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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattagttttggccattttgttccctgctctaataacttagtgaataacttctatctccttatcaaacactcttttaacggattgaactttgtaataccgaatactgattgaatataatgttttcctgttgcagAATATGTATGCTCAGTTGTTGCCTCTTGCTTTGCCTGCACCGCCAATGCCTGGAATGGGAGGAGGCTTTGCCCCTCCCCCTCCAATGGGTGGATTGGGGA

Basic information

species Glycine max
transcript GLYMA11G35460.1
intron # 28
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 28
lower sequence: GRMZM5G804382_T01 (Zea mays), 3'ss of exon 6
gtaattagttttggccattttgttccctgctctaataacttagtgaataacttctatctccttat-caaacactcttttaacggattgaactttgtaataccgaa--tactgattgaatataatgttttcc-tgttgcagAATATGTATGCTCAGTTGTTGCCTCTTGCTTTGCCTGCACCGCCAATGCCTGGAATGGGAGGAGGCTTTGCCCCTCCCCCTCCAATGGGTGGATTGGGGA---------
                                                 || ||||  || | || || |   ||| ||   | | | ||   | | || | ||      ||     | |   |   |||| | |||||||| |||||||| || ||| | ||||||||||||||||| |||||||||||||| ||||| ||         |||||| ||||| ||||||||  |||| |         
-----------------------------------------------gtacatctaaatcttcattcacatgttctgttcgtgtaattaatcatttcatcctgaggcagttggcatgacaagttacgttccattttgcagAACATGTATGCGCAATTGCTTCCTCTTGCTTTGCCTGCTCCGCCAATGCCTGGCATGGGTGG---------CCCTCCACCTCCGATGGGTGGGATGGGCATGCCTCCAA

upper sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 28
lower sequence: GRMZM2G057576_T01 (Zea mays), 3'ss of exon 28
gtaattagttttggccattttgttccctgctctaataacttagtgaataacttctatctccttatcaaacactctt-ttaacggattgaa-ctttgtaataccgaatactgattgaatataatgttttcctgttgcagAATATGTATGCTCAGTTGTTGCCTCTTGCTTTGCCTGCACCGCCAATGCCTGGAATGGGAGGAGGCTTTGCCCCTCCCCCTCCAATGGGTGGATTGGGGA---------
                                            | | | ||   | | |  |  ||     | || ||  ||   |||  | |||  ||  | | |     |   ||   ||||         |||||| |||||||| ||| || | ||||| |||||||| || |||||||||||||| ||||| ||          ||||| ||||| ||||||||| |||| |         
--------------------------------------------gtaaacctaaaaccgcgctcgcatgtgtttttgtttccgtgctgaggcattgacatgacaagttgcattcttatgcgatgt---------gcagAACATGTATGCGCAGCTGCTTCCTCTCGCTTTGCCGGCGCCGCCAATGCCTGGCATGGGTGG---------TCCTCCACCTCCGATGGGTGGAATGGGCATGCCTCCCA

upper sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 28
lower sequence: GRMZM2G115138_T01 (Zea mays), 3'ss of exon 13
gtaattagttttggccattttgttccctgctctaataacttagtgaataacttctatctccttatcaaacactcttttaacggattgaa-ctttgtaataccgaatactgattgaatataatgttttcctgttgcagAATATGTATGCTCAGTTGTTGCCTCTTGCTTTGCCTGCACCGCCAATGCCTGGAATGGGAGGAGGCTTTGCCCCTCCCCCTCCAATGGGTGGATTGGGGA---------
                                            | | | ||   | | |  |  |      | | ||  ||   |||  | |||  ||  | | |     |   ||   ||||         |||||| |||||||| ||| || | ||||| |||||||| || |||||||||||||| ||||| ||         |||||| ||||| ||||||||| |||| |         
--------------------------------------------gtaaacctaaaaccgcgctcgcgtgtgttttgtttccgtgctgaggcattgacatgacaagttgcattcttatgcgatgt---------gcagAACATGTATGCGCAGCTGCTTCCTCTCGCTTTGCCAGCGCCGCCAATGCCTGGCATGGGTGG---------CCCTCCACCTCCGATGGGTGGAATGGGCATGCCTCCCA

upper sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 28
lower sequence: GRMZM2G091121_T01 (Zea mays), 3'ss of exon 9
gtaattagttttggccattttgttccctgctctaataacttagtgaataacttctatctccttatcaaacactcttttaacggattgaa-ctttgtaataccgaatactgattgaatataatgttttcctgttgcagAATATGTATGCTCAGTTGTTGCCTCTTGCTTTGCCTGCACCGCCAATGCCTGGAATGGGAGGAGGCTTTGCCCCTCCCCCTCCAATGGGTGGATTGGGGA---------
                                            | | | ||   | | |  |  |      | | ||  ||   |||  | |||  ||  | | |     |   ||   ||||         |||||| |||||||| ||| || | ||||| |||||||| || |||||||||||||| ||||| ||         |||||| ||||| ||||||||| |||| |         
--------------------------------------------gtaaacctaaaaccgcgctcgcgtgtgttttgtttccgtgctgaggcattgacatgacaagttgcattcttatgcgatgt---------gcagAACATGTATGCACAGCTGCTTCCTCTCGCTTTGCCAGCGCCGCCAATGCCTGGCATGGGTGG---------CCCTCCACCTCCGATGGGTGGAATGGGCATGCCTCCCA

upper sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 28
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 29
gtaattagttttggccattttgttccctgctctaataacttagtgaataacttctatctccttatcaaacactcttttaacggattgaactttgtaataccgaatactgattgaatataatgttttcctgttgcagAATATGTATGCTCAGTTGTTGCCTCTTGCTTTGCCTGCACCGCCAATGCCTGGAATGGGAGGAGGC------TTTGCCCCTCCCCCTCCAATGGGTGGATTGGGGA
                                  |  |||||    | | || |   ||   |||||  |     |||| |   ||||    |  | |    |  | | ||    | |  | || |  |    ||||| |||||||| ||  ||||||| |||||||| |||||||| || ||||| ||||||||||| ||       | ||  ||||| || | |||||| ||        
--------------------------------gtactacttatgacacagctaca--ctggatatcatccgactctttatc---ttgacagatacact-taaaggagtaatatgtttttcttttgtttttaaacagAACATGTATGCCCAAATGTTGCCACTTGCTTTACCTGCACCACCGATGCCAGGAATGGGAGGTGGTGGTGGGTATGGTCCTCCACCACAAATGGGCGGTA------

upper sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 28
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 29
gtaattagttttggccattttgttccctgctctaataacttagtgaataacttctatctccttatcaaacactcttttaacggattgaactttgtaataccgaatactgattgaatataatgttttcct---gttgcagAATATGTATGCTCAGTTGTTGCCTCTTGCTTTGCCTGCACCGCCAATGCCTGGAATGGGAGGAG------------GCTTTGCCCCTCCCCCTCCAATGGGTGGATTGGGGA
                                 | |  | | | |  |  |||| ||| |||| |   |     | || ||    | || ||| ||     | |  || || |||  |||| | || |    | ||||||||||||||||||||||| |||| ||||||||||||||||| || ||||| || ||||||||||            |   |     ||| ||||| ||||            
---------------------------------agtggcatggcgtttttcttc-atccccttctgtta----ttattgaccatcttaa-tttatagctgggcaatctaatagaaactaatatgttacattggctgcagAATATGTATGCTCAGTTGCTGCCCCTTGCTTTGCCTGCACCTCCGATGCCCGGCATGGGAGGAGCTGGGATGGCAGGAGGTTTTGTTCCACCTCCCATGG------------

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|5058537|gb|AI737013.1|AI737013
EST:     ACCAAGTGAAAGCTAAAGAGCAAGAAGAGAAGGAAGTAATTGCTCAACAG                         AATATGTATGCTCAGTTGTTGCCTCTTGCTTTGCCTGCACCGCCAATGCCT
genomic: ACCAAGTGAAAGCTAAAGAGCAAGAAGAGAAGGAAGTAATTGCTCAACAGgtaattagtt ... cctgttgcagAATATGTATGCTCAGTTGTTGCCTCTTGCTTTGCCTGCACCGCCAATGCCT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggattgaactttgtaataccgaatactgattgaatataatgttttcctgttgcagAATATGTATGCTCAGTTGTTGCCTCTTGCTTTGCCTGCACCGCCAATGCCTGGAATGGGAGGAGGCTTTGCCCCTCCCCCTCCAATGGGTGGATTGGGGA
                       tactgat  putative branch site (score: 2)
                                         ttttcctgtt  putative PPT
                            attgaatataatgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattagttttggccattttgttccctgctctaataacttagtgaataacttctatctccttatcaaacactcttttaacggattgaactttgtaataccgaatactgattgaatataatgttttcctgttgcagAATATGTATGCTCAGTTGTTGCCTCTTGCTTTGCCTGCACCGCCAATGCCTGGAATGGGAGGAGGCTTTGCCCCTCCCCCTCCAATGGGTGGATTGGGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA