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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtcatatcctggtcgtggagatgtgatgaatacatagtttcttattgtttccttacctgaagaatactgttacatttgcactttctggattgttcaatagGCTCTTTATGAAGCACTAATGAGGCAAGAAGAGCTGCTTGCTTACATTGATAGTCAAGAAAAAGCTAGGTTACGG

Basic information

species Glycine max
transcript GLYMA11G12260.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G12260.1 (Glycine max), 3'ss of exon 12
lower sequence: AT4G39170.2 (Arabidopsis thaliana), 3'ss of exon 7
gtcatatcctggtcgtggagat-gtgatgaatacatagtttcttattgtttccttacctgaagaatactgttacatttgcactttctggattgttcaa--tagGCTCTTTATGAAGCACTAATGAGGCAAGAAGAGCTGCTTGCTTACATTGATAGTCAAGAAAAAGCTAGGTTACGG
          |    || | |   || | || |  |     |        |    ||||||    |         | |  |   | |   || ||  |   |||||||||||||||| || ||||| ||||||||  | || |||||||||||  |||||||   ||||  |   | |
----------gtaactgaataccatgttcaacaattgaaacccaccaaaattagaacctgagacgtttcacgttctctaaaaactgtttgttatttgaagcagGCTCTTTATGAAGCTCTGATGAGACAAGAAGAATTACTCGCTTACATTGACCGTCAAGAGGCAGCTCAGCACCAG
















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|15288281|gb|BI472180.1|BI472180
EST:     CTGTATGTCGGGTGGATGCTTTGGAAGCAGAGCTAATTGCAACTAAAAAG                         GCTCTTTATGAAGCACTAATGAGGCAAGAAGAGCTGCTTGCTTACATTGAT
genomic: CTGTATGTCGGGTGGATGCTTTGGAAGCAGAGCTAATTGCAACTAAAAAGgtaggatgct ... tgttcaatagGCTCTTTATGAAGCACTAATGAGGCAAGAAGAGCTGCTTGCTTACATTGAT
EST: gi|209719530|gb|BW651008.1|BW651008
EST:     CTGTATGTCGGGTGGATGCTTTGGAAGCAGAGCTAATTGCAACTAAAAAG                         GCTCTTTATGAAGCACTAATGAGGCAAGAAGAGCTGCTTGCTTACATTGAT
genomic: CTGTATGTCGGGTGGATGCTTTGGAAGCAGAGCTAATTGCAACTAAAAAGgtaggatgct ... tgttcaatagGCTCTTTATGAAGCACTAATGAGGCAAGAAGAGCTGCTTGCTTACATTGAT
EST: gi|209713243|gb|BW681782.1|BW681782
EST:     CTGTATGTCGGGTGGATGCTTTGGAAGCAGAGCTAATTGCAACTAAAAAG                         GCTCTTTATGAAGCACTAATGAGGCAAGAAGAGCTGCTTGCTTACATTGAT
genomic: CTGTATGTCGGGTGGATGCTTTGGAAGCAGAGCTAATTGCAACTAAAAAGgtaggatgct ... tgttcaatagGCTCTTTATGAAGCACTAATGAGGCAAGAAGAGCTGCTTGCTTACATTGAT
EST: gi|214004554|gb|DB985333.1|DB985333
EST:     CTGTATGTCGGGTGGATGCTTTGGAAGCAGAGCTAATTGCAACTAAAAAG                         GCTCTTTATGAAGCACTAATGAGGCAAGAAGAGCTGCTTGCTTACATTGAT
genomic: CTGTATGTCGGGTGGATGCTTTGGAAGCAGAGCTAATTGCAACTAAAAAGgtaggatgct ... tgttcaatagGCTCTTTATGAAGCACTAATGAGGCAAGAAGAGCTGCTTGCTTACATTGAT
EST: gi|58015266|gb|CX702008.1|CX702008
EST:     CTGTATGTCGGGTGGATGCTTTGGAAGCAGAGCTAATTGCAACTAAAAAG                         GCTCTTTATGAAGCACTAATGAGGCAAGAAGAGCTGCTTGCTTACATTGAT
genomic: CTGTATGTCGGGTGGATGCTTTGGAAGCAGAGCTAATTGCAACTAAAAAGgtaggatgct ... tgttcaatagGCTCTTTATGAAGCACTAATGAGGCAAGAAGAGCTGCTTGCTTACATTGAT
EST: gi|58019538|gb|CX706280.1|CX706280
EST:     CTGTATGTCGGGTGGATGCTTTGGAAGCAGAGCTAATTGCAACTAAAAAG                         GCTCTTTATGAAGCACTAATGAGGCAAGAAGAGCTGCTTGCTTACATTGAT
genomic: CTGTATGTCGGGTGGATGCTTTGGAAGCAGAGCTAATTGCAACTAAAAAGgtaggatgct ... tgttcaatagGCTCTTTATGAAGCACTAATGAGGCAAGAAGAGCTGCTTGCTTACATTGAT
EST: gi|208125799|gb|GD925939.1|GD925939
EST:     CTGTATGTCGGGTGGATGCTTTGGAAGCAGAGCTAATTGCAACTAAAAAG                         GCTCTTTATGAAGCACTAATGAGGCAAGAAGAGCTGCTTGCTTACATTGAT
genomic: CTGTATGTCGGGTGGATGCTTTGGAAGCAGAGCTAATTGCAACTAAAAAGgtaggatgct ... tgttcaatagGCTCTTTATGAAGCACTAATGAGGCAAGAAGAGCTGCTTGCTTACATTGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtttccttacctgaagaatactgttacatttgcactttctggattgttcaatagGCTCTTTATGAAGCACTAATGAGGCAAGAAGAGCTGCTTGCTTACATTGATAGTCAAGAAAAAGCTAGGTTACGG
    tccttac  putative branch site (score: 2)
                        ttacattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcatatcctggtcgtggagatgtgatgaatacatagtttcttattgtttccttacctgaagaatactgttacatttgcactttctggattgttcaatagGCTCTTTATGAAGCACTAATGAGGCAAGAAGAGCTGCTTGCTTACATTGATAGTCAAGAAAAAGCTAGGTTACGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - ggtcgtg
- - - - - - - - - - -tgtgatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - acctgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgttac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcactt