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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCGGGATATTGGCTCCGGGAATTTCGGCGTCGCAAGGCTTATGAGGGATAAACAGACGCAAGAGCTTGTTGCTGTCAAGTATATTGAACGCGGAGATAAGgttagtgccaatcaacaaaaaaaaataaaggttttcgatttttttggggtggcaaggagaaaaaggaaggaaaaaaaataattcacatgatcgttttcct...

Basic information

species Glycine max
transcript GLYMA01G39020.2
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G39020.2 (Glycine max), 5'ss of exon 1
lower sequence: AT5G66880.1 (Arabidopsis thaliana), 5'ss of exon 1
TCGGGATATTGGCTCCGGGAATTTCGGCGTCGCAAGGCTTATGAGGGATAAACAGACGCAAGAGCTTGTTGCTGTCAAGTATATTGAACGCGGAGATAAGgttagtgccaatcaacaaaaaaaaataaaggttttcgatttttttggggtggcaaggagaaaaaggaaggaaaaaaaataattcaca-tgatcgttttcct------
|  ||||||||| || || |||||||| || ||  | |||||||| |||||||  ||  |||||||||||||||||||||| || ||  | ||||| ||||||     || |      |||||  | |   ||||| ||||||    | ||   |     |    |       |    | |||   | || | | |||         
TAAGGATATTGGTTCTGGTAATTTCGGTGTTGCTCGTCTTATGAGAGATAAACTCACTAAAGAGCTTGTTGCTGTCAAGTACATCGAGAGAGGAGACAAGgtt----tcattttt---aaaaatctcatctttttctatttttggaagttgatgatatttatttagtccagtgatcgttcatttttagtgtttggtttagctttcac

upper sequence: GLYMA01G39020.2 (Glycine max), 5'ss of exon 1
lower sequence: PP1S218_59V6.1 (Physcomitrella patens), 5'ss of exon 1
TCGGGATATTGGCTCCGGGAATTTCGGCGTCGCAAGGCTTATGAGGGATAAACAGACGCAAGAGCTTGTTGCTGTCAAGTATATTGAACGCGGAGATAAGgttagtgccaatcaacaaaaaaaaataaaggttttcgatttttttggggtggca---aggagaaaaaggaaggaaaaaaaataattcacatgatcgttttcct
    || ||||| || ||||||||||| ||||| ||||| ||| | |||||  ||||    ||||| ||||||||||||||||| |||||||| || |||||  || |   ||     ||    ||   ||   |  | |  |    |    ||   ||  |     |   |             | |   ||      |   
GAAAGACATTGGGTCGGGGAATTTCGGGGTCGCCAGGCTCATGCGCGATAAGAAGACCAGGGAGCTCGTTGCTGTCAAGTATATCGAACGCGGGGAGAAGgtgcgt-cggttcggtttaacgtgatttggggactgaagtactgcaagtgttcattcagttgttcgtgtgtgtttccggttgcggtgatgcgacgacggtg--
















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|6071033|gb|AW100420.1|AW100420
EST:     AACAGACGCAAGAGCTTGTTGCTGTCAAGTATATTGAACGCGGAGATAAG                         ATTGATGAAAATGTTATAAGAGAAATCATTGATCACAGGTCTCTAAGACAT
genomic: AACAGACGCAAGAGCTTGTTGCTGTCAAGTATATTGAACGCGGAGATAAGgttagtgcca ... tgtgtcacagATTGATGAAAATGTTAAAAGAGAAATCATTAATCACAGGTCTCTAAGACAT
EST: gi|19453479|gb|BM954889.1|BM954889
EST:     AACAGACGCAAGAGCTTGTTGCTGTCAAGTATATTGAACGCGGAGATAAG                         ATTGATGAAAATGTTAAAAGAGAAATCATTAATCACAGGTCTCTAAGACAT
genomic: AACAGACGCAAGAGCTTGTTGCTGTCAAGTATATTGAACGCGGAGATAAGgttagtgcca ... tgtgtcacagATTGATGAAAATGTTAAAAGAGAAATCATTAATCACAGGTCTCTAAGACAT
EST: gi|11412769|gb|BF424780.1|BF424780
EST:     AACAGACGCAAGAGCTTGTTGCTGTCAAGTATATTGAACGCGGAGATAAG                         ATTGATGAAAATGTTAAAAGAGAAATCATTAATCACAGGTCTCTAAGACAT
genomic: AACAGACGCAAGAGCTTGTTGCTGTCAAGTATATTGAACGCGGAGATAAGgttagtgcca ... tgtgtcacagATTGATGAAAATGTTAAAAGAGAAATCATTAATCACAGGTCTCTAAGACAT
EST: gi|14259499|gb|BG882407.1|BG882407
EST:     AACAGACGCAAGAGCTTGTTGCTGTCAAGTCTATTGAACGCGGAGATAAG                         ATTGATGAAAATGTTAAAAGAGAAATCATTAATCACAGGTCTCTAAGACAT
genomic: AACAGACGCAAGAGCTTGTTGCTGTCAAGTATATTGAACGCGGAGATAAGgttagtgcca ... tgtgtcacagATTGATGAAAATGTTAAAAGAGAAATCATTAATCACAGGTCTCTAAGACAT
EST: gi|4291115|gb|AI441715.1|AI441715
EST:     AACAGACGCAAGAGCTTGTTGCTGTCAAGTATATTGAACGCGGAGATAAG                         ATTGATGAAAATGTTAAAAGAGAAATCATTAATCACAGGTCTCTAAGACAT
genomic: AACAGACGCAAGAGCTTGTTGCTGTCAAGTATATTGAACGCGGAGATAAGgttagtgcca ... tgtgtcacagATTGATGAAAATGTTAAAAGAGAAATCATTAATCACAGGTCTCTAAGACAT
EST: gi|4285128|gb|AI440867.1|AI440867
EST:     AACAGACGCAAGAGCTTGTTGCTGTCAAGTATATTGAACGCGGAGATAAG                         ATTGATGAAAATGTTAAAAGAGAAATCATTAATCACAGGTCTCTAAGACAT
genomic: AACAGACGCAAGAGCTTGTTGCTGTCAAGTATATTGAACGCGGAGATAAGgttagtgcca ... tgtgtcacagATTGATGAAAATGTTAAAAGAGAAATCATTAATCACAGGTCTCTAAGACAT
EST: gi|27424851|gb|CA936371.1|CA936371
EST:     GCGGAGATAAG                         ATTGATGAAAATGTTAAAAGAGAAATCATTAATCACAGGTCTCTAAGACAT
genomic: GCGGAGATAAGgttagtgcca ... tgtgtcacagATTGATGAAAATGTTAAAAGAGAAATCATTAATCACAGGTCTCTAAGACAT
EST: gi|18040782|gb|BM309076.1|BM309076
EST:     AACAGACGCAAGAGCTTGTTGCTGTCAAGTATATTGAACGCGGAGATAAG                         ATTGATGAAAATGTTAAAAGAGAAATCATTAATCACAGGTCTCTAAGACAT
genomic: AACAGACGCAAGAGCTTGTTGCTGTCAAGTATATTGAACGCGGAGATAAGgttagtgcca ... tgtgtcacagATTGATGAAAATGTTAAAAGAGAAATCATTAATCACAGGTCTCTAAGACAT
EST: gi|4286595|gb|AI441069.1|AI441069
EST:     AACAGACGCAAGAGCTTGTTGCTGTCAAGTATATTGAACGCGGAGATAAG                         ATTGATGAAAATGTTAAAAGAGAAATCATTAATCACAGGTCTCTAAGACAT
genomic: AACAGACGCAAGAGCTTGTTGCTGTCAAGTATATTGAACGCGGAGATAAGgttagtgcca ... tgtgtcacagATTGATGAAAATGTTAAAAGAGAAATCATTAATCACAGGTCTCTAAGACAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCGGGATATTGGCTCCGGGAATTTCGGCGTCGCAAGGCTTATGAGGGATAAACAGACGCAAGAGCTTGTTGCTGTCAAGTATATTGAACGCGGAGATAAGgttagtgccaatcaacaaaaaaaaataaaggttttcgatttttttggggtggcaaggagaaaaaggaaggaaaaaaaataattcacatgatcgttttcct

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT