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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcctgcataactgccatttgatattgcatctggtataaataatcgtaaggttgcatgatctatcctgtttccccaaatattaatttgcatattttgcagATAACAGGGCAATCATGTCCATTATCATTCAAGGGAAGCCCCTATTGGATGGCTCCTGAG

Basic information

species Glycine max
transcript GLYMA09G24970.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G24970.2 (Glycine max), 3'ss of exon 6
lower sequence: Vv16s0050g00770.t01 (Vitis vinifera), 3'ss of exon 6
----ttcctgcataactgccatttgatattgcatctggtataaataatcgtaaggttgcatgatcta-tcctgtttccccaa-atattaatttgcatattttgcagATAACAGGGCAATCATGTCCATTATCATTCAAGGGAAGCCCCTATTGGATGGCTCCTGAG
    ||| ||  || |    || | |   |     ||   |   || || | | ||| |||| |  | ||| | || ||  | |||||   || ||| |  ||||||| || ||||| |||||||| |||||||||||||||||||| || |||||||| ||||||
tagtttcttgtgtatcga--atatcaacctatgcttgacct---tagtcatgatgtt-catgttaaaatccagcttacctgacatatttcattacatgtcatgcagATCACTGGGCAGTCATGTCCTTTATCATTCAAGGGAAGCCCATACTGGATGGCACCTGAG

upper sequence: GLYMA09G24970.2 (Glycine max), 3'ss of exon 6
lower sequence: PP1S8_299V6.1 (Physcomitrella patens), 3'ss of exon 8
----ttcctgcataactgccatttgatattgcatctggtataaataat-cgtaaggttgcatgatctatcctgtttccccaaatattaatttgcatattttgcagATAACAGGGCAATCATGTCCATTATCATTCAAGGGAAGCCCCTATTGGATGGCTCCTGAG
       | |   || | |   ||     | | |  | | | |  ||| | |    ||||| ||    |   | |     |  |  | |  | | |  | |||||||  | |  ||||| | ||     || || ||||||||||| ||||||||||||||||||
ctcaagacggttaaaatacttctttgcgct-ccttggttgttagcaattcatggtattgcaaga---gtagggatcttatacttcctgacatac-tgctctgcagATTTCTGCTCAATCTTTTCTCAAGTCCTTTAAGGGAAGCCCGTATTGGATGGCTCCTGAG

upper sequence: GLYMA09G24970.2 (Glycine max), 3'ss of exon 6
lower sequence: PP1S10_200V6.2 (Physcomitrella patens), 3'ss of exon 8
---ttcctgcataactgccatttgatattgcatctggtataaataatcgtaaggttgcatgatctatcctgtttccccaaatattaatttgcat-attttgcagATAACAGGGCAATCATGTCCATTATCATTCAAGGGAAGCCCCTATTGGATGGCTCCTGAG
   ||  | ||   ||    |||   | |||  ||  | |  ||  || |   |||  | | |      |||| || ||  |||       |||  |  |||||||  | |  ||||| | ||     || |||||||||||||| || |||||||||||||||
gtatttttccagtccttggtttttgaaatgctgct--tttcgattctc-tcttgttagaaggtactctttgtt-cctcatgtatcctgagacattgtgatgcagATTTCTGCTCAATCCTTTCTCCAGTCTTTCAAGGGAAGCCCTTACTGGATGGCTCCTGAG

upper sequence: GLYMA09G24970.2 (Glycine max), 3'ss of exon 6
lower sequence: PP1S387_39V6.1 (Physcomitrella patens), 3'ss of exon 6
-----ttcctgcataactgccatttgatattgcatctggtataaataatcgtaaggttgcatgatctatcctgtttccccaaatattaatttgcatattttgcagATAACAGGGCAATCATGTCCATTATCATTCAAGGGAAGCCCCTATTGGATGGCTCCTGAG
      ||  | |  |  | | || |   |     |||  |  | |   | |   || ||| ||  |||    | || |    |  |     |  |  | |||||||  | |  ||||| | ||     || |||||||||||||| ||||||||||||||||||
gttaagtcacgtaggataggccttcgtgttcctcactgtcagcagt--ccatgctgtcgcaagag-tatgg-atctcacgtgctcctggcacgt-tgctctgcagATTTCTGCTCAATCTTTTCTCCAGTCTTTCAAGGGAAGCCCTTATTGGATGGCTCCTGAG

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|5753494|gb|AI960781.1|AI960781
EST:     TAGATACTAATGGCCGGGTTAAGTTGGCAGACTTTGGCATGGCAAAGCAT                         ATAACAGGGCAATC
genomic: TAGATACTAATGGCCGGGTTAAGTTGGCAGACTTTGGCATGGCAAAGCATgtaagcttgg ... tattttgcagATAACAGGGCAATC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaaggttgcatgatctatcctgtttccccaaatattaatttgcatattttgcagATAACAGGGCAATCATGTCCATTATCATTCAAGGGAAGCCCCTATTGGATGGCTCCTGAG
                                 tattaat  putative branch site (score: 2)
                              aaatattaatttgcat  TA-rich tract