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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcaggtgcatgtaattccaatttgtgggaaggggatgtaaaatcaaaaatcctaccctgaacctatagtgataacataagttttgtaatttgtattacagATGGGATAAACCAATACTACTTGCTTGGGGATTATCAGACAAGTACTTGCCCCAGTCTGTGGCAGAGCAGTTTCAGAAAGGAAATCCAGCACAAATCCAG

Basic information

species Glycine max
transcript GLYMA07G03260.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G03260.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G117531_T04 (Zea mays), 3'ss of exon 9
tcaggtgcatg-taattccaatttgtgggaaggggatgtaaaatcaaaaatcctaccctgaac--ctatagtgataacataagttttgtaatttgtattacagATGGGATAAACCAATACTACTTGCTTGGGGATTATCAGACAAGTACTTGCCCCAGTCTGTGGCAGAGCAGTTTCAGAAAGGAAATCCAGCACAAATCCAG
| || ||| | | | ||| | | | | | | | | || | ||||| || || | | || | |||| ||| ||||| ||||||||||| ||||| |||||| |||| ||||||||||| || | || | || ||| | || || ||| ||||| | | |
-aaagttcattctgaatacaagcaattgatatatactagtcatgtgggcccttggcaacgtattgctgttctgata-caaaaaaatgatcatct-tattgcagTTGGGAAAAACCAATACTGCTTGCATGGGGAATATCTGACAAGTACTTACCGCTCTCGATAGCTGAGGAATTCAAGCAAGCTAATCCTGGCGTTGTAAAA

upper sequence: GLYMA07G03260.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv09s0002g07500.t01 (Vitis vinifera), 3'ss of exon 9
-tcaggtgcatgtaattccaatttgtgggaaggggatgtaaaatcaaaaatcctaccctgaacct-atagtgataacataagttttgtaatttgt-attacagATGGGATAAACCAATACTACTTGCTTGGGGATTATCAGACAAGTACTTGCCCCAGTCTGTGGCAGAGCAGTTTCAGAAAGGAAATCCAGCACAAATCCAG
| || | || | ||| || | | | | || | | | | ||| | || | | | |||| | | ||| |||||||||||||||||| |||| |||||| ||||||||||||| |||| || || |||||||| ||||||| || ||||| || | | || |
tttgtgtattttcaaaattcacctgta--aactattcttcatgctgctgacctcgccttttattttaccatga-attatgaatgaatgactttgggaattcagGTGGGATAAACCAATACTAGTTGCATGGGGAATATCAGACAAGTATCTGCCTCAATCAGTGGCAGAAGAGTTTCAAAAGGGAAACCCTGATTATATAAAA
















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|31312540|gb|CD397743.1|CD397743
EST:     AACTTCAAAGGTACTTTCAGTGAAATATCAGCAGGATTTACAACTGAGAG                         ATGGGATAAACCAATGCTACTTGCTTGGGGATTATCAGACAAGTACTTGCC
genomic: AACTTCAAAGGTACTTTCAGTGAAATATCAGCAGGATTTACAACTGAGAGgtatatttat ... tgtattacagATGGGATAAACCAATACTACTTGCTTGGGGATTATCAGACAAGTACTTGCC
EST: gi|31472542|gb|CD414570.1|CD414570
EST:     AACTTCAAAGGTACTTTCAGTGAAATATCATCAGGATTTACAACTGAGAG                         ATGGGATAAACCAATGCTACTTGCTTGGGGATTATCAGACAAGTACTTGCC
genomic: AACTTCAAAGGTACTTTCAGTGAAATATCAGCAGGATTTACAACTGAGAGgtatatttat ... tgtattacagATGGGATAAACCAATACTACTTGCTTGGGGATTATCAGACAAGTACTTGCC
EST: gi|5510083|gb|AI856467.1|AI856467
EST:     TTACAACTGAGAG                         ATGGGATAAACCAATACTACTTGCTTGGGGATTATCAGACAAGTACTTGCC
genomic: TTACAACTGAGAGgtatatttat ... tgtattacagATGGGATAAACCAATACTACTTGCTTGGGGATTATCAGACAAGTACTTGCC
EST: gi|209727722|gb|BW658459.1|BW658459
EST:     AACTTCAAAGGTACTTTCAGTGAAATATCAGCAGGATTTACAACTGAGAG                         ATGGGATAAACCAATGCTACTTGCTTGGGGATTATCAGACAAGTACTTGCC
genomic: AACTTCAAAGGTACTTTCAGTGAAATATCAGCAGGATTTACAACTGAGAGgtatatttat ... tgtattacagATGGGATAAACCAATACTACTTGCTTGGGGATTATCAGACAAGTACTTGCC
EST: gi|31466823|gb|CD408851.1|CD408851
EST:     AACTTCAAAGGTACTTTCAGTGAAATATCAGCAGGATTTACAACTGAGAG                         ATGGGATAAACCAATGCTACTTGCTTGGGGATTATCAGACAAGTACTTGCC
genomic: AACTTCAAAGGTACTTTCAGTGAAATATCAGCAGGATTTACAACTGAGAGgtatatttat ... tgtattacagATGGGATAAACCAATACTACTTGCTTGGGGATTATCAGACAAGTACTTGCC
EST: gi|16342366|gb|BI967961.1|BI967961
EST:     AACTTCAAAGGTACTTTCAGTGAAATATCAGCAGGATTTACAACTGAGAG                         ATGGGATAAACCAATACTACTTGCTTGGGGATTATCAGACAAGTACTTGCC
genomic: AACTTCAAAGGTACTTTCAGTGAAATATCAGCAGGATTTACAACTGAGAGgtatatttat ... tgtattacagATGGGATAAACCAATACTACTTGCTTGGGGATTATCAGACAAGTACTTGCC
EST: gi|31476274|gb|CD418302.1|CD418302
EST:     AGGATTTACAACTGAGAG                         ATGGGATAAACCAATGCTACTTGCTTGGGGATTATCAGACAAGTACTTGCC
genomic: AGGATTTACAACTGAGAGgtatatttat ... tgtattacagATGGGATAAACCAATACTACTTGCTTGGGGATTATCAGACAAGTACTTGCC
EST: gi|209703109|gb|BW673294.1|BW673294
EST:     AACTTCAAAGGTACTTTCAGTGAAATATCAGCAGGATTTACAACTGAGAG                         ATGGGATAAACCAATGCTACTTGCTTGGGGATTATCAGACAAGTACTTGCC
genomic: AACTTCAAAGGTACTTTCAGTGAAATATCAGCAGGATTTACAACTGAGAGgtatatttat ... tgtattacagATGGGATAAACCAATACTACTTGCTTGGGGATTATCAGACAAGTACTTGCC
EST: gi|5510381|gb|AI856698.1|AI856698
EST:     AACTTCAAAGGTACTTTCAGTGAAATATCAGCAGGATTTACAACTGAGAG                         ATGGGATAAACCAATACTACTTGCTTGGGGATTATCAGACAAGTACTTGCC
genomic: AACTTCAAAGGTACTTTCAGTGAAATATCAGCAGGATTTACAACTGAGAGgtatatttat ... tgtattacagATGGGATAAACCAATACTACTTGCTTGGGGATTATCAGACAAGTACTTGCC
EST: gi|31463415|gb|CD405443.1|CD405443
EST:     AACTTCAAAGGTACTTTCAGTGAAATATCAGCAGGATTTACAACTGAGAG                         ATGGGATAAACCAATGCTACTTGCTTGGGGATTATCAGACAAGTACTTGCC
genomic: AACTTCAAAGGTACTTTCAGTGAAATATCAGCAGGATTTACAACTGAGAGgtatatttat ... tgtattacagATGGGATAAACCAATACTACTTGCTTGGGGATTATCAGACAAGTACTTGCC
EST: gi|31466761|gb|CD408789.1|CD408789
EST:     AACTTCAAAGGTACTTTCAGTGAAATATCAGCAGGATTTACAACTGAGAG                         ATGGGATAAACCAATGCTACTTGCTTGGGGATTATCAGACAAGTACTTGCC
genomic: AACTTCAAAGGTACTTTCAGTGAAATATCAGCAGGATTTACAACTGAGAGgtatatttat ... tgtattacagATGGGATAAACCAATACTACTTGCTTGGGGATTATCAGACAAGTACTTGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaatcctaccctgaacctatagtgataacataagttttgtaatttgtattacagATGGGATAAACCAATACTACTTGCTTGGGGATTATCAGACAAGTACTTGCCCCAGTCTGTGGCAGAGCAGTTTCAGAAAGGAAATCCAGCACAAATCCAG
                       tgataac  putative branch site (score: 2)
 ataacataagttttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcaggtgcatgtaattccaatttgtgggaaggggatgtaaaatcaaaaatcctaccctgaacctatagtgataacataagttttgtaatttgtattacagATGGGATAAACCAATACTACTTGCTTGGGGATTATCAGACAAGTACTTGCCCCAGTCTGTGGCAGAGCAGTTTCAGAAAGGAAATCCAGCACAAATCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - gcatgta
- - - - - - - - - - -ttgtggg
- - - - - - - - - - - - - - - ggggatg