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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcaaagtcgtggtgcttttattctcacttgtgcttatttgatttcacatagtttaaactctctttcatctgtaaccagGCAATCAACAAAAGTTTATCATCACTGAGTGATGTTATATTCGCCTTAGCCAAGAAGGAGGATCATGTGCCATTCAGGAACTCAAAGCTTACATATCTCC

Basic information

species Glycine max
transcript GLYMA12G16580.1
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G16580.1 (Glycine max), 3'ss of exon 15
lower sequence: LOC_Os04g53760.1 (Oryza sativa), 3'ss of exon 14
gtatgcaaagtcgtggtgcttttattctcacttgtgcttatttgatt-tcacatagtttaaactctctttcatctgtaa---ccagGCAATCAACAAAAGTTTATCATCACTGAGTGATGTTATATTCGCCTTAGCCAAGAAGGAGGATCATGTGCCATTCAGGAACTCAAAGCTTACATATCTCC
||  |     || |      ||||   |      | ||||||||||  |||||| || | | || | | |  ||| ||     ||||||||||| ||||| || ||| | || || |||||||| || ||  | || ||    || ||||||||||| |||||||||||||| |||||||| ||  
gtgagtgtgttcatcacaaatttacaat-----attcttatttgataatcacattgtcttatctgtttgttttctttatgtttcagGCAATCAATAAAAGCTTGTCAGCTCTTAGCGATGTTATCTTTGCAATTGCGAAAGGAGACGATCATGTGCCCTTCAGGAACTCAAAACTTACATACCTTT

upper sequence: GLYMA12G16580.1 (Glycine max), 3'ss of exon 15
lower sequence: AT5G54670.1 (Arabidopsis thaliana), 3'ss of exon 15
gtatgcaaagtcgtggtgcttttattctcacttgtgcttatttg--atttcacatagtttaaactctctttcatctgtaaccagGCAATCAACAAAAGTTTATCATCACTGAGTGATGTTATATTCGCCTTAGCCAAGAAGGAGGATCATGTGCCATTCAGGAACTCAAAGCTTACATATCTCC
||| |     |  | |     | |  |    || || ||  |||  ||||    |   ||||||| || ||| |   |   |||||||||||||||||||| || || ||  | ||||| |||||||||||||| ||||| || |||||||| |||||| | ||||||||||| |||||||| |
gtacgtt---tgatagaaacataaaacatgattatggtttcttgcaatttttagtctcttaaactttcattctttctt---cagGCAATCAACAAAAGTTTGTCGTCGCTAGGCGATGTCATATTCGCCTTAGCAAAGAAAGAAGATCATGTACCATTCCGAAACTCAAAGCTCACATATCTTC

upper sequence: GLYMA12G16580.1 (Glycine max), 3'ss of exon 15
lower sequence: AT4G27180.1 (Arabidopsis thaliana), 3'ss of exon 15
-----gtatgcaaagtcgtggtgcttttattctcacttgtgcttatttgatttcacat-agtttaa--actctctttcatctgtaaccagGCAATCAACAAAAGTTTATCATCACTGAGTGATGTTATATTCGCCTTAGCCAAGAAGGAGGATCATGTGCCATTCAGGAACTCAAAGCTTACATATCTCC
     || ||| || || | ||      ||| | |      |  |   ||||| | ||  | ||||  | | ||||     |      |||||||||||||||| ||||| || ||  | ||||| ||||| |||||||| ||||| || ||||| || || ||||| ||||||||||| || ||||| |
gtaatgtctgcgaa-tcttagtaaacacatttttag--agacacaagagatttaatattggcttaatgattttcttcttcttactgaaagGCAATCAACAAAAGCTTATCGTCTCTAGGCGATGTCATATTTGCCTTAGCGAAGAAAGAAGATCACGTTCCTTTCAGAAACTCAAAGCTCACTTATCTTC

upper sequence: GLYMA12G16580.1 (Glycine max), 3'ss of exon 15
lower sequence: Vv19s0014g05070.t01 (Vitis vinifera), 3'ss of exon 14
-------------gtatgcaaagtcgtggtgcttttattctcacttgtgcttatttgatttcacatagtttaaactctctttcatctgtaaccagGCAATCAACAAAAGTTTATCATCACTGAGTGATGTTATATTCGCCTTAGCCAAGAAGGAGGATCATGTGCCATTCAGGAACTCAAAGCTTACATATCTCC
                   | |  | |  | || ||| | | |||| |  ||||     || | ||   |  |  |   |||||  | | || |||| ||||| || ||| | |||||| | |||||||||||||| ||| | || ||||||||||| ||||| ||||| ||||||||||||||||| ||||| |
gtatttgagaaacactgatacaagcttaattctgttaattttacttatcattatgcatctttatatttatatatattcttttcaattatgac-agGCCATCAATAAGAGTCTGTCATCATTAAGTGATGTTATATTTGCCCTGGCAAAGAAGGAGGACCATGTACCATTTAGGAACTCAAAGCTTACGTATCTTC

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|4313552|gb|AI460671.1|AI460671
EST:     AGTGGATCAACCGGGGACCGGTTGAAAGAAACTCTA                         GCAATCAACAAAAGTTTATCATCACTGAGTGATGTTATATTCGCCTTAGCC
genomic: AGTGGATCAACCGGGGACCGGTTGAAAGAAACTCAAgtatgcaaag ... ctgtaaccagGCAATCAACAAAAGTTTATCATCACTGAGTGATGTTATATTCGCCTTAGCC
EST: gi|18733417|gb|BM527595.1|BM527595
EST:     AGCGGCTTTCAAAGAGTGGATCAACCGGGGACCGGTTGAAAGAAACTCAA                         GCAATCAACAAAAGTTTATCATCACTGAGTGATGTTATATTCGCCTTAGCC
genomic: AGCGGCTTTCAAAGAGTGGATCAACCGGGGACCGGTTGAAAGAAACTCAAgtatgcaaag ... ctgtaaccagGCAATCAACAAAAGTTTATCATCACTGAGTGATGTTATATTCGCCTTAGCC
EST: gi|12688191|gb|BG154527.1|BG154527
EST:     AGCGGCTTTCAAAGAGTGGATCAACCGGGGACCGGTTGAAAGAAACTCAA                         GCAATCAACAAAAGTTTATCATCACTGAGTGATGTTATATTCGCCTTAGCC
genomic: AGCGGCTTTCAAAGAGTGGATCAACCGGGGACCGGTTGAAAGAAACTCAAgtatgcaaag ... ctgtaaccagGCAATCAACAAAAGTTTATCATCACTGAGTGATGTTATATTCGCCTTAGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcacttgtgcttatttgatttcacatagtttaaactctctttcatctgtaaccagGCAATCAACAAAAGTTTATCATCACTGAGTGATGTTATATTCGCCTTAGCCAAGAAGGAGGATCATGTGCCATTCAGGAACTCAAAGCTTACATATCTCC
                                  ctctctttcatctgt  CT-rich tract
          ttatttgattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgcaaagtcgtggtgcttttattctcacttgtgcttatttgatttcacatagtttaaactctctttcatctgtaaccagGCAATCAACAAAAGTTTATCATCACTGAGTGATGTTATATTCGCCTTAGCCAAGAAGGAGGATCATGTGCCATTCAGGAACTCAAAGCTTACATATCTCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT