAACCAGGAACTGGGAAGACATTGCTTGCAAAG                         GCTGTGGCAAACTCAACATCAGCAACCTTTTTGCGTGTTGTTGGTAGTGAA
genomic: GAGTTATTTTATATGGGGAACCAGGAACTGGGAAGACATTGCTTGCAAAGgtgtgcattt ... ttactttcagGCTGTGGCAAACTCAACATCAGCAACCTTTTTGCGTGTTGTTGGTAGTGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCTGACACATCCTGAACTGTATGAAGACATTGGTATCAAGCCTCCTAAGGGAGTTATTTTATATGGGGAACCAGGAACTGGGAAGACATTGCTTGCAAAGgtgtgcattttttggggtttcttatatggtgttgaaatatattatcaacatattttctatttctcattttctatgtttaatacgaagtttgaatttcttt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttggggt