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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtctttatgaattgtgattgttgtttgttattagcaaaaaaaaatttcgttgaacttgggtgttttaattttgacccaaatttaattgtgcctgctacagGAACTTTCACGCTTTCCAATTTGGGTATGTTTGGAGTTGACAGGTTTGATGCCATACTTCCACCAGGCCAG

Basic information

species Glycine max
transcript GLYMA20G24830.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G24830.2 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os08g33440.1 (Oryza sativa), 3'ss of exon 3
gtgtctttatgaattgtgattgttgtttgttattagcaaaaaaaaatttcgttgaacttgggtgttttaattttgacccaaatttaattgtgcctgctacagGAACTTTCACGCTTTCCAATTTGGGTATGTTTGGAGTTGACAGGTTTGATGCCATACTTCCACCAGGCCAG
          | || |    || |||||     | | | |      ||       |  ||    || || ||   |||  ||   ||||| |    || |||| || || || || || || |||||||||||||| ||||| || |||||||| || |||||||| ||||||
----------gtatggaacctgatgtttcagtcttgtagatcgttgttgaaaaacatgtgaaaattgtactt---acctgaag--aattg-gtggtctgcagGGACATTTACACTGTCAAACTTGGGTATGTTTGGTGTTGATAGATTTGATGCAATTCTTCCACCTGGCCAG

upper sequence: GLYMA20G24830.2 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G117786_T01 (Zea mays), 3'ss of exon 3
gtgtctttatgaattgtgattgttgtttgttattagcaaaaaaaaatttcgttgaac-ttgggtgttttaattttgacccaaatttaattgtgcctgctacagGAACTTTCACGCTTTCCAATTTGGGTATGTTTGGAGTTGACAGGTTTGATGCCATACTTCCACCAGGCCAG
  || |  |     || | |  | |  |   || ||   |  |   | || |||||  |    |||    ||  | |||  ||    ||| ||     | |||| ||||| || || ||||| |||||||||||||| || ||  |||||||||| || |||||||| ||||||
--gtatggaactcatgggctcatggcattgcat-agtgtattaggttgtctttgaaaatctcatgtgaacatgcttacctgaa---gattttgttatttgcagGGACTTTTACACTGTCCAACTTGGGTATGTTTGGTGTAGATCGGTTTGATGCAATCCTTCCACCTGGCCAG

upper sequence: GLYMA20G24830.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv01s0011g03380.t01 (Vitis vinifera), 3'ss of exon 3
--------------gtgtctttatgaattgtgattgttgtttgttattag--caaaaaaaaatttcgttgaacttgggtgttttaattttgacccaaatttaattgtgcctgcta------cagGAACTTTCACGCTTTCCAATTTGGGTATGTTTGGAGTTGACAGGTTTGATGCCATACTTCCACCAGGCCAG
               | | | | ||  || |  |   | |  | | || |  ||   ||||  |  ||||  |||   | ||||       | | ||||| | |||| | |   |      |||| || ||||| || ||||||||||| |||||||| || |||||||||||||| || || || || || |||
gttttcattgtttaatttttctgtgtcttctcctctctatacggttttggggcacttaaaatgtgggttgttctttcttcttttggagc-aaacaaaattaagttgtacttctcattcatccagGGACCTTCACTCTGTCCAATTTGGGCATGTTTGGTGTAGACAGGTTTGATGCTATTCTGCCTCCTGGTCAG

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|6069878|gb|AW099474.1|AW099474
EST:     AGTGGAAAAAGCTCGTGCAAAGCAGTTGCAACCTCATGAGTATAATTCAG                         GAACTTTCACGCTTTCCAATTTGNGTATGNTNTG-AGTTGACAGGTT-GAT
genomic: AGTGGAAAAAGCTCGTGCAAAGCAGTTGCAACCTCATGAGTATAATTCAGgtgtctttat ... cctgctacagGAACTTTCACGCTTTCCAATTTGGGTATGTT-TGGAGTTGACAGGTTTGAT
EST: gi|208134819|gb|GD930022.1|GD930022
EST:     AGTGGAAAAAGCTCGTGCAAAGCAGTTGCAACCTCATGAGTATAATTCAG                         GAACCTTCACGCTTTCCAATTTGGGTATGTTTGGAGTTGACAGGTTTGACG
genomic: AGTGGAAAAAGCTCGTGCAAAGCAGTTGCAACCTCATGAGTATAATTCAGgtgtctttat ... cctgctacagGAACTTTCACGCTTTCCAATTTGGGTATGTTTGGAGTTGACAGGTTTGATG
EST: gi|19053677|gb|BM732344.1|BM732344
EST:     AGTGGAAAAAGCTCGTGCAAAGCAGTTGCAACCTCATGAGTATAATTCAG                         GAACTTTCACGCTTTCCAATTTGGGTATGTTTGGAGTTGACAGGTTTGATG
genomic: AGTGGAAAAAGCTCGTGCAAAGCAGTTGCAACCTCATGAGTATAATTCAGgtgtctttat ... cctgctacagGAACTTTCACGCTTTCCAATTTGGGTATGTTTGGAGTTGACAGGTTTGATG
EST: gi|193458208|gb|FK422499.1|FK422499
EST:     AGTGGAAAAAGCTCGTGCAAAGCAGTTGCAACCTCATGAGTATAATTCAG                         GAACTTTCACGCT
genomic: AGTGGAAAAAGCTCGTGCAAAGCAGTTGCAACCTCATGAGTATAATTCAGgtgtctttat ... cctgctacagGAACTTTCACGCT
EST: gi|6134907|gb|AW133300.1|AW133300
EST:     AGTGGAAAAAGCTCGTGCAAAGCAGTTGCAACCTCATGAGTATAATTCAG                         GAACTTTCACGCTTTCCAATTTGGGTATGTNTTGGAGTTGACAGGTTTGAT
genomic: AGTGGAAAAAGCTCGTGCAAAGCAGTTGCAACCTCATGAGTATAATTCAGgtgtctttat ... cctgctacagGAACTTTCACGCTTTCCAATTTGGGTATGT-TTGGAGTTGACAGGTTTGAT
EST: gi|193558726|gb|FK512927.1|FK512927
EST:     AGTGGAAAAAGCTCGTGCAAAGCAGTTGCAACCTCATGAGTATAATTCAG                         GAACTTTCACGCT
genomic: AGTGGAAAAAGCTCGTGCAAAGCAGTTGCAACCTCATGAGTATAATTCAGgtgtctttat ... cctgctacagGAACTTTCACGCT
EST: gi|22525077|gb|BU083888.1|BU083888
EST:     AGTGGAAAAAGCTCGTGCAAAGCAGTTGCAACCTCATGAGTATAATTCAG                         GAACTTTCACGCTTTCCAATTTGGGTATGTTTGGAGTTGACAGGTTTGATG
genomic: AGTGGAAAAAGCTCGTGCAAAGCAGTTGCAACCTCATGAGTATAATTCAGgtgtctttat ... cctgctacagGAACTTTCACGCTTTCCAATTTGGGTATGTTTGGAGTTGACAGGTTTGATG
EST: gi|7478035|gb|AW666112.1|AW666112
EST:     AGTGGAAAAAGCTCGTGCAAAGCAGCTGCAACCTCATGAGTATAATTCAC                         GAACTTTCACGCTTTCCAATTTGGGTATGTTTGGAGTTGACAGGTTTGATG
genomic: AGTGGAAAAAGCTCGTGCAAAGCAGTTGCAACCTCATGAGTATAATTCAGgtgtctttat ... cctgctacagGAACTTTCACGCTTTCCAATTTGGGTATGTTTGGAGTTGACAGGTTTGATG
EST: gi|14011336|gb|BG726189.1|BG726189
EST:     AGTGGAAAAAGCTCGTGCAAAGCAGTTGCAACCTCATGAGTATAATTCAG                         GAACTTTCACGCTTTCCAATTTGGGTATGTTTGGAGTTGACAGGTTTGATG
genomic: AGTGGAAAAAGCTCGTGCAAAGCAGTTGCAACCTCATGAGTATAATTCAGgtgtctttat ... cctgctacagGAACTTTCACGCTTTCCAATTTGGGTATGTTTGGAGTTGACAGGTTTGATG
EST: gi|31464480|gb|CD406508.1|CD406508
EST:     AGTGGAAAAAGCTCGTGCAAAGCAGTTGCAACCTCATGAGTATAATTCAG                         GAACTTTCACGCTTTCCAATTTGGGTATGTTTGGAGTTGACAGGTTTGATG
genomic: AGTGGAAAAAGCTCGTGCAAAGCAGTTGCAACCTCATGAGTATAATTCAGgtgtctttat ... cctgctacagGAACTTTCACGCTTTCCAATTTGGGTATGTTTGGAGTTGACAGGTTTGATG
EST: gi|193489031|gb|FK456728.1|FK456728
EST:     AGTGGAAAAAGCTCGTGCAAAGCAGTTGCAACCTCATGAGTATAATTCAG                         GAACTTTCACGCT
genomic: AGTGGAAAAAGCTCGTGCAAAGCAGTTGCAACCTCATGAGTATAATTCAGgtgtctttat ... cctgctacagGAACTTTCACGCT
EST: gi|208054335|gb|GD854472.1|GD854472
EST:     AAAGCTCGTGCAAAGCAGTTTGCAACCTCATGAGTATAATTCAG                         GAACTTTCACGCTTTCCAATTTGGGTATGTTTGGAGTTGACAGGTTTGATG
genomic: AAAGCTCGTGCAAAGCAG-TTGCAACCTCATGAGTATAATTCAGgtgtctttat ... cctgctacagGAACTTTCACGCTTTCCAATTTGGGTATGTTTGGAGTTGACAGGTTTGATG
EST: gi|31466163|gb|CD408191.1|CD408191
EST:     AGTGGAAAAAGCTCGTGCAAAGCAGTTGCAACCTCATGAGTATAATTCAG                         GAACTTTCACGCTTTCCAATTTGGGTATGTTTGGAGTTGACAGGTTTGATG
genomic: AGTGGAAAAAGCTCGTGCAAAGCAGTTGCAACCTCATGAGTATAATTCAGgtgtctttat ... cctgctacagGAACTTTCACGCTTTCCAATTTGGGTATGTTTGGAGTTGACAGGTTTGATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcgttgaacttgggtgttttaattttgacccaaatttaattgtgcctgctacagGAACTTTCACGCTTTCCAATTTGGGTATGTTTGGAGTTGACAGGTTTGATGCCATACTTCCACCAGGCCAG
               tgttttaattttga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtctttatgaattgtgattgttgtttgttattagcaaaaaaaaatttcgttgaacttgggtgttttaattttgacccaaatttaattgtgcctgctacagGAACTTTCACGCTTTCCAATTTGGGTATGTTTGGAGTTGACAGGTTTGATGCCATACTTCCACCAGGCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG