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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcatgcattatatgtttgaatactgataactaaattgcatttcttttcacttttgttgaccctcatgaatcttctgtgctaaaggtgaaactttttatagGTGAAGTTATGGTGTGACTGCCCTTTCTGGCCTGATGATGGCATGTGCCGGTTGCGGGACTGTAGTGTGTGTGAATGCCCTGAAAGCGAGTTCCCCGAAT

Basic information

species Glycine max
transcript GLYMA09G10830.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G10830.2 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os03g52340.1 (Oryza sativa), 3'ss of exon 2
tcatgcattatatgtttgaatactgataactaaattgcatttcttttcacttttg----ttgaccctcatgaatcttctgtgctaaaggtgaaactttttatagGTGAAGTTATGGTGTGACTGCCCTTTCTGGCCTGATGATGGCATGTGCCGGTTGCGGGACTGTAGTGTGTGTGAATGCCCTGAAAGCGAGTTCCCCGAAT
      ||| ||| | | ||   ||   |    ||||||      |      |||    |  || ||||  ||  |||  |  |  |  ||     || | ||||| || || |||||||||||||||||||||||||||||||| ||||| ||| |  |||| |||||||| ||||| ||||| || |  ||||| || ||  
--gactattttatttgttaactttgtgtat--gattgcaccaaaatatgacattgaaaataaacactcaaaaaaattcacttgtttatttgctttcttgtttagGTTAAATTGTGGTGTGACTGCCCTTTCTGGCCTGATGATGGAATGTGTCGGCTTAGGGATTGTAGTGTCTGTGAGTGCCCAGAGAATGAGTTTCCTGAGC

upper sequence: GLYMA09G10830.2 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G521844_T01 (Zea mays), 3'ss of exon 2
--tcatgcattatatgtttgaatactgataactaaattgcatttcttttcacttttgttgaccctcatgaatcttctgtgctaaaggtgaaactttttatagGTGAAGTTATGGTGTGACTGCCCTTTCTGGCCTGATGATGGCATGTGCCGGTTGCGGGACTGTAGTGTGTGTGAATGCCCTGAAAGCGAGTTCCCCGAAT
  | ||||     |  |    | | | | ||  |||      | |  |   |  | | | | |      ||    | |||||     |     ||| || |||| || || ||||||||||||||||| ||||| |||||||| ||||||  | |  | || |||||||| ||||| ||| | || |  |||||||||||| 
tgtgatgccaccaaaatactcacattaaaaataaaaaatttctgcagtggccagtggctcatctgttctaagtcac-gtgctgttccttgtcttttgta-agGTTAAATTGTGGTGTGACTGCCCTTTTTGGCCCGATGATGGAATGTGCAAGCTTAGAGATTGTAGTGTTTGTGAGTGCTCAGAGAATGAGTTCCCCGAAC

upper sequence: GLYMA09G10830.2 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G108115_T01 (Zea mays), 3'ss of exon 2
tcatgcattatatgtttgaatactgataactaaattgcatttcttttcacttttgttgaccctca-tgaatcttctgtgctaaag---gtgaaactttttat------agGTGAAGTTATGGTGTGACTGCCCTTTCTGGCCTGATGATGGCATGTGCCGGTTGCGGGACTGTAGTGTGTGTGAATGCCCTGAAAGCGAGTTCCCCGAAT
          ||| | |||||| |||  || ||| |||   | ||   | |    ||      || ||  || ||||| ||||     |||    |  || |      |||| || || ||||||||||||||||| ||||| |||||||| ||||||  | |  | || |||||||| ||||| || || || |  |||||||| ||| 
---------ctatatgtgaata-tgactaccaaaatgctcatattaaaaataaaatttttaagcaatggttcatctgttctaagtcgtgtgttgttccttgtcttttaagGTTAAATTGTGGTGTGACTGCCCTTTTTGGCCCGATGATGGAATGTGCAAGCTTAGAGATTGTAGTGTTTGTGAGTGTCCGGAGAATGAGTTCCCTGAAC

upper sequence: GLYMA09G10830.2 (Glycine max), 3'ss of exon 2
lower sequence: AT2G38960.3 (Arabidopsis thaliana), 3'ss of exon 2
tcatgcattatatgtttgaatactgataactaaattgcatttcttttcacttttgttgaccctcatgaatcttctgtgctaaaggtgaa-actttttatagGTGAAGTTATGGTGTGACTGCCCTTTCTGGCCTGATGATGGCATGTGCCGGTTGCGGGACTGTAGTGTGTGTGAATGCCCTGAAAGCGAGTTCCCCGAAT
   |   ||  || |||      |||| |  ||| |              | | |  ||   |      | |  |||| ||    ||||  | ||| |||||| ||  | |||||||| ||||| || ||||||||||||||||||||||||||  | ||||| ||||| |||||||| ||||||||||||||||| ||| 
--gttggtt-catatttcttctttgatcatgaaagta-------------tctagaggat--ttggaggtgtgttgtgataggtttgaatgcgtttaatagGTTAAACTGTGGTGTGATTGCCCGTTTTGGCCTGATGATGGCATGTGCCGGTTAAGAGACTGCAGTGTTTGTGAATGTCCTGAAAGCGAGTTCCCTGAAG

upper sequence: GLYMA09G10830.2 (Glycine max), 3'ss of exon 2
lower sequence: Vv10s0003g03950.t01 (Vitis vinifera), 3'ss of exon 2
tcatgcattatatgtttgaatactgataactaaattgcatttcttttcacttttg-ttgaccctcatga-atcttctgtg--ctaaaggtgaaacttttta-tagGTGAAGTTATGGTGTGACTGCCCTTTCTGGCCTGATGATGGCATGTGCCGGTTGCGGGACTGTAGTGTGTGTGAATGCCCTGAAAGCGAGTTCCCCGAAT
        | |||  |   |||||   |   | ||||  |||    | |   |||  |||||   ||   || |||||    ||   | |  |  | | |  ||||  ||||| ||||||||||||||||||||||  |||||||| |||||||  |||||||| || ||||| ||||||||||| ||||  |||||||| ||| 
-----ttgtttattctgttatacttcaattgatattgtgttttcgcttatgcttgactgacctatatcccattttctgaagcctgttgatccatttctatggtagGCTAAGTTGTGGTGTGACTGCCCTTTCTGGCTAGATGATGGTATGTGCCACTTGCGGGATTGCAGTGTTTGTGAATGCCCCGAAAATGAGTTCCCTGAAA

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|192326501|gb|FK018808.1|FK018808
EST:     ACCCCTCCCTCCAGGAGCTCGTGAAGACCCCTTTCTTTCGATATTTTAAG                         GTGAAGTTATGGTGTGACTGCCCTTTCTGGCCTGATGATGGCATGTGCCGG
genomic: ACCCCTCCCTCCAGGAGCTCGTGAAGACCCCTTTCTTTCGATATTTTAAGgtttgcttat ... ctttttatagGTGAAGTTATGGTGTGACTGCCCTTTCTGGCCTGATGATGGCATGTGCCGG
EST: gi|254313612|gb|GR831241.1|GR831241
EST:     ACCCCTCCCTCCAGGAGCTCGTGAAGACCCCTTTCTTTCGATATTTTAAG                         GTGAAGTTATGGTGTGACTGCCCTTTCTGGCCTGATGATGGCATGTGCCGG
genomic: ACCCCTCCCTCCAGGAGCTCGTGAAGACCCCTTTCTTTCGATATTTTAAGgtttgcttat ... ctttttatagGTGAAGTTATGGTGTGACTGCCCTTTCTGGCCTGATGATGGCATGTGCCGG
EST: gi|209704078|gb|BW673678.1|BW673678
EST:     ACCCCTCCCTCCAGGAGCTCGTGAAGACCCCTTTCTTTCGATATTTTAAG                         GTGAAGTTATGGTGTGACTGCCCTTTCTGGCCTGATGATGGCATGTGCCGG
genomic: ACCCCTCCCTCCAGGAGCTCGTGAAGACCCCTTTCTTTCGATATTTTAAGgtttgcttat ... ctttttatagGTGAAGTTATGGTGTGACTGCCCTTTCTGGCCTGATGATGGCATGTGCCGG
EST: gi|209720049|gb|BW659448.1|BW659448
EST:     ACCCCTCCCTCCAGGAGCTCGTGAAGACCCCTTTCTTTCGATATTTTAAG                         GTGAAGTTATGGTGTGACTGCCCTTTCTGGCCTGATGATGGCATGTGCCGG
genomic: ACCCCTCCCTCCAGGAGCTCGTGAAGACCCCTTTCTTTCGATATTTTAAGgtttgcttat ... ctttttatagGTGAAGTTATGGTGTGACTGCCCTTTCTGGCCTGATGATGGCATGTGCCGG
EST: gi|17519016|gb|BM188058.1|BM188058
EST:     ACCCCTCCCTCCAGGAGCTCGTGAAGACCCCTTTCTTTCGATATTTTAAG                         GTGAAGTTATGGTGTGACTGCCCTTTCTGGCCTGATGATGGCATGTGCCGG
genomic: ACCCCTCCCTCCAGGAGCTCGTGAAGACCCCTTTCTTTCGATATTTTAAGgtttgcttat ... ctttttatagGTGAAGTTATGGTGTGACTGCCCTTTCTGGCCTGATGATGGCATGTGCCGG
EST: gi|213596204|gb|DB960164.1|DB960164
EST:     ACCCCTCCCTCCAGGAGCTCGTGAAGACCCCTTTCTTTCGATATTTTAAG                         GTGAAGTTATGGTGTGACTGCCCTTTCTGGCCTGATGATGGCATGTGCCGG
genomic: ACCCCTCCCTCCAGGAGCTCGTGAAGACCCCTTTCTTTCGATATTTTAAGgtttgcttat ... ctttttatagGTGAAGTTATGGTGTGACTGCCCTTTCTGGCCTGATGATGGCATGTGCCGG
EST: gi|254329295|gb|GR833667.1|GR833667
EST:     ACCCCTCCCTCCAGGAGCTCGTGAAGACCCCTTTCTTTCGATATTTTAAG                         GTGAAGTTATGGTGTGACTGCCCTTTCTGGCCTGATGATGGCA
genomic: ACCCCTCCCTCCAGGAGCTCGTGAAGACCCCTTTCTTTCGATATTTTAAGgtttgcttat ... ctttttatagGTGAAGTTATGGTGTGACTGCCCTTTCTGGCCTGATGATGGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcacttttgttgaccctcatgaatcttctgtgctaaaggtgaaactttttatagGTGAAGTTATGGTGTGACTGCCCTTTCTGGCCTGATGATGGCATGTGCCGGTTGCGGGACTGTAGTGTGTGTGAATGCCCTGAAAGCGAGTTCCCCGAAT
                               tgctaaa  putative branch site (score: 2)
                                             ctttttat  putative PPT
                                        tgaaactttttata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcatgcattatatgtttgaatactgataactaaattgcatttcttttcacttttgttgaccctcatgaatcttctgtgctaaaggtgaaactttttatagGTGAAGTTATGGTGTGACTGCCCTTTCTGGCCTGATGATGGCATGTGCCGGTTGCGGGACTGTAGTGTGTGTGAATGCCCTGAAAGCGAGTTCCCCGAAT

tcatgca
- - - - - -atgtttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - accctca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tctgtgc