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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctacatatattttcattgtggcatgcagattaatcattatgtatttttttctgctcttgttttgaactggtcactaaaaccttgtcaatttgaaatatagGGAGCCATGTTGTTTGGAAAGCGATTGGAGGTCAACTATTCGAAGCATGCGAACATAACCCAAGGTGCTGATACACATGAGTATGTCAATTCAAATCTCA

Basic information

species Glycine max
transcript GLYMA16G27970.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G27970.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv18s0072g00310.t01 (Vitis vinifera), 3'ss of exon 13
ctacatatattttcattgtggcatgcagattaatcattatgtatttttttctgctcttgttttgaactggtcactaaaaccttgtcaa--tttgaaatatagGGAGCCATGTTGTTTGGAAAGCGATTGGAGGTCAACTATTCGAAGCATGCGAACATAACCCAAGGTGCTGATACACATGAGTATGTCAATTCAAATCTCA
 ||  |||    ||| |  |      |  ||      | | | | || |  ||   || |||| | ||||  ||||||| | | ||||  || | |  ||||||||||||| | ||||||||| |||||||||| ||||  |||||| || | ||||||||   ||||||||||||||| |||||| | || |||| ||| |
ttatgtatgccatcact-cgatccataatttgtgttctctttgtattgtggtgaagttcttttta-ctgggaactaaaatcctttcaaaattgggatgatagGGAGCCATGCTATTTGGAAAGAGATTGGAGGTGAACTTCTCGAAGTATTCAAACATAACTACAGGTGCTGATACACACGAGTATATGAACTCAAGTCTTA
















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|7284482|gb|AW597072.1|AW597072
EST:     TCCAAATGGGAGATGGTTTCCAAGCTGAATTGGCAGTACATTTTCTGAAG                         GGAGCCATGTTGTTAGGAAAGCGATTGGAGGTCAACTATTCGAAGCATGCT
genomic: TCCAAATGGGAGATGGTTTCCAAGCTGAATTGGCAGTACATTTTCTGAAGgtttgtttct ... tgaaatatagGGAGCCATGTTGTTTGGAAAGCGATTGGAGGTCAACTATTCGAAGCATGCG
EST: gi|61241638|gb|DN591029.1|DN591029
EST:     TCCAAATGGGAGATGGTTTCCAAGCTGAATTGGCAGTACATTTTCTGAAG                         GGAGCCATGTTGTTTGGAAAGCGATTGGAGGTCAACTATTCGAAGCATGCG
genomic: TCCAAATGGGAGATGGTTTCCAAGCTGAATTGGCAGTACATTTTCTGAAGgtttgtttct ... tgaaatatagGGAGCCATGTTGTTTGGAAAGCGATTGGAGGTCAACTATTCGAAGCATGCG
EST: gi|193567354|gb|FK524727.1|FK524727
EST:     TCCAAATGGGAGATGGTTTCCAAGCTGAATTGGCAGTACA-TTTCTGAAG                         GGAGCCATGTTGTTTGGAAAGCGATTGGAGGTCAACTATTCGAAGCATGCG
genomic: TCCAAATGGGAGATGGTTTCCAAGCTGAATTGGCAGTACATTTTCTGAAGgtttgtttct ... tgaaatatagGGAGCCATGTTGTTTGGAAAGCGATTGGAGGTCAACTATTCGAAGCATGCG
EST: gi|21994596|gb|BQ786124.1|BQ786124
EST:     GGAGATGGTTTCCAAGCTGAATTGGCAGTACATTTTCTGAAG                         GGAGCCATGTTGTTTGGAAAGCGATTGGAGGTCAACTATTCGAAGCATGCG
genomic: GGAGATGGTTTCCAAGCTGAATTGGCAGTACATTTTCTGAAGgtttgtttct ... tgaaatatagGGAGCCATGTTGTTTGGAAAGCGATTGGAGGTCAACTATTCGAAGCATGCG
EST: gi|17023569|gb|BM094603.1|BM094603
EST:     TCCAAATGGGAGATGGTTTCCAAGCTGAATTGGCAGTACATTTTCTGAAG                         GGAGCCATGTTGTTTGGAAAGCGATTGGAGGTCAACTATTCGAAGCATGCG
genomic: TCCAAATGGGAGATGGTTTCCAAGCTGAATTGGCAGTACATTTTCTGAAGgtttgtttct ... tgaaatatagGGAGCCATGTTGTTTGGAAAGCGATTGGAGGTCAACTATTCGAAGCATGCG
EST: gi|14989899|gb|BI315589.1|BI315589
EST:     TCCAAATGGGAGATGGTTTCCAAGCTGAATTGGCAGTACATTTTCTGAAG                         GGAGCCATGTTGTTTGGAAAGCGATTGGAGGTCAACTATTCGAAGCATGCG
genomic: TCCAAATGGGAGATGGTTTCCAAGCTGAATTGGCAGTACATTTTCTGAAGgtttgtttct ... tgaaatatagGGAGCCATGTTGTTTGGAAAGCGATTGGAGGTCAACTATTCGAAGCATGCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttctgctcttgttttgaactggtcactaaaaccttgtcaatttgaaatatagGGAGCCATGTTGTTTGGAAAGCGATTGGAGGTCAACTATTCGAAGCATGCGAACATAACCCAAGGTGCTGATACACATGAGTATGTCAATTCAAATCTCA
                          cactaaa  putative branch site (score: 2)
                                       tcaatttgaaatata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctacatatattttcattgtggcatgcagattaatcattatgtatttttttctgctcttgttttgaactggtcactaaaaccttgtcaatttgaaatatagGGAGCCATGTTGTTTGGAAAGCGATTGGAGGTCAACTATTCGAAGCATGCGAACATAACCCAAGGTGCTGATACACATGAGTATGTCAATTCAAATCTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - gcatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccttgtc