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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcaaattattaatggggtaaagaagtatacaatttttgcgtggtgctaattaattctagtgctatgtatgcttttaatctaatattttaaggcattgtagGTGGCAGCCAGTGTTGCTTTTCTAATTGCAAGATATTTTGCTCGTGAGCGAATTGTAAAACTAGTGGAAGGAAATAAGAAGTTTGTTGCTATTGACAAAG

Basic information

species Glycine max
transcript GLYMA08G26000.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G26000.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv18s0001g03830.t01 (Vitis vinifera), 3'ss of exon 3
-------------------------tcaaatta-ttaatggggtaaagaagtatacaatttttgcgtggtgctaattaattctagtgctatgtatgcttttaatctaatatttt----aaggcattgtagGTGGCAGCCAGTGTTGCTTTTCTAATTGCAAGATATTTTGCTCGTGAGCGAATTGTAAAACTAGTGGAAGGAAATAAGAAGTTTGTTGCTATTGACAAAG
                         |  ||  | |||      | |||   | | |  ||| |   | ||  ||| |       |  |  | | | ||   ||    |||||||    ||  | ||  |||| ||||| |||||||| ||  ||||||| ||||||||||||||||| || ||| | ||| |||| |||||||| || || ||| |||| ||||||||||
gtaagttgtttttctgcaattaaaatagaacaacttagcaaccttaagtgcttttctttttctttattgttttaaatgtgatgggcacagtttttactaaaaaatgtatattttttttaacccttttcagGTTGCAGCAAGTGTTGCCTTCTTAATTGCCAGATATTTTGCTCGTGAACGTATTCTTAAATTAGTTGAAGGAAACAAAAAATTTCTTGCAATTGACAAAG
















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|120533380|gb|EH261513.1|EH261513
EST:     TTCTATTTGGATCTGTTGTCGGCACTATCATAGTCTCTATCAGCGGAACA                         GTGGCAGCCAGTGTTGCTTTTCTAATTGCAAGATATTTTGCTCGTGAGCGA
genomic: TTCTATTTGGATCTGTTGTCGGCACTATCATAGTCTCTATCAGCGGAACAgtgagtcaat ... ggcattgtagGTGGCAGCCAGTGTTGCTTTTCTAATTGCAAGATATTTTGCTCGTGAGCGA
EST: gi|209699648|gb|BW655727.1|BW655727
EST:     TTCTATTTGGATCTGTTGTCGGCACTATCATAGTCTCTATCAGCGGAACA                         GTGGCAGCCAGTGTTGCTTTTCTAATTGCAAGATATTTTGCTCGTGAGCGA
genomic: TTCTATTTGGATCTGTTGTCGGCACTATCATAGTCTCTATCAGCGGAACAgtgagtcaat ... ggcattgtagGTGGCAGCCAGTGTTGCTTTTCTAATTGCAAGATATTTTGCTCGTGAGCGA
EST: gi|120530346|gb|EH258479.1|EH258479
EST:     TTCTATTTGGATCTGTTGTCGGCACTATCATAGTCTCTATCAGCGGAACA                         GTGGCAGCCAGTGTTGCTTTTCTAATTGCAAGATATTTTGCTCGTGAGCGA
genomic: TTCTATTTGGATCTGTTGTCGGCACTATCATAGTCTCTATCAGCGGAACAgtgagtcaat ... ggcattgtagGTGGCAGCCAGTGTTGCTTTTCTAATTGCAAGATATTTTGCTCGTGAGCGA
EST: gi|120530968|gb|EH259101.1|EH259101
EST:     TCTATTTGGATCTGTTGTCGGCACTATCATAGTCTCTAATCAGCGGAACA                         GTGGCAGCCAGTGTTGCTTTTCTAAATTGCAAGATATTTTGCTCGTGAGCG
genomic: TCTATTTGGATCTGTTGTCGGCACTATCATAGTCTCTA-TCAGCGGAACAgtgagtcaat ... ggcattgtagGTGGCAGCCAGTGTTGCTTTTCTAA-TTGCAAGATATTTTGCTCGTGAGCG
EST: gi|120531813|gb|EH259946.1|EH259946
EST:     TTCTATTTGGATCTGTTGTCGGCACTATCATAGTCTCTATCAGCGGAACA                         GTGGCAGCCAGTGTTGCTTTTCTAATTGCAAGATATTTTGCTCGTGAGCGA
genomic: TTCTATTTGGATCTGTTGTCGGCACTATCATAGTCTCTATCAGCGGAACAgtgagtcaat ... ggcattgtagGTGGCAGCCAGTGTTGCTTTTCTAATTGCAAGATATTTTGCTCGTGAGCGA
EST: gi|51337968|gb|CO981834.1|CO981834
EST:     TTCTATTTGGATCTGTTGTCGGCACTATCATAGTCTCTATCAGCGGAACA                         GTGGCAGCCAGTGTTGCTTTTCTAATTGCAAGATATTTTGCTCGTGAGCGA
genomic: TTCTATTTGGATCTGTTGTCGGCACTATCATAGTCTCTATCAGCGGAACAgtgagtcaat ... ggcattgtagGTGGCAGCCAGTGTTGCTTTTCTAATTGCAAGATATTTTGCTCGTGAGCGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctaattaattctagtgctatgtatgcttttaatctaatattttaaggcattgtagGTGGCAGCCAGTGTTGCTTTTCTAATTGCAAGATATTTTGCTCGTGAGCGAATTGTAAAACTAGTGGAAGGAAATAAGAAGTTTGTTGCTATTGACAAAG
                 tatgtatgcttttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcaaattattaatggggtaaagaagtatacaatttttgcgtggtgctaattaattctagtgctatgtatgcttttaatctaatattttaaggcattgtagGTGGCAGCCAGTGTTGCTTTTCTAATTGCAAGATATTTTGCTCGTGAGCGAATTGTAAAACTAGTGGAAGGAAATAAGAAGTTTGTTGCTATTGACAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - -atggggt
- - - - - - - - - - - - - - - - - - - - tggtgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - -ctagtgc