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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgcagaagagctcatctaacctgtgttccaaatcagcttccattttgtagatttttttaaaatatttcatttttcatcccttgacttgttgcttgtcagGCCGAGAAGGAATTGCAGCCATGGATTGCCAAAGATGACAATCTAGGTCAGAAGTTGTGGAGAATCAATCAGCGGATTGTAAAATTGATAACTGAACTAT

Basic information

species Glycine max
transcript GLYMA09G07240.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G07240.2 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os01g08700.2 (Oryza sativa), 3'ss of exon 13
------------------------------------------------------------------------------------------atgcagaagagctcat-ctaacctgt--gttccaaatcagcttccattttgtagattttt--ttaaaatatttcatttttcatc--ccttgacttgt---tgcttgtcagGCCGAGAAGGAATTGCAGCCATGGATTGCCAAAGATGACAATCTAGGTCAGAAGTTGTGGAGAATCAATCAGCGGATTGTAAAATTGATAACTGAACTAT
                                                                                           || ||      |  | || |  | |  ||| |||| || |  |    ||   ||| |    |  |   ||||| |   |||||  ||  ||||  |   |  ||  |||||||||||||| |||||||| ||||||||   ||||||  | | |||||||||| |||||||| |||| ||||| || || ||  ||||| | || ||  
gtcaagatattgttattgttatatttacatacttgttatcatatttaaaagcttcatattgtatgtacctttgaaaaaaaaagttccatactgtagcttcttttgttctcatttcttggtttcaaagcatcagcatcattaccgatataaaatatacccatttcctcagtcatcttccccgactcttgtatctttcacagGCCGAGAAGGACTTGCAGCCCTGGATTGCTCGAGATGATGAGCAAGGTCAGAAGATGTGGAGAGTCAACCAGCGAATAGTTAAGCTGATAGCAGAGCTTA

upper sequence: GLYMA09G07240.2 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G107101_T03 (Zea mays), 3'ss of exon 13
atgcagaagagctcatctaacctgtgttccaaat-cagcttccattt----tgtagatttttttaaaatatttcatttttcatcccttgacttgttgcttgtcagGCCGAGAAGGAATTGCAGCCATGGATTGCCAAAGATGACAATCTAGGTCAGAAGTTGTGGAGAATCAATCAGCGGATTGTAAAATTGATAACTGAACTAT
       | | ||  |  ||      ||  || | ||    | |  |    | | ||  | |||   |  |   |||| |   | |||   || ||  | | |||||||||||||| |||||||| |||||||| | ||||||| | | |||||||||| |||||||| |||| ||||| || || ||  | ||| |||| ||  
---tctgacatctatttcaaaacacattttaactacaatgcctaggtggaatatggacctgtttccta-gtcatatttcttgacgcttattttttttttcg-cagGCCGAGAAGGACTTGCAGCCTTGGATTGCTAGAGATGACGAACAAGGTCAGAAGATGTGGAGAGTCAACCAGCGTATAGTGAAGCTTATAGCTGAGCTTA

upper sequence: GLYMA09G07240.2 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM5G844173_T01 (Zea mays), 3'ss of exon 12
atgcagaagagctcatctaacctgtgttccaaatcagcttccattttgtagatttttttaaaatat-ttcatttttcatcc-cttgacttgttgcttgtcagGCCGAGAAGGAATTGCAGCCATGGATTGCCAAAGATGACAATCTAGGTCAGAAGTTGTGGAGAATCAATCAGCGGATTGTAAAATTGATAACTGAACTAT
 |      |       |  | || | ||| |||   | ||  | |     |  | | | || ||     | |||   || | | |  || |    ||  |||||||||||||| |||||||| |||||||| | ||| ||| | | ||| |||||| |||||||| |||| || || || || ||  | ||| | || ||  
-tttttttgtttctgacagatctct-ttcgaaacacgttttaactacaatgcctatgtgaatatgcacccgtttcctattcacgtttctagaattttcgcagGCCGAGAAGGACTTGCAGCCTTGGATTGCTAGAGACGACGAACAAGGCCAGAAGATGTGGAGAGTCAACCAACGTATAGTGAAGCTTATAGCGGAGCTCA

upper sequence: GLYMA09G07240.2 (Glycine max), 3'ss of exon 12
lower sequence: Vv18s0157g00020.t01 (Vitis vinifera), 3'ss of exon 13
atgcagaagagctcatctaacctgtgttccaaatcagcttcc-attttgtagatttttttaaa-------atatttcattttt-catcccttgacttgt-tgcttgtcagGCCGAGAAGGAATTGCAGCCATGGATTGCCAAAGATGACAATCTAGGTCAGAAGTTGTGGAGAATCAATCAGCGGATTGTAAAATTGATAACTGAACTAT
        ||  |    |  |  |||| ||||||||||  |  ||||| |||  | ||||||        | ||   ||  |  | |   |||  |||| |||||||||||| |||| |||||||||||| |||||||| ||||||||  |||||||||||||| ||||||||||||| ||  | ||||||||||||||    || ||| 
--------gatgttgcttg-caggtgt-ccaaatcagcaacttattttctagtctattttaagttcaaccacatcatatactcacttttattgcattgtgtgcttgtcagGCTGAGAGGGAATTGCAGCCTTGGATTGCTAAAGATGATGATCTAGGTCAGAAGATGTGGAGAATCAACCAAAGAATTGTAAAATTGATCGTGGAGCTAA

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|17402189|gb|BM178971.1|BM178971
EST:     AGGTTGTATCTGCATCTCCTACGAAAGCAGCTATGGCAGTTGTTCTTCAG                         GCCGAGAAGGAATTGCAGCCATGGATTGCCAAAGATGACAATCTAGGTCAG
genomic: AGGTTGTATCTGCATCTCCTACGAAAGCAGCTATGGCAGTTGTTCTTCAGgtctattttt ... tgcttgtcagGCCGAGAAGGAATTGCAGCCATGGATTGCCAAAGATGACAATCTAGGTCAG
EST: gi|192305785|gb|FG995727.1|FG995727
EST:     AGGTTGTATCTGCATCTCCTACGAAAGCAGCTATGGCAGTTGTTCTTCAG                         GCCGAGAAGGAATTGCAGCCATGGATTACCAAAGATGACAATCTAGGTCAG
genomic: AGGTTGTATCTGCATCTCCTACGAAAGCAGCTATGGCAGTTGTTCTTCAGgtctattttt ... tgcttgtcagGCCGAGAAGGAATTGCAGCCATGGATTGCCAAAGATGACAATCTAGGTCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtagatttttttaaaatatttcatttttcatcccttgacttgttgcttgtcagGCCGAGAAGGAATTGCAGCCATGGATTGCCAAAGATGACAATCTAGGTCAGAAGTTGTGGAGAATCAATCAGCGGATTGTAAAATTGATAACTGAACTAT
                                  ccttgac  putative branch site (score: 4)
      atttttttaaaatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgcagaagagctcatctaacctgtgttccaaatcagcttccattttgtagatttttttaaaatatttcatttttcatcccttgacttgttgcttgtcagGCCGAGAAGGAATTGCAGCCATGGATTGCCAAAGATGACAATCTAGGTCAGAAGTTGTGGAGAATCAATCAGCGGATTGTAAAATTGATAACTGAACTAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - cctgtgt
- - - - - - - - - - - - - - - - - cagcttc