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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctttatccatgttttttggtatagatataacttaaattagtatagagctttatccattaaaactggtacgaatttttgaaatgcttttctgtatttgcagGAACCTTTCTGTCATTGGGAAAGAAGAGAGGTGAACTCAAGGTTTTATGGACAAGAGGGGAACCAAAAATACCTTGCCCTCACATCCAAGAGGATCAATC

Basic information

species Glycine max
transcript GLYMA09G39500.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G39500.1 (Glycine max), 3'ss of exon 13
lower sequence: Vv15s0046g02460.t01 (Vitis vinifera), 3'ss of exon 13
-------ctttatccatgttttttggtatagatataacttaaattagtatagagctttatccattaaaactggtacgaatttttgaaatgcttttctgtatttgcagGAACCTTTCTGTCATTGGGAAAGAAGAGAGGTGAACTCAAGGTTTTATGGACAAGAGGGGAACCAAAAATACCTTGCCCTCACATCCAAGAGGATCAATC
         ||||||  ||||||  | |   || ||     ||   ||    | ||| |    ||  |  |  |   || ||    |||  ||   | ||  | |||| ||||||||| ||||||||||||||||||| || ||||||  | ||||||||| ||| |||||  |||  || ||||| |||||||||     ||||| 
gtcatgttcttatccgagtttttgagga---atttattgacaaggggttgtcaccttgagttttttcattttttgttaactt----aatctttggttctaaattcagGCACCTTTCTGGCATTGGGAAAGAAGAGAGGCGATCTCAAGACTCTATGGACAAAAGGAGAACCCGAAAGGCCATGCCCGCACATCCAACCTTCTCAATA
















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|254320216|gb|GR829404.1|GR829404
EST:     GGATGGACATGGTCAACCAGCTTTGCTTTATATAGTCCCATTTACACTTG                         GAACCTTTCTGTCATTGGGAAAGAAGAGAGGTGAACTCAAGGTTTTATGGA
genomic: GGATGGACATGGTCAACCAGCTTTGCTTTATATAGTCCCATTTACACTTGgttagtaaaa ... gtatttgcagGAACCTTTCTGTCATTGGGAAAGAAGAGAGGTGAACTCAAGGTTTTATGGA
EST: gi|9258837|gb|BE346984.1|BE346984
EST:     GGATGGACATGGTCAACCAGCTTTGCTTTATATAGTCCCATTTACACTTG                         GAACCTTTCTGTCATTGGGAAAGAAGAGAGGTGAACTCAAGGTTTTATGGA
genomic: GGATGGACATGGTCAACCAGCTTTGCTTTATATAGTCCCATTTACACTTGgttagtaaaa ... gtatttgcagGAACCTTTCTGTCATTGGGAAAGAAGAGAGGTGAACTCAAGGTTTTATGGA
EST: gi|22524144|gb|BU082955.1|BU082955
EST:     GGATGGACATGGTCAACCAGCTTTGCTTTATATAGTCCCATTTACACTTG                         GAACCTTTTTGTCATTGGGAAAGAAGAGAGGTGAACTCAAGGTTTTATGGA
genomic: GGATGGACATGGTCAACCAGCTTTGCTTTATATAGTCCCATTTACACTTGgttagtaaaa ... gtatttgcagGAACCTTTCTGTCATTGGGAAAGAAGAGAGGTGAACTCAAGGTTTTATGGA
EST: gi|207749000|gb|GD721411.1|GD721411
EST:     GGATGGACATGGTCAACCAGCTTTGCTTTATATAGTCCCATTTACACTTG                         GAACCTTTCTGTCATTGGGAAAGAAGAGAGGTGAACTCAAGGTTTTATGGA
genomic: GGATGGACATGGTCAACCAGCTTTGCTTTATATAGTCCCATTTACACTTGgttagtaaaa ... gtatttgcagGAACCTTTCTGTCATTGGGAAAGAAGAGAGGTGAACTCAAGGTTTTATGGA
EST: gi|208088299|gb|GD889467.1|GD889467
EST:     GGATGGACATGGTCAACCAGCTTTGCTTTATATAGTCCCATTTACACTTG                         GAACCTTTTTGTCATTGGGAAAGAAGAGAGGTGAACTCAAGGTTTTANGGA
genomic: GGATGGACATGGTCAACCAGCTTTGCTTTATATAGTCCCATTTACACTTGgttagtaaaa ... gtatttgcagGAACCTTTCTGTCATTGGGAAAGAAGAGAGGTGAACTCAAGGTTTTATGGA
EST: gi|22523945|gb|BU082756.1|BU082756
EST:     GGATGGACATGGTCAACCAGCTTTGCTTTATATAGTCCCATTTACACTTG                         GAACCTTTTTGTCATTGGGAAAGAAGAGAGGTGAACTC
genomic: GGATGGACATGGTCAACCAGCTTTGCTTTATATAGTCCCATTTACACTTGgttagtaaaa ... gtatttgcagGAACCTTTCTGTCATTGGGAAAGAAGAGAGGTGAACTC
EST: gi|254320215|gb|GR829403.1|GR829403
EST:     GGATGGACATGGTCAACCAGCTTTGCTTTATATAGTCCCATTTACACTTG                         GAACCTTTCTGTCATTGGGAAAGAAGAGAGGTGAACTCAAGGTTTTATGGA
genomic: GGATGGACATGGTCAACCAGCTTTGCTTTATATAGTCCCATTTACACTTGgttagtaaaa ... gtatttgcagGAACCTTTCTGTCATTGGGAAAGAAGAGAGGTGAACTCAAGGTTTTATGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agctttatccattaaaactggtacgaatttttgaaatgcttttctgtatttgcagGAACCTTTCTGTCATTGGGAAAGAAGAGAGGTGAACTCAAGGTTTTATGGACAAGAGGGGAACCAAAAATACCTTGCCCTCACATCCAAGAGGATCAATC
                                      cttttctgt  CT-rich tract
                         aatttttgaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctttatccatgttttttggtatagatataacttaaattagtatagagctttatccattaaaactggtacgaatttttgaaatgcttttctgtatttgcagGAACCTTTCTGTCATTGGGAAAGAAGAGAGGTGAACTCAAGGTTTTATGGACAAGAGGGGAACCAAAAATACCTTGCCCTCACATCCAAGAGGATCAATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - ccatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - -ccattaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctggtac