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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAGAATGTGGGGCTTCTAGGAAGCAATCGTATTGGTAGTAGAAGGGTCATTCAAGTTTCAGCTGGCTTTATGATATTCTTCTCAATGTTAGgtgagcggactaacataagtgtgtaaattaattccaattattttcatagttttacttaaagttcataatttgcttctttcttcag

Basic information

species Glycine max
transcript GLYMA08G12360.1
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G12360.1 (Glycine max), 5'ss of exon 12
lower sequence: Vv10s0003g01460.t01 (Vitis vinifera), 5'ss of exon 11
AGAGAATGTGGGGCTTCTAGGAAGCAATCGTATTGGTAGTAGAAGGGTCATTCAAGTTTCAGCTGGCTTTATGATATTCTTCTCAATGTTAGgtgagcgga---ctaacataagtgtgtaaattaattccaattattttcatagttt--tacttaaagttcataatttgcttctttctt-cag
||| |||||||| ||||| |||   | |||  |||| ||  | |||||||||||| |||||||||| ||||||||||||||||||||  |||||||||       || ||||  |   ||       |  ||||| ||      |||    ||||||  ||||  ||   ||  | ||| |||
AGAAAATGTGGGCCTTCTTGGATCAACTCGCGTTGGAAGCCGCAGGGTCATTCAAATTTCAGCTGGTTTTATGATATTCTTCTCAATACTAGgtgagcaacaatttatcatacatac-tactgcttcttgaattacttcttctctttgtcccttaaaactcatttttctttttgtacttgcag
















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|193585013|gb|FK542416.1|FK542416
EST:     ATTCTTCTCAATGTTAG                         GAAAATTTGGAGCTCTATTTGCATCAATACCATTCCCCATGTTTGCTGCTG
genomic: ATTCTTCTCAATGTTAGgtgagcggac ... ctttcttcagGAAAATTTGGAGCTCTATTTGCATCAATACCATTCCCCATGTTTGCTGCTG
EST: gi|58017520|gb|CX704262.1|CX704262
EST:     AAGGGTCATTCAAGTTTCAGCTGGCTTTATGATATTCTTCTCAATGTTAG                         GAAAATTTGGAGCTCTATTTGCATCAATACCATTCCCCATGTTTGCTGCTG
genomic: AAGGGTCATTCAAGTTTCAGCTGGCTTTATGATATTCTTCTCAATGTTAGgtgagcggac ... ctttcttcagGAAAATTTGGAGCTCTATTTGCATCAATACCATTCCCCATGTTTGCTGCTG
EST: gi|22525738|gb|BU084549.1|BU084549
EST:     AAGGGTCATTCAAGTTTCAGCTGGCTTTATGATATTCTTCTCAATGTTAG                         GAAAATTTGGAGCTCTATTTGCATCA
genomic: AAGGGTCATTCAAGTTTCAGCTGGCTTTATGATATTCTTCTCAATGTTAGgtgagcggac ... ctttcttcagGAAAATTTGGAGCTCTATTTGCATCA
EST: gi|58014211|gb|CX700953.1|CX700953
EST:     AAGGGTCATTCAAGTTTCAGCTGGCTTTATGATATTCTTCTCAATGTTAG                         GAAAATTTGGAGCTCTATTTGCATCAATACCATTCCCCATGTTTGCTGCTG
genomic: AAGGGTCATTCAAGTTTCAGCTGGCTTTATGATATTCTTCTCAATGTTAGgtgagcggac ... ctttcttcagGAAAATTTGGAGCTCTATTTGCATCAATACCATTCCCCATGTTTGCTGCTG
EST: gi|31473755|gb|CD415783.1|CD415783
EST:     AAGGGTCATTCAAGTTTCAGCTGGCTTTATGATATTCTTCTCAATGTTAG                         GTAAATTTGGAGCTCTATTTGCATCAATACCATTCCCCATGTTTGCTGCTG
genomic: AAGGGTCATTCAAGTTTCAGCTGGCTTTATGATATTCTTCTCAATGTTAGgtgagcggac ... ctttcttcagGAAAATTTGGAGCTCTATTTGCATCAATACCATTCCCCATGTTTGCTGCTG
EST: gi|58024713|gb|CX711454.1|CX711454
EST:     AAGGGTCATTCAAGTTTCAGCTGGCTTTATGATATTCTTCTCAATGTTAG                         GAAAATTTGGAGCTCTATTTGCATCAATACCATTCCCCATGTTTGCTGCTG
genomic: AAGGGTCATTCAAGTTTCAGCTGGCTTTATGATATTCTTCTCAATGTTAGgtgagcggac ... ctttcttcagGAAAATTTGGAGCTCTATTTGCATCAATACCATTCCCCATGTTTGCTGCTG
EST: gi|22525586|gb|BU084397.1|BU084397
EST:     AAGGGTCATTCAAGTTTCAGCTGGCTTTATGATATTCTTCTCAATGTTAG                         GAAAATTTGGAGCTCTATTTGCATCAA
genomic: AAGGGTCATTCAAGTTTCAGCTGGCTTTATGATATTCTTCTCAATGTTAGgtgagcggac ... ctttcttcagGAAAATTTGGAGCTCTATTTGCATCAA
EST: gi|58018670|gb|CX705412.1|CX705412
EST:     AAGGGTCATTCAAGTTTCAGCTGGCTTTATGATATTCTTCTCAATGTTAG                         GAAAATTTGGAGCTCTATTTGCATCAATACCATTCCCCATGTTTGCTGCTG
genomic: AAGGGTCATTCAAGTTTCAGCTGGCTTTATGATATTCTTCTCAATGTTAGgtgagcggac ... ctttcttcagGAAAATTTGGAGCTCTATTTGCATCAATACCATTCCCCATGTTTGCTGCTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAGAATGTGGGGCTTCTAGGAAGCAATCGTATTGGTAGTAGAAGGGTCATTCAAGTTTCAGCTGGCTTTATGATATTCTTCTCAATGTTAGgtgagcggactaacataagtgtgtaaattaattccaattattttcatagttttacttaaagttcataatttgcttctttcttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG