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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctcagcattgcacaagggacacattttttttgtttggtttgtgttgtttaaggatgtaaagttaggcttttttttatttatttattgtttcgcctgacagGGCTGAGAAGTGTGTGATGGCTTCATCTGGCTTTCAAGCTGATGTCAAAGCTTTGCAGAAGGTTTTGTCTGCTAGGCATTTG

Basic information

species Glycine max
transcript GLYMA08G39420.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G39420.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os08g41730.1 (Oryza sativa), 3'ss of exon 1
----ctcagcattgcacaagggacacattttttttgtttggtttgtgttgtttaaggatgtaaagttaggcttttttttatttatttattgtttcgcctgacagGGCTGAGAAGTGTGTGATGGCTTCATCTGGCTTTCAAGCTGATGTCAAAGCTTTGCAGAAGGTTTTGTCTGCTAGGCATTTG
    | |  |   ||    |    |||| ||| |||    | |     | |||     | | ||   ||   |  |    |||   ||    |||   |   || || || || |||||  |||| |||||||| ||||||| |||||| ||||||||||||| |    |  |||| | | | |||
taatcacgacgcagc-tgcgcataacatatttgttggaaagctctctctctttttttttctgaataaagtgctaatgccgtttccctaaaccttcaatt---agAGCGGATAAATGTGTTTTGGCCTCATCTGGATTTCAAGGTGATGTTAAAGCTTTGCAGAGGAACCTTACTGCCAAGGAATTG

upper sequence: GLYMA08G39420.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G124417_T01 (Zea mays), 3'ss of exon 1
ctcagcattgcacaagggacacattttttttgtttggtttgtgttgtttaaggatgtaaagttaggcttttttttatttatttattgtttcgcctg--acagGGCTGAGAAGTGTGTGATGGCTTCATCTGGCTTTCAAGCTGATGTCAAAGCTTTGCAGAAGGTTTTGTCTGCTAGGCATTTG
    |  ||  | |  | ||     || ||| | |  |    |   | ||   || | |  ||     |    | ||   ||   || |||       ||||| | || || |||||  ||||||||||||| ||||||| |||| |||||||||||||||||| | || |||||| | | || 
aattgtcttctaaagtgaacctgccttatttttataataacagaaatgtat--atctgatattgtcactgagctaatgctttctctgcttccttgagaacagGTCAGACAAATGTGTTTTGGCTTCATCTGGGTTTCAAGGTGATATCAAAGCTTTGCAGAAGGCTCTGGCTGCTAAGGAATTA

upper sequence: GLYMA08G39420.1 (Glycine max), 3'ss of exon 2
lower sequence: AT3G60820.1 (Arabidopsis thaliana), 3'ss of exon 2
----ctcagcattgcacaag-ggacacattttttttgtttggtttgtgttgtttaaggatgtaaagttaggcttttttttatttatttattgtttcgcctgacagGGCTGAGAAGTGTGTGATGGCTTCATCTGGCTTTCAAGCTGATGTCAAAGCTTTGCAGAAGGTTTTGTCTGCTAGGCATTTG
     |||    |    ||   || | | || |  |||||  ||  | || | |||   |||||   |    | ||      || | |  | ||     |  ||| || || |    |||  || |||| |||||||| || |||||||| |||||||||||||||||| |     | || || |||
agtattcattcgtatggaaatagatagaattctcgtgttt--ttcatcttatgtaact-tgtaagact--cttgttaagctgttgtcttcttttaacttttccagAGCGGACAGAGCTGTTTTGTCTTCCTCTGGCTTCCAGGCTGATGTGAAAGCTTTGCAGAAGGTTCTCAAATCCAGACACTTG

upper sequence: GLYMA08G39420.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv15s0048g00900.t01 (Vitis vinifera), 3'ss of exon 2
-ctcagcattgcacaagggacacattttttttgtttggtttgtgttgtttaaggatgtaaagttaggcttttttttatttatttattgtttcgcctgacagGGCTGAGAAGTGTGTGATGGCTTCATCTGGCTTTCAAGCTGATGTCAAAGCTTTGCAGAAGGTTTTGTCTGCTAGGCATTTG
  | |    || | || ||| | |  |||||   ||| | |     ||| |   ||   ||   ||  |||| | |  || ||| ||  |   |||  ||| || || || ||||| ||||| |||||||| |||||||||||||| | |||||| ||||||   ||| | |||||||| |||
cattatttatggagaatggaaagaggtttttaaattgttatacaaagttcagttatactaaagcagtgttttatattgttcttt-tttctcaaccttgcagAGCAGACAAATGTGTAATGGCCTCATCTGGATTTCAAGCTGATGTAAGAGCTTTACAGAAGCACTTGGCAGCTAGGCACTTG

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|16280179|gb|BI943833.1|BI943833
EST:     TCCACCGGTTACAACATCCTCACTCGCGATTACTCCAAAATCTCCCAACT                         GGCTGAGAAGTGTGTGATGGCTTCATCTGGCTTTCAAGCTGATGTCAAAGC
genomic: TCCACCGGTTACAACATCCTCACTCGCGATTACTCCAAAATCTCCCAACTgtatgttttt ... cgcctgacagGGCTGAGAAGTGTGTGATGGCTTCATCTGGCTTTCAAGCTGATGTCAAAGC
EST: gi|207799339|gb|GD769178.1|GD769178
EST:     TCCACCGGTTACAACATCCTCACTCGCGATTACTCCAAAATCTCCCAACT                         GGCTGAGAAGTGTGTGATGGCTTCATCTGGCTTTCAAGCTGATGTCAAAGC
genomic: TCCACCGGTTACAACATCCTCACTCGCGATTACTCCAAAATCTCCCAACTgtatgttttt ... cgcctgacagGGCTGAGAAGTGTGTGATGGCTTCATCTGGCTTTCAAGCTGATGTCAAAGC
EST: gi|19345885|gb|BM890765.1|BM890765
EST:     TCCACCGGTTACAACATCCTCACTCGCGATTACTCCAAAATCTCCCAACT                         GGCTGAGAAGTGTGTGATGGCTTCATCTGGCTTTCAAGCTGATGTCAAAGC
genomic: TCCACCGGTTACAACATCCTCACTCGCGATTACTCCAAAATCTCCCAACTgtatgttttt ... cgcctgacagGGCTGAGAAGTGTGTGATGGCTTCATCTGGCTTTCAAGCTGATGTCAAAGC
EST: gi|298165462|gb|HO011511.1|HO011511
EST:     TCCACCGGTTACAACATCCTCACTCGCGATTACTCCAAAATCTCCCAACT                         GGCTGAGAAGTGTGTGATGGCTTCATCTGGCTTTCAAGCTGATGTCAAAGC
genomic: TCCACCGGTTACAACATCCTCACTCGCGATTACTCCAAAATCTCCCAACTgtatgttttt ... cgcctgacagGGCTGAGAAGTGTGTGATGGCTTCATCTGGCTTTCAAGCTGATGTCAAAGC
EST: gi|193614307|gb|FK562279.1|FK562279
EST:     TCCACCGGTTACAACATCCTCACTCGCGATTACTCCAAAATCTCCCAACT                         GGCTGAGAAGTGTGTGATGGCTTCATCTGGCTTTCAAGCTGATGTCAAAGC
genomic: TCCACCGGTTACAACATCCTCACTCGCGATTACTCCAAAATCTCCCAACTgtatgttttt ... cgcctgacagGGCTGAGAAGTGTGTGATGGCTTCATCTGGCTTTCAAGCTGATGTCAAAGC
EST: gi|120534402|gb|EH262535.1|EH262535
EST:     GTTACAACATCCTCACTCGCGATTACTCCAAAATCTCCCAACT                         GGCTGAGAAGTGTGTGATGGCTTCATCTGGCTTTCAAGCTGATGTCAAAGC
genomic: GTTACAACATCCTCACTCGCGATTACTCCAAAATCTCCCAACTgtatgttttt ... cgcctgacagGGCTGAGAAGTGTGTGATGGCTTCATCTGGCTTTCAAGCTGATGTCAAAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttaaggatgtaaagttaggcttttttttatttatttattgtttcgcctgacagGGCTGAGAAGTGTGTGATGGCTTCATCTGGCTTTCAAGCTGATGTCAAAGCTTTGCAGAAGGTTTTGTCTGCTAGGCATTTG
                                          tttcgcct  CT-rich tract
           taaagttaggcttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctcagcattgcacaagggacacattttttttgtttggtttgtgttgtttaaggatgtaaagttaggcttttttttatttatttattgtttcgcctgacagGGCTGAGAAGTGTGTGATGGCTTCATCTGGCTTTCAAGCTGATGTCAAAGCTTTGCAGAAGGTTTTGTCTGCTAGGCATTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - tgcacaa
- - - - - - - - - - - - - - -ttgtttg
- - - - - - - - - - - - - - - - - - gtttgtg