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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctgtctggatatctactgtttgccttataaatgcatgtattacttcccctctctttctgcaaggtgtgcaaattgactgcttgtcctttttgaaatcagAAAGTTAGTTTAGCTCGGAGATTTGCTTTAGTTCCCCTGGGACCTCCTTTACTGTCCTACCAAAGCAACTGCAAGGCAATGCTAACTGCTGTTGATGGCG

Basic information

species Glycine max
transcript GLYMA19G22520.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G22520.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os12g13460.1 (Oryza sativa), 3'ss of exon 5
----------tctgtctggatatctactgtttgccttataaatgcatgtattacttcccctctctttctgcaaggtgtgcaaattgactgcttgtcctttttgaaatcagAAAGTTAGTTTAGCTCGGAGATTTGCTTTAGTTCCCCTGGGACCTCCTTTACTGTCCTACCAAAGCAACTGCAAGGCAATGCTAACTGCTGTTGATGGCG
            |    | ||  |  |  |||   |||| | || ||  || |||   |||     ||   ||| | |    |||         |    ||  | | |||||||||||||||||||| ||||||||  |||||||  |||| || ||  || || ||||| | ||||||||||| |||||||| || ||||||| ||   
gggatcaacagttcatagcatgccagccttttattttattactggataaat-actgaacctgctcgtcgctaagttatttttatt---------tttcattgaagaacagAAAGTTAGTTTAGCTCGAAGATTTGCGCTAGTTCCATTGGGCCCACCACTATTGACCTACAAGAGCAACTGCAAAGCAATGCTGACAGCTGTTGGTGATT

upper sequence: GLYMA19G22520.1 (Glycine max), 3'ss of exon 5
lower sequence: AT5G14260.2 (Arabidopsis thaliana), 3'ss of exon 5
tctgtctggatatctactgtttgcc--ttataaatgcatgta-ttacttcccctctctttctgcaaggtgtgcaaattgactgcttgtcctttttgaaatcagAAAGTTAGTTTAGCTCGGAGATTTGCTTTAGTTCCCCTGGGACCTCCTTTACTGTCCTACCAAAGCAACTGCAAGGCAATGCTAACTGCTGTTGATGGCG
    |||  |  |   ||    ||   | ||  | ||| ||| | |  |      | || || |      |  | ||||  |  |  | ||| ||| | |||||| ||  |||| |||||  | |||||||| ||||| || || ||||| ||  || ||||      |||||||||||||||||| |||||||||||||| |
-gaatctaaagtttagcttgcagctcatcatttaagcaagtagtcaggtggtgcttgttgcttcttctaatttagattg--ttatgcttcttcttgtactcagAATGTCGGTTTGGCTCGTCGGTTTGCTTTGGTTCCTCTTGGTCCTCCCTTGTTGGCCTATTGTTCCAACTGCAAGGCAATGCTTACTGCTGTTGATGGTG
















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|15287126|gb|BI471017.1|BI471017
EST:     TTTTCAAACAAGCCTTTGCTGCTATTCAGTCTTGTGTGGTGCATTTACAG                         AAAGTTAGTTTAGCTCGGAGATTTGCTTTAGTTCCCCTGGGACCTCCTTTA
genomic: TTTTCAAACAAGCCTTTGCTGCTATTCAGTCTTGTGTGGTGCATTTACAGgtaaagtttc ... ttgaaatcagAAAGTTAGTTTAGCTCGGAGATTTGCTTTAGTTCCCCTGGGACCTCCTTTA
EST: gi|197661912|gb|FD480321.1|FD480321
EST:     TTTTCAAACAAGCCTTTGCTGCTATTCAGTCTTGTGTGGTGCATTTACGG                         AAAGTTAGTTTAGCTCGGAGATTTGCTTTAGTTCCCCTGGGACCTCCTTTA
genomic: TTTTCAAACAAGCCTTTGCTGCTATTCAGTCTTGTGTGGTGCATTTACAGgtaaagtttc ... ttgaaatcagAAAGTTAGTTTAGCTCGGAGATTTGCTTTAGTTCCCCTGGGACCTCCTTTA
EST: gi|20815055|gb|BQ299533.1|BQ299533
EST:     TTTTCAAACAAGCCTTTGCTGCTATTCAGTCTTGTGTGGTGCATTTACAG                         AAAGTTAGTTTAGCTCGGAGATTTGCTTTAGTTCCCCTGGGACCTCCTTTA
genomic: TTTTCAAACAAGCCTTTGCTGCTATTCAGTCTTGTGTGGTGCATTTACAGgtaaagtttc ... ttgaaatcagAAAGTTAGTTTAGCTCGGAGATTTGCTTTAGTTCCCCTGGGACCTCCTTTA
EST: gi|17153028|gb|BM142961.1|BM142961
EST:     TTTTCAAACAAGCCTTTGCTGCTATTCAGTCTTGTGTGGTGCATTTACAG                         AAAGTTAGTTTAGCTCGGAGATTTGCTTTAGTTCCCCTGGGACCTCCTTTA
genomic: TTTTCAAACAAGCCTTTGCTGCTATTCAGTCTTGTGTGGTGCATTTACAGgtaaagtttc ... ttgaaatcagAAAGTTAGTTTAGCTCGGAGATTTGCTTTAGTTCCCCTGGGACCTCCTTTA
EST: gi|19348347|gb|BM892879.1|BM892879
EST:     TTTTCAAACAAGCCTTTGCTGCTATTCAGTCTTGTGTGGTGCATTTACAG                         AAAGTTAGTTTAGCTCGGAGATTTGCTTTAGTTCCCCTGGGACCTCCTTTA
genomic: TTTTCAAACAAGCCTTTGCTGCTATTCAGTCTTGTGTGGTGCATTTACAGgtaaagtttc ... ttgaaatcagAAAGTTAGTTTAGCTCGGAGATTTGCTTTAGTTCCCCTGGGACCTCCTTTA
EST: gi|26058132|gb|CA801046.1|CA801046
EST:     TTTTCAAACAAGCCTTTGCTGCTATTCAGTCTTGTGTGGTGCATTTACAG                         AAAGTTAGTTTAGCTCGGAGATTTGCTTTAGTTCCCCTGGGACCTCCTTTA
genomic: TTTTCAAACAAGCCTTTGCTGCTATTCAGTCTTGTGTGGTGCATTTACAGgtaaagtttc ... ttgaaatcagAAAGTTAGTTTAGCTCGGAGATTTGCTTTAGTTCCCCTGGGACCTCCTTTA
EST: gi|20814963|gb|BQ299441.1|BQ299441
EST:     TTTTCAAACAAGCCTTTGCTGCTATTCAGTCTTGTGTGGTGCATTTACAG                         AAAGTTAGTTTAGCTCGGAGATTTGCTTTAGTTCCCCTGGGACCTCCTTTA
genomic: TTTTCAAACAAGCCTTTGCTGCTATTCAGTCTTGTGTGGTGCATTTACAGgtaaagtttc ... ttgaaatcagAAAGTTAGTTTAGCTCGGAGATTTGCTTTAGTTCCCCTGGGACCTCCTTTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcccctctctttctgcaaggtgtgcaaattgactgcttgtcctttttgaaatcagAAAGTTAGTTTAGCTCGGAGATTTGCTTTAGTTCCCCTGGGACCTCCTTTACTGTCCTACCAAAGCAACTGCAAGGCAATGCTAACTGCTGTTGATGGCG
                          aattgac  putative branch site (score: 3)
                                ctgcttgtccttttt  CT-rich tract
                                          tttttgaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctgtctggatatctactgtttgccttataaatgcatgtattacttcccctctctttctgcaaggtgtgcaaattgactgcttgtcctttttgaaatcagAAAGTTAGTTTAGCTCGGAGATTTGCTTTAGTTCCCCTGGGACCTCCTTTACTGTCCTACCAAAGCAACTGCAAGGCAATGCTAACTGCTGTTGATGGCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT