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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttttgctatttctttcctcatcataaaaaaggccaagaagaatctaaatgctagttgggtgttaaatgcgataatgtagaatatgcttctatgttgtagGATCCAAGAAGTAAGGATATTGAGGATGTCTTGATTCTTTCCGGGGATCACCTCTACCGAATGGACTATATGGACTTTGTTCAA

Basic information

species Glycine max
transcript GLYMA07G38820.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G38820.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os03g52460.1 (Oryza sativa), 3'ss of exon 4
-cttttgctatttctttcctcatcataaaaaaggccaagaagaatctaaatgctagttgggtgttaaatgcgataatg-tagaatatgcttctatgttgtagGATCCAAGAAGTAAGGATATTGAGGATGTCTTGATTCTTTCCGGGGATCACCTCTACCGAATGGACTATATGGACTTTGTTCAA
   ||| | |||   | |||  | ||   |  |  | |    | |  |||  ||  |   |      |    ||  |  |  |   ||||    | ||||||||| | | |  ||| || || || |||||  |||||||||| || ||||| |||||||| |||||||| |||||||||||||| 
aacttttcaatta--tcccttgttatttgatcgtactattctactgaaaaacctcatcatgctccttacataattttaatgcatcgtgctatcgttttgtagGATGCCAAAGCTAAAGACATCGATGATGTGCTGATTCTTTCTGGTGATCATCTCTACCGCATGGACTACATGGACTTTGTTCAG

upper sequence: GLYMA07G38820.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G391936_T02 (Zea mays), 3'ss of exon 4
-cttttgctatttct--ttcctcatcataaaaaaggccaagaagaatctaaatgctagttgggtgttaaatgcgataatgtagaatatgcttctatgttgtagGATCCAAGAAGTAAGGATATTGAGGATGTCTTGATTCTTTCCGGGGATCACCTCTACCGAATGGACTATATGGACTTTGTTCAA
      |  | | |   ||||  ||      |      || |  | | ||| | | |    | ||||   ||    ||| |  ||||   |  | | ||||||||| ||| |  ||| || ||||| |||||  |||||||||| || || || |||||||| |||||||| |||||||||||||| 
ttcaaagggactgccagttccctattgctttactttgtaatattattataa-taccacaaagctgttccttgaagaaat-tgtaataca-taatgttttgtagGATGCAAAATCTAAAGACATTGAAGATGTGCTGATTCTTTCTGGTGACCATCTCTACCGTATGGACTACATGGACTTTGTTCAG

upper sequence: GLYMA07G38820.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G19220.1 (Arabidopsis thaliana), 3'ss of exon 4
cttttgctatttctttcctcatcataaaaaaggccaagaagaatctaaatgctagttgggtgttaaatgcgataatgtagaatatgcttctatgttgtagGATCCAAGAAGTAAGGATATTGAGGATGTCTTGATTCTTTCCGGGGATCACCTCTACCGAATGGACTATATGGACTTTGTTCAA
                            | |   ||     || |||  |  |  |      | ||  |  |    ||  || || ||| |      |||||| ||||||| ||||| || |||||||| ||||| ||||| || |||||||||||| | ||||| || ||||| ||| | || 
--------------------------gtagaaatcagacttaaactagcttatcatc--acatcaatagacaagcggtccaacattctttt----catagGATGCAAGAAGCAAGGACATAGAGGATGTATTGATCCTTTCTGGAGATCACCTCTACAGGATGGATTACATGGATTTTATACAG

upper sequence: GLYMA07G38820.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv05s0020g02880.t01 (Vitis vinifera), 3'ss of exon 4
cttttgctatttctttcctcatcataaaaaaggccaagaagaatctaaatgctagttgggtgttaaatgcgataatgtagaatatgcttctatgttgtagGATCCAAGAAGTAAGGATATTGAGGATGTCTTGATTCTTTCCGGGGATCACCTCTACCGAATGGACTATATGGACTTTGTTCAA
       ||    | |     |  ||   | |     |  | | | ||    |||  || | | |||      |  ||   | |   ||  ||  | ||||||| |||||||||||| |||||||||||  ||||||| || || |||||  | ||||||||||||||||||||||||||||| 
------gtacccatatttcacttctagttaggattctggggtaaccaa----tagacgg-tatcaaaccaagaagggtgttaaagcttttcatcctatagGATCAAAGAAGTAAGGAAATTGAGGATGTGCTGATTCTGTCTGGAGATCATTTATACCGAATGGACTATATGGACTTTGTTCAG

upper sequence: GLYMA07G38820.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ23417 (Selaginella moellendorffii), 3'ss of exon 5
cttttgctatttctttcctcatcataaaaaaggccaagaagaatctaaatgctagttgggtgttaaatgcgataatgtagaatatgcttctatgttgta-gGATCCAAGAAGTAAGGATATTGAGGATGTCTTGATTCTTTCCGGGGATCACCTCTACCGAATGGACTATATGGACTTTGTTCAA
                                             | |    |     ||||||     || ||   |    | |  || | | |   | ||||   ||||  |||||  | ||  | ||  |  |||| ||||| |||||||||||||| |||||||| ||||||||||| || 
--------------------------------------gtactctttaccatttccaaggtgttgggctcg-tatgctgaggtttcgttttgtatgacaagGATGTGAGAAACAAGGACGTCGACTACGTGCTTGTTCTCTCCGGTGATCACCTCTACCGCATGGACTACATGGACTTTGTCCAG

upper sequence: GLYMA07G38820.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ25399 (Selaginella moellendorffii), 3'ss of exon 4
cttttgctatttctttcctcatcataaaaaaggccaagaagaatctaaatgctagttgggtgttaaatgcg-ataatgtagaatatgcttctatgttgtagGATCCAAGAAGTAAGGATATTGAGGATGTCTTGATTCTTTCCGGGGATCACCTCTACCGAATGGACTATATGGACTTTGTTCAA
                                         | ||| |    |     ||||||  |  || ||  ||  |  |    || ||||    |||||   ||||  |||||  | ||  | ||  |  |||| ||||| |||||||||||||| |||||||| ||||||||||| || 
---------------------------------------gtactcttaccatttccaaggtgttggactcgcatgctgaggtttcgttttgtatgaca-agGATGTGAGAAACAAGGACGTCGACTACGTGCTTGTTCTCTCCGGTGATCACCTCTACCGCATGGACTACATGGACTTTGTCCAG

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|151404121|gb|EV273931.1|EV273931
EST:     GGTTTCAAGGTACTGCTGATGCTGTGAGGCAGTTCCACTGGCTCTTTGAG                         GATCCAAGAAGTAAGGATATTGAGGATGTCTTGATTCTTTCCGGGGATCAC
genomic: GGTTTCAAGGTACTGCTGATGCTGTGAGGCAGTTCCACTGGCTCTTTGAGgtattaagtt ... tatgttgtagGATCCAAGAAGTAAGGATATTGAGGATGTCTTGATTCTTTCCGGGGATCAC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaatgctagttgggtgttaaatgcgataatgtagaatatgcttctatgttgtagGATCCAAGAAGTAAGGATATTGAGGATGTCTTGATTCTTTCCGGGGATCACCTCTACCGAATGGACTATATGGACTTTGTTCAA
 atctaaa  putative branch site (score: 3)
                                       tgcttct  putative PPT
                          ataatgtagaatat  TA-rich tract