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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaccctggttattatataaatcatgaaaagtctgtacatgttgcatttatgtgaatgctttgtccatagttttgtttacaaatgtgcaatttctttgtagGTAAATTCAAGCCCGTGATCAAGAAAGCAATGGTGGAGCTTGAAG

Basic information

species Glycine max
transcript GLYMA09G01050.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G01050.1 (Glycine max), 3'ss of exon 13
lower sequence: AT1G12000.1 (Arabidopsis thaliana), 3'ss of exon 13
aaccctggttattatataaatcatgaaaagtctgtacatgttgcatttatgtgaatgctttgtccatagttttgtttacaaatgtgcaatttc--tttgtagGTAAATTCAAGCCCGTGATCAAGAAAGCAATGGTGGAGCTTGAAG
             ||||||||||   ||||  |    | |   |||||   ||||       || | |  ||     |  |  ||   |||||   ||| |||||| |||||||| ||||||||||||||||||||||| |||||||
-----gtacagaaatataaatca-ataaagcttac-taagacacattt---tgaa------atctagatattaaaaaatcagagt-tgatttcaacttgcagGTAAGTTCAAGCCTGTGATCAAGAAAGCAATGGTGGAACTTGAAG

upper sequence: GLYMA09G01050.1 (Glycine max), 3'ss of exon 13
lower sequence: AT4G04040.1 (Arabidopsis thaliana), 3'ss of exon 13
aaccctggttattatataaatcatgaaaagtctgtacatgttgcatttatgtgaatgctttgtccatagttttgtttacaaatgtgcaatttctttgtagGTAAATTCAAGCCCGTGATCAAGAAAGCAATGGTGGAGCTTGAAG
           | |||||| ||   |  |   || |  ||||  ||     |  || ||||  | | | | |  |||    ||||          || ||||||||||||||| || ||||||||||| ||||| || |||||||
----------gtaatataagtcgatactatcgtgaa-gtgtttgataagattatattcttttccaacattctcttttttttatgt----------tgcagGTAAATTCAAGCCTGTTATCAAGAAAGCTATGGTTGAACTTGAAG

upper sequence: GLYMA09G01050.1 (Glycine max), 3'ss of exon 13
lower sequence: Vv10s0116g00360.t01 (Vitis vinifera), 3'ss of exon 13
aaccctggttattatataaatcatgaaaagtctgtacatgttgcatttatgtgaatgctttgtccatagttttgtttacaaatgtgcaatttctttgtagGTAAATTCAAGCCCGTGATCAAGAAAGCAATGGTGGAGCTTGAAG
| |  |  | |         ||||   |  ||      |     |||||    |     |   |  |   |   |||   |||    ||  |  ||| |||||| |||||||| ||||||||||| |||||||| || ||||| |
agcatttatcaggggggttctcatctcagttcatcgtttccattatttagtacatcagctaacctttccatccctttctgaattctaaaactgcttgcagGTAAGTTCAAGCCTGTGATCAAGAAGGCAATGGTTGAACTTGATG

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|4313688|gb|AI460807.1|AI460807
EST:     TGTTGGTGGAACTGCACTCACCTCAATGATGGATGTGGAGAGGAGGCATG                         GTAAATTCAAGCCCGTGATCAAGAAAGCAATGGTGGAGCTTGAAG
genomic: TGTTGGTGGAACTGCACTCACCTCAATGATGGATGTGGAGAGGAGGCATGgtacacactt ... ttctttgtagGTAAATTCAAGCCCGTGATCAAGAAAGCAATGGTGGAGCTTGAAG
EST: gi|213598262|gb|DB979705.1|DB979705
EST:     TGTACAAGGAACTGCACTCACCTCAATGATGGATGTGGAGAGGAGGCATG                         GTAAATTCAAGCCCGTGATCAAGAAAGCAATGGTGGAGCTTGAAG
genomic: TGTTGGTGGAACTGCACTCACCTCAATGATGGATGTGGAGAGGAGGCATGgtacacactt ... ttctttgtagGTAAATTCAAGCCCGTGATCAAGAAAGCAATGGTGGAGCTTGAAG
EST: gi|15813400|gb|BI785675.1|BI785675
EST:     TGTTGGTGGAACTGCACTCACCTCAATGATGGATGTGGAGAGGAGGCATG                         GTAAATTCAAGCCCGTGATCAAGAAAGCAATGGTGGAGCTTGAAG
genomic: TGTTGGTGGAACTGCACTCACCTCAATGATGGATGTGGAGAGGAGGCATGgtacacactt ... ttctttgtagGTAAATTCAAGCCCGTGATCAAGAAAGCAATGGTGGAGCTTGAAG
EST: gi|7284788|gb|AW597213.1|AW597213
EST:     TGTTGGTGGAACTGCACTCACCTCAATGATGGATGTGGAGAGGAGGCATG                         GTAAATTCAAGCCCGTGATCAAGAAAGCAATGGTGGAGCTTGAAG
genomic: TGTTGGTGGAACTGCACTCACCTCAATGATGGATGTGGAGAGGAGGCATGgtacacactt ... ttctttgtagGTAAATTCAAGCCCGTGATCAAGAAAGCAATGGTGGAGCTTGAAG
EST: gi|4313349|gb|AI460468.1|AI460468
EST:     TGTTGGTGGAACTGCACTCACCTCAATGATGGATGTGGAGAGGAGGCATG                         GTAAATTCAAGCCCGTGATCAAGAAAGCAATGGTGGAGCTTGAAG
genomic: TGTTGGTGGAACTGCACTCACCTCAATGATGGATGTGGAGAGGAGGCATGgtacacactt ... ttctttgtagGTAAATTCAAGCCCGTGATCAAGAAAGCAATGGTGGAGCTTGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttatgtgaatgctttgtccatagttttgtttacaaatgtgcaatttctttgtagGTAAATTCAAGCCCGTGATCAAGAAAGCAATGGTGGAGCTTGAAG
                                            tttctttgt  CT-rich tract
                        ttttgtttacaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaccctggttattatataaatcatgaaaagtctgtacatgttgcatttatgtgaatgctttgtccatagttttgtttacaaatgtgcaatttctttgtagGTAAATTCAAGCCCGTGATCAAGAAAGCAATGGTGGAGCTTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
aaccctg
- - - - - - - - - - -catgaaa
- - - - - - - - - - - - - - - tctgtac
- - - - - - - - - - - - - - - - - - - - -tgcattt
- - - - - - - - - - - - - - - - - - - - - - - - - gtgaatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtgcaa