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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtggcttctaagtttgaaactagaaaatttactatgtcatattgttatttgtgtttaggtatcacttccttttaacattgtttattattactttctatgcttttagGTCACTGGCAAGGCAGTAATGCTAGATGAAATCATCAACTATGTACAGTCACTTCAACGACAGGTTGAG

Basic information

species Glycine max
transcript GLYMA02G13860.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G13860.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G137541_T01 (Zea mays), 3'ss of exon 3
gtggcttctaagtttgaaactagaaaatttactatgtcatattgttatttgtgtttaggtatcacttccttttaacattgtttattattactttctatgctt-----ttagGTCACTGGCAAGGCAGTAATGCTAGATGAAATCATCAACTATGTACAGTCACTTCAACGACAGGTTGAG
|| | |    |  |||  |  | ||||   | ||   | |  |  | |  ||| ||   | ||| | |   ||| || |    || |  || ||| |  |||       |||||||||||||||| || ||||| || || ||||||||||| || ||||| || ||| |||| ||||||
gtaggtct--atcttgccaaaaaaaaaaggaatagaacttgct--tgtgagtgctttatt-tcattgctgattatcagtacaaatgaacaccttcgacccttgaaatccagGTCACTGGCAAGGCGGTGATGCTTGACGAGATCATCAACTACGTTCAGTCCCTGCAAAGACAAGTTGAG

upper sequence: GLYMA02G13860.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G26260.1 (Arabidopsis thaliana), 3'ss of exon 3
gtggcttctaagtttgaaactagaaaatttactatgtcatattgttatttgtgtttaggtatcacttccttttaacattgtttat-tattactttctatgcttttagGTCACTGGCAAGGCAGTAATGCTAGATGAAATCATCAACTATGTACAGTCACTTCAACGACAGGTTGAG
||   | ||    ||     |   |  || |      ||| | |     ||      |       || ||||| | ||   |     ||| | ||   ||  | ||||| ||||| |||||||| ||||| ||||||||||| |||||||| || ||||||||| | ||  | |||
gtaagtccttttctt----tttagatgttgatgtctacatgtagaagaatggaagctgaagctgttttcttttcatataaatgggacattgcatttattg--tgtagGTGACTGGTAAGGCAGTTATGCTCGATGAAATCATTAACTATGTGCAATCACTTCAATGCCAAATCGAG

upper sequence: GLYMA02G13860.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv01s0010g00740.t01 (Vitis vinifera), 3'ss of exon 4
-gtggcttct--aagtttgaaactagaaaat--ttactatgtcatattgttatttgtgtttaggtatcacttccttttaacattgtttattattactttctatgcttttagGTCACTGGCAAGGCAGTAATGCTAGATGAAATCATCAACTATGTACAGTCACTTCAACGACAGGTTGAG
  ||| || |   | ||   |||| |   |   | | ||  |   ||| |  | ||   || | | |  ||||| |    ||||   |   | |    |  ||  || ||||||||||||||||| || ||||||||||||||||| |||||||| || ||||||||||| |||||||||
gttggtttgttggaattaataacttggggaccataattagattgaattatc-tatggaattcgatgttgcttccgtggctcattccatgggaat-tgcttgatttttgtagGTCACTGGCAAGGCGGTCATGCTAGATGAAATCATTAACTATGTGCAATCACTTCAACGGCAGGTTGAG

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|193469602|gb|FK435962.1|FK435962
EST:     TAAGTGAGAGGATGAAGTTTCTTCAAGACCTTGTACCTGGATGCAGCAAG                         GTCACTGGCAAGGCAGTAATGCTAGATGAAATCATCAACTATGTACAGTCA
genomic: TAAGTGAGAGGATGAAGTTTCTTCAAGACCTTGTACCTGGATGCAGCAAGgtggcttcta ... atgcttttagGTCACTGGCAAGGCAGTAATGCTAGATGAAATCATCAACTATGTACAGTCA
EST: gi|208266542|gb|GE062805.1|GE062805
EST:     TAAGTGAGAGGATGAAGTTTCTTCAAGACCTTGTACCTGGATGCAGCAAG                         GTCACTGGCAAGGCAGTAATGCTAGATGAAATCATCAACTATGTACAGTCA
genomic: TAAGTGAGAGGATGAAGTTTCTTCAAGACCTTGTACCTGGATGCAGCAAGgtggcttcta ... atgcttttagGTCACTGGCAAGGCAGTAATGCTAGATGAAATCATCAACTATGTACAGTCA
EST: gi|208316755|gb|GE115383.1|GE115383
EST:     TAAGTGAGAGGATGAAGTTTCTTCAAGACCTTGTACCTGGATGCAGCAAG                         GTCACTGGCAAGGCAGTAATGCTAGATGAAATCATCAACTATGTACAGTCA
genomic: TAAGTGAGAGGATGAAGTTTCTTCAAGACCTTGTACCTGGATGCAGCAAGgtggcttcta ... atgcttttagGTCACTGGCAAGGCAGTAATGCTAGATGAAATCATCAACTATGTACAGTCA
EST: gi|193448449|gb|FK412404.1|FK412404
EST:     TAAGTGAGAGGATGAAGTTTCTTCAAGACCTTGTACCTGGATGCAGCAAG                         GTCACTGGCAAGGCAGTAATGCTAGATGAAA
genomic: TAAGTGAGAGGATGAAGTTTCTTCAAGACCTTGTACCTGGATGCAGCAAGgtggcttcta ... atgcttttagGTCACTGGCAAGGCAGTAATGCTAGATGAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtttaggtatcacttccttttaacattgtttattattactttctatgcttttagGTCACTGGCAAGGCAGTAATGCTAGATGAAATCATCAACTATGTACAGTCACTTCAACGACAGGTTGAG
                  ttttaac  putative branch site (score: 2)
                                       ctttctatgctttt  putative PPT
                  ttttaacattgtttat  TA-rich tract