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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttttgcattcaatgtgttttcaattttaaaatatgtacttctaattaatgagatggtaacaactgaccatcctttccagATAAGGGCAGACATTGAAACAAAAGGAGAATTCATTAATGACCTTATAAGAAAAGTAGTAGATGCAGCCTTCACGGATATTGAAGAGGTCCTAAAGTTTG

Basic information

species Glycine max
transcript GLYMA17G04640.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G04640.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv05s0020g00920.t01 (Vitis vinifera), 3'ss of exon 3
gtaagttttgcattcaatgtgttttcaattttaaaatatg-----tacttctaattaatgagatggtaacaactgaccatcctttccagATAAGGGCAGACATTGAAACAAAAGGAGAATTCATTAATGACCTTATAAGAAAAGTAGTAGATGCAGCCTTCACGGATATTGAAGAGGTCCTAAAGTTTG
|||||  ||  |     || |  || | | ||    | |      |  ||||| |     | |   ||| |     | | |  |   ||||||  ||||||||||||||||||||||| ||||| ||||  |||||    | |||  | | |||| | |   | ||||| |||||  |  | || ||||
gtaagcatttaaaattttgggacttaattattggtttgttgttgctgtttctactcgtctataaactaata-tcatctaacaatgatagATAAAAGCAGACATTGAAACAAAAGGAGACTTCATCAATGGTCTTATCCAGAGAGTGCTGGCTGCATCTTATTCAGATATGGAAGACATTGTGAAATTTG
















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|192331028|gb|FK020248.1|FK020248
EST:     ACAGTAGCATTGTTGGAGAAATTCAGAACCGTTCAGCTCATCTTTTAGCA                         ATAAGGGCAGACATTGAAACAAAAGGAGAATTCATTAATGACCTTATAAGA
genomic: ACAGTAGCATTGTTGGAGAAATTCAGAACCGTTCAGCTCATCTTTTAGCAgtaagttttg ... tcctttccagATAAGGGCAGACATTGAAACAAAAGGAGAATTCATTAATGACCTTATAAGA
EST: gi|7691495|gb|AW759621.1|AW759621
EST:     ACAGTAGCATTGTTGGAGAAATTCAGAACCGTTCAGCTCATCTGTTAGCA                         ATAAGGGCAGACATTGAAACAAAAGGAGAATTCATTAATGACCTTATAAGA
genomic: ACAGTAGCATTGTTGGAGAAATTCAGAACCGTTCAGCTCATCTTTTAGCAgtaagttttg ... tcctttccagATAAGGGCAGACATTGAAACAAAAGGAGAATTCATTAATGACCTTATAAGA
EST: gi|12774798|gb|BG239746.1|BG239746
EST:     ACAGTAGCATTGTTGGAGAAATTCAGAACCGTTCAGCTCATCTTTTAGCA                         ATAAGGGCAGACATTGAAACAAAAGGAGAATTCATTAATGACCTTATAAGA
genomic: ACAGTAGCATTGTTGGAGAAATTCAGAACCGTTCAGCTCATCTTTTAGCAgtaagttttg ... tcctttccagATAAGGGCAGACATTGAAACAAAAGGAGAATTCATTAATGACCTTATAAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttaaaatatgtacttctaattaatgagatggtaacaactgaccatcctttccagATAAGGGCAGACATTGAAACAAAAGGAGAATTCATTAATGACCTTATAAGAAAAGTAGTAGATGCAGCCTTCACGGATATTGAAGAGGTCCTAAAGTTTG
                                    aactgac  putative branch site (score: 2)
                                          ccatcctttcc  CT-rich tract
           tacttctaattaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttttgcattcaatgtgttttcaattttaaaatatgtacttctaattaatgagatggtaacaactgaccatcctttccagATAAGGGCAGACATTGAAACAAAAGGAGAATTCATTAATGACCTTATAAGAAAAGTAGTAGATGCAGCCTTCACGGATATTGAAGAGGTCCTAAAGTTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG