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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgatgaaataatggtgttagttgttagatctccctttggtgttgtgatcttttagctgtagttatcatgctgagttttgggtcttgtgttttttcttcagTAAAGAAGAAACCTTTCTCTTTGCGCGTGTCCCGTTCTCTTCTCCAATCCTCCTCCATCCCCACTGTGTGATCTGATCCTAAACCTTATAGCCATGACTA

Basic information

species Glycine max
transcript GLYMA08G06280.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G06280.1 (Glycine max), 3'ss of exon 1
lower sequence: AT4G21560.2 (Arabidopsis thaliana), 3'ss of exon 2
--------------tgatgaaata-atggtgttagtt---gttagatctccctttggt-gttgtgatcttttagct-gtagttatcatgctgagttttgggtcttgtgttttttcttcagTAAAGAAGAAACCTTTCTCTTTGCGCGTGTCCCGTTCTCTTCTCCAATCCTCCTCCATCCCCACTGTGTGATCTGATCCTAAACCTTATAGCCATGACTA
              |||| |  |  ||     | |||   ||||||| |   | |  |   |||||| | ||| || |    |||     |   | |  | |     | |||||  |   |            ||  |||||||||||||||| |||||||||||||   ||| | ||    |  |||  | || |||  ||    | ||||  |     
ttttctatcttctatgatcacctgcatttctcttgttttggttagatgttaatctccttagtgtgatttattaacttggtactattgattttgatatcagCTAGGAAGCTTTTTGCTTTTTG---------TTTTCGTCTTTGCGCGTGTCCCATTCTCTTCTCCAAAGTTCC-CTATA---ATAGTGAAAGCTCATC--AAGTTATTTAGCTCT-----
















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|208253627|gb|GE054345.1|GE054345
EST:     CAAACCATAAGCAACAACAACGCACCATTCGATAACGTCTTCTGGTTCTT                         TAAAGAAGAAACCTTTCTCTTTGCGCGTGTCCCGTTCTCTTCTCCAATCCT
genomic: CAAACCATAAGCAACAACAACGCACCATTCGATAACGTCTTCTGGTTCTTgtaagtctcc ... ttttcttcagTAAAGAAGAAACCTTTCTCTTTGCGCGTGTCCCGTTCTCTTCTCCAATCCT
EST: gi|151399297|gb|EV269168.1|EV269168
EST:     CAAACCATAAGCAACGACAACGCACCATTCGATAACGTCTTCTGGTTCTT                         TAAAGAAGAAACCTTTCTCTTTGCGCGTGTCCCGTTCTCTTCTCCAATCCT
genomic: CAAACCATAAGCAACAACAACGCACCATTCGATAACGTCTTCTGGTTCTTgtaagtctcc ... ttttcttcagTAAAGAAGAAACCTTTCTCTTTGCGCGTGTCCCGTTCTCTTCTCCAATCCT
EST: gi|298193934|gb|HO040582.1|HO040582
EST:     CAAACCATAAGCAACAACAACGCACCATTCGATAACGTCTTCTGGTTCTT                         TAAAGAAGGAACCTTTCTCTTTGCGCGTGTCCCGTTCTCTTCTCCAATCCT
genomic: CAAACCATAAGCAACAACAACGCACCATTCGATAACGTCTTCTGGTTCTTgtaagtctcc ... ttttcttcagTAAAGAAGAAACCTTTCTCTTTGCGCGTGTCCCGTTCTCTTCTCCAATCCT
EST: gi|11274957|gb|BF325281.1|BF325281
EST:     TTCTGGTTCTT                         TAAAGAAGAAACCTTTCTCTTTGCGCGTGTCCCGTTCTCTTCTCCAATCCT
genomic: TTCTGGTTCTTgtaagtctcc ... ttttcttcagTAAAGAAGAAACCTTTCTCTTTGCGCGTGTCCCGTTCTCTTCTCCAATCCT
EST: gi|9819537|gb|BE555050.1|BE555050
EST:     CGATAACGTCTTCTGGTTCTT                         TAAAGAAGAAACCTTTCTCTTTGCGCGTGTCCCGTTCTCTTCTCCAATCCT
genomic: CGATAACGTCTTCTGGTTCTTgtaagtctcc ... ttttcttcagTAAAGAAGAAACCTTTCTCTTTGCGCGTGTCCCGTTCTCTTCTCCAATCCT
EST: gi|120534210|gb|EH262343.1|EH262343
EST:     TCTTCTGGTTCTT                         TAAAGAAGAAACCTTTCTCTTTGCGCGTGTCCCGTTCTCTTCTCCAATCCT
genomic: TCTTCTGGTTCTTgtaagtctcc ... ttttcttcagTAAAGAAGAAACCTTTCTCTTTGCGCGTGTCCCGTTCTCTTCTCCAATCCT
EST: gi|209700570|gb|BW670314.1|BW670314
EST:     ACCATTCGATAACGTCTTCTGGTTCTT                         TAAAGAAGAAACCTTTCTCTTTGCGCGTGTCCCGTTCTCTTCTCCAATCCT
genomic: ACCATTCGATAACGTCTTCTGGTTCTTgtaagtctcc ... ttttcttcagTAAAGAAGAAACCTTTCTCTTTGCGCGTGTCCCGTTCTCTTCTCCAATCCT
EST: gi|208236648|gb|GE031660.1|GE031660
EST:     CAAACCATAAGCAACAACAACGCACCATTCGATAACGTCTTCTGGTTCTT                         TAAAGAAGAAACCTTTCTCTTTGCGCGTGTCCCGTTCTCTTCTCCAATCCT
genomic: CAAACCATAAGCAACAACAACGCACCATTCGATAACGTCTTCTGGTTCTTgtaagtctcc ... ttttcttcagTAAAGAAGAAACCTTTCTCTTTGCGCGTGTCCCGTTCTCTTCTCCAATCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatcttttagctgtagttatcatgctgagttttgggtcttgtgttttttcttcagTAAAGAAGAAACCTTTCTCTTTGCGCGTGTCCCGTTCTCTTCTCCAATCCTCCTCCATCCCCACTGTGTGATCTGATCCTAAACCTTATAGCCATGACTA
                                    tcttgtgttttttctt  CT-rich tract
                                           ttttttctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgatgaaataatggtgttagttgttagatctccctttggtgttgtgatcttttagctgtagttatcatgctgagttttgggtcttgtgttttttcttcagTAAAGAAGAAACCTTTCTCTTTGCGCGTGTCCCGTTCTCTTCTCCAATCCTCCTCCATCCCCACTGTGTGATCTGATCCTAAACCTTATAGCCATGACTA

- - - - -aatggtg
- - - - - - - - - - - - - - -ctccctt
- - - - - - - - - - - - - - - - - - -ggtgttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - gctgtag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcttgtg