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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agaattgtggaactaattcccacactagttctatttttattttaatttagttctctttggaaatttgattttgtttctcttctatgtttaacacattcagGTTTGCTCGTGTTGGATCAGTTGTTTTAGCACTTCATGATGCTAGCGATGTGTTTCTAGAGATAGGGAAAATGTCCAAATACAGTGGTGCTGAAACAATG

Basic information

species Glycine max
transcript GLYMA16G12080.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G12080.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os02g37080.2 (Oryza sativa), 3'ss of exon 3
------------------------------------------------------------------------------agaatt-gtggaactaattccca-cactagttctatttttattttaatttagttctctttg--gaaatttgat---tttgtttctcttctatgtttaacacattcagGTTTGCTCGTGTTGGATCAGTTGTTTTAGCACTTCATGATGCTAGCGATGTGTTTCTAGAGATAGGGAAAATGTCCAAATACAGTGGTGCTGAAACAATG
                                                                               || || || | ||     |  |  | |   |||    | | |||| || | |  | |||    | | || |    ||| |||||    | | | |     |  |||||||||| | ||||| ||||| || || ||| |||||||||| || |||||||| || ||  ||||||||||| ||||||| ||   |  |||     | 
gtctctttttgtctaacttttaatttttgttgtttcttgaatatgaactttttttaccttgattcaagcattactctatgagttagtagcacagggccttaatattttatcttcactgagtttatttcactcatttttattaacacttaactaatttatttctgaaatttttcttcatgaaccagGTTTGCTAGAGTTGGCTCAGTAGTATTGGCAATTCATGATGCAAGTGATGTGTTCCTGGAAGTAGGGAAAATGGCCAAATATAGCCATTGTGATTTGCTT

upper sequence: GLYMA16G12080.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G016551_T01 (Zea mays), 3'ss of exon 1
-agaattgtggaactaattcccacactagttctatttttattttaatttag-ttctctttggaaatttgattt---tgtttctcttctatgtttaacacattcagGTTTGCTCGTGTTGGATCAGTTGTTTTAGCACTTCATGATGCTAGCGATGTGTTTCTAGAGATAGGGAAAATGTCCAAATACAGTGGTGCTGAAACAATG
     || |   |  || ||| |    ||     ||   ||| |  |  |   |     | | | | |||  |   ||| |   |  | ||  || || |  ||| |||||||||||||| || ||||||||||| ||||||||||| || ||| | || |||||||| ||||| ||| |||| |||||| |    ||     | 
gtattttttaataaaaaatcctaggacagggtgtttgccattcttttgcaaactgatactagcattatgacctaactgtattgttattgtgcctatcaaa--cagATTTGCTCGTGTTGGCTCTGTTGTTTTAGCCCTTCATGATGCAAGTGATATATTCCTAGAGATTGGGAAGATGGCCAAGTACAGTAGCTGCGAGTGGCTA

upper sequence: GLYMA16G12080.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G163426_T01 (Zea mays), 3'ss of exon 3
--agaattgtggaactaattcccacactagttctatttttattttaatttag-ttctctttggaaatttgattt---tgtttctcttctatgtttaacacattcagGTTTGCTCGTGTTGGATCAGTTGTTTTAGCACTTCATGATGCTAGCGATGTGTTTCTAGAGATAGGGAAAATGTCCAAATACAGTGGTGCTGAAACAATG
  |   || |   |  | |||| |    ||    |||   ||| |  |  |   |     | | |   |||  |   ||| |   |  | ||  || || |  ||| || |||||||||||  | ||||||||||| ||||||||||| || ||| | || |||||||| ||||| ||| |||| |||||| |    ||     | 
gtatttttttaataaaatttcctaggagagggtgattgccattcttttgcaaactgatactagcatcatgacctagctgtattgttgttgtgcctatcaaa--cagATTCGCTCGTGTTGGCACTGTTGTTTTAGCCCTTCATGATGCAAGTGATATATTCCTAGAGATTGGGAAGATGGCCAAGTACAGTAGCTGCGAGTGGCTA

upper sequence: GLYMA16G12080.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G13580.2 (Arabidopsis thaliana), 3'ss of exon 3
--agaattgtggaactaattcccacacta-gttctatttttattttaatttagttc-tctttggaaatttgattttgtt-tctcttctatgtttaacacattcagGTTTGCTCGTGTTGGATCAGTTGTTTTAGCACTTCATGATGCTAGCGATGTGTTTCTAGAGATAGGGAAAATGTCCAAATACAGTGGTGCTGAAACAATG
  |   ||        |  ||| |  |||   |  |         | |||   ||  ||        |||||| || || | |||| |    || |    |  || ||  | |||||||| || |||||| | |||||||| |||||||| ||||||||||| ||| | ||||||||||| ||||| ||||| ||||||| ||| 
gtatgcttccatcgtcacatcctattctatactgaaaaacagaactgattccttttgtccacattgttttgatcttcttgtttctttttctctttatcgctgtagCTTCTCCCGTGTTGGTTCTGTTGTTCTGGCACTTCACGATGCTAGTGATGTGTTTCTTGAGGTTGGGAAAATGTCTAAATATAGTGGAGCTGAAAGAATC

upper sequence: GLYMA16G12080.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G25540.1 (Arabidopsis thaliana), 3'ss of exon 4
agaattgtggaactaattcccacactagttctatttttattttaatttagttctctttggaaatttgattttgtttctcttctatgtttaacacattcagGTTTGCTCGTGTTGGATCAGTTGTTTTAGCACTTCATGATGCTAGCGATGTGTTTCTAGAGATAGGGAAAATGTCCAAATACAGTGGTGCTGAAACAATG
                | |  | | ||  |  | || | || |     |            | | |  ||||||||   ||  ||||| |  | ||  || ||  |||||| ||| || ||| || | |||||||||||||| ||||||||||| || || || ||||||||||| |||||  | || || ||||   | 
---------------gtacgtatatta--tacacttgtgttgtggaggaaaggatacactgactcttgttttgttt---ttggatgttgatgatat--agATTAACTCGTGCTGGTTCTGTTATTCTTGCACTTCATGATGCGAGCGATGTGTTCCTTGAAATTGGGAAAATGTCTAAATATTGCGGAGCGGAAAGTCTC

upper sequence: GLYMA16G12080.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv01s0010g01110.t01 (Vitis vinifera), 3'ss of exon 3
agaattgtggaactaattcccacactagttctatttttattttaatttagttctctttggaaatttgattttgtttctcttctatgtttaacacattcagGTTTGCTCGTGTTGGATCAGTTGTTTTAGCACTTCATGATGCTAGCGATGTGTTTCTAGAGATAGGGAAAATGTCCAAATACAGTGGTGCTGAAACAATG
| |||  | | | |   |   | |  |  | |  |   || ||  |||  |||| | |   |  ||  |||| |||||||   || | |  | | | ||| || || |||||||| || ||||||||||| |||||||||||||| ||||| ||||| ||| ||||||| |||||||||||||  ||||||||||| |  
aaaatgtttggatttcatagtaaataatcttttatgcaatatttctttctttctttctttcatcttttttttttttctctctgatttctgtctcttgcagATTCGCCCGTGTTGGTTCTGTTGTTTTAGCTCTTCATGATGCTAGTGATGTCTTTCTGGAGGTAGGGAAGATGTCCAAATACAAAGGTGCTGAAACCACT

upper sequence: GLYMA16G12080.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S13_229V6.1 (Physcomitrella patens), 3'ss of exon 3
agaattgtggaactaattcccacactagttc--tatttttattttaatttagttctctttggaaatttg---attttgtttc--tcttctatgtttaacacattcagGTTTGCTCGTGTTGGATCAGTTGTTTTAGCACTTCATGATGCTAGCGATGTGTTTCTAGAGATAGGGAAAATGTCCAAATACAGTGGTGCTGAAACAATG
    ||| |||| |  |  | | | |  ||        || ||| | || ||  |     ||||||      | |  | ||     | | ||||||        ||| || |||||||||||||| || ||  | ||  | ||||||||||||||||| |||||||| |||||||| ||| | ||||| || |||   || |  || 
----ttgaggaa-tgctgacaaaagtgatttatcgacgttctttcagttgagaaccgcgaggaaatacacaaactgagctttgacgtgccatgtttggttgg--cagATTAGCTCGTGTTGGATCTGTGGTCCTGGCTGTGCATGATGCTAGCGATGTATTTCTAGAAATAGGGAAGATGACAAAATATAGCGGTCTGGAGATCATT

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|5760327|gb|AI965754.1|AI965754
EST:     AGTCATCATGTTGCTACTGTAATTCTTATTGTTCTGTCTTACATTNTTAG                         GTTTGCTCGTCGT-GGATCAGTTGTTNTAGCACTTCATGATGCTAGCGATG
genomic: AGTCATCATGTTGCTACTGTAATTCTTATTGTTCTGTCTTACATTTTTAGgtatcttttt ... acacattcagGTTTGCTCGT-GTTGGATCAGTTGTTTTAGCACTTCATGATGCTAGCGATG
EST: gi|151411962|gb|EV281773.1|EV281773
EST:     AGTCATCATGTTGCTACTGTAATTCTTATTGTTCTGTCTTACATTTTTAG                         GTTTGCTCGTGTTGGATCAGTTGTTTTAGCACTTCATGATGCTAGCGATGT
genomic: AGTCATCATGTTGCTACTGTAATTCTTATTGTTCTGTCTTACATTTTTAGgtatcttttt ... acacattcagGTTTGCTCGTGTTGGATCAGTTGTTTTAGCACTTCATGATGCTAGCGATGT
EST: gi|151408094|gb|EV277902.1|EV277902
EST:     AGTCATCATGTTGCTACTGTAATTCTTATTGTTCTGTCTTACATTTTTAG                         GTTTGCTCGTGTTGGATCAGTTGTTTTAGCACTTCATGATGCTAGCGATGT
genomic: AGTCATCATGTTGCTACTGTAATTCTTATTGTTCTGTCTTACATTTTTAGgtatcttttt ... acacattcagGTTTGCTCGTGTTGGATCAGTTGTTTTAGCACTTCATGATGCTAGCGATGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttagttctctttggaaatttgattttgtttctcttctatgtttaacacattcagGTTTGCTCGTGTTGGATCAGTTGTTTTAGCACTTCATGATGCTAGCGATGTGTTTCTAGAGATAGGGAAAATGTCCAAATACAGTGGTGCTGAAACAATG
                                        gtttaac  putative branch site (score: 3)
               aaatttgattttgttt  TA-rich tract