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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatgatgtctttatactatgagtatatcaatgtatatactatgtagtttcaatttttagttattgcttgggaatgtttaaattttgttgttattgattagATTGATGATACGGAGAAGTTGTTGGAGATCACAAAGCAAGCAGCGAAGGAAGGTGCTTTCCTTGTGTATACTTTAGCTGACCCATCATTGGCTTCAACTG

Basic information

species Glycine max
transcript GLYMA20G27860.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G27860.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv10s0116g00390.t01 (Vitis vinifera), 3'ss of exon 1
aatgatgtctttatactatgagtatatcaatgtatatactatgtagtttcaatttttagtt--attgcttgggaatgtttaaattttgttgttattgattagATTGATGATACGGAGAAGTTGTTGGAGATCACAAAGCAAGCAGCGAAGGAAGGTGCTTTCCTTGTGTATACTTTAGCTGACCCATCATTGGCTTCAACTG
| ||  |  | | |  |||     |  |   || |      |  |  |      || |  |  ||   ||| | || ||| |   |  |   |  |  ||||||||||||| | |||  |||| |||||||   |||||||||||| || ||||||||  | ||||| || |||||||||||||| ||| |||||  | |||
attg--gattctgttgtatagagctgccggagttttggtcttagaactcttgcattaaaatggatgatttgagtatatttgatggtcatctatgcttgttagATTGATGATGCAGAGCCGTTGGTGGAGATAGTAAAGCAAGCAGCTAAAGAAGGTGCAATGCTTGTTTACACTTTAGCTGACCCTTCAATGGCTGAATCTG
















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|209714749|gb|BW674274.1|BW674274
EST:     ACTGCTTGGTCGACCGTGGCTGCCCCGTCAGTACCCATTTGTTTTCTGGG                         ATTGATGATACGGAGAAGTTGTTGGAGATCACAAAGCAAGCAGCGAAGGAA
genomic: ACTGCTTGGTCGACCGTGGCTGCCCCGTCAGTACCCATTTGTTTTCTGGGgtaagcaaat ... tattgattagATTGATGATACGGAGAAGTTGTTGGAGATCACAAAGCAAGCAGCGAAGGAA
EST: gi|120528751|gb|EH256885.1|EH256885
EST:     ACTGCTTGGTCGACCGTGGCTGCCCCGTCAGTACCCATTTGTTTTCTGGG                         ATTGATGATACGGAGAAGTTGTTGGAGATCACAAAGCAAGCAGCGAAGGAA
genomic: ACTGCTTGGTCGACCGTGGCTGCCCCGTCAGTACCCATTTGTTTTCTGGGgtaagcaaat ... tattgattagATTGATGATACGGAGAAGTTGTTGGAGATCACAAAGCAAGCAGCGAAGGAA
EST: gi|254343704|gb|GR857460.1|GR857460
EST:     ACTGCTTGGTCGACCGTGGCTGCCCCGTCAGTACCCATTTGTTTTCTGGG                         ATTGATGATACGGAGAAGTTGTTGGAGATCACAAAGCAAGCAGCGAAGGAA
genomic: ACTGCTTGGTCGACCGTGGCTGCCCCGTCAGTACCCATTTGTTTTCTGGGgtaagcaaat ... tattgattagATTGATGATACGGAGAAGTTGTTGGAGATCACAAAGCAAGCAGCGAAGGAA
EST: gi|10232963|gb|BE801851.1|BE801851
EST:     ACTGCTTGGTCGACCGTGGCTGCCCCGTCAGTACCCATTTGTTTTCTGGG                         ATTGATGATACGGAGAAGTTGTTGGAGATCACAAAGCAAGCAGCGAAGGAA
genomic: ACTGCTTGGTCGACCGTGGCTGCCCCGTCAGTACCCATTTGTTTTCTGGGgtaagcaaat ... tattgattagATTGATGATACGGAGAAGTTGTTGGAGATCACAAAGCAAGCAGCGAAGGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttcaatttttagttattgcttgggaatgtttaaattttgttgttattgattagATTGATGATACGGAGAAGTTGTTGGAGATCACAAAGCAAGCAGCGAAGGAAGGTGCTTTCCTTGTGTATACTTTAGCTGACCCATCATTGGCTTCAACTG
                          aatgtttaaattttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatgatgtctttatactatgagtatatcaatgtatatactatgtagtttcaatttttagttattgcttgggaatgtttaaattttgttgttattgattagATTGATGATACGGAGAAGTTGTTGGAGATCACAAAGCAAGCAGCGAAGGAAGGTGCTTTCCTTGTGTATACTTTAGCTGACCCATCATTGGCTTCAACTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- tgatgtc
- - - - - - - -ctatgag
- - - - - - - - - - - - - -caatgta
- - - - - - - - - - - - - - - - - - - -tatgtag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcttgg