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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CACCTTCACAAACTTATCTTTAGTGTGGTCTAAAGAAGTGGAACTCTATTCAACTAATCAGAATTGCGTGAAGATGCTAGTTGGAAATAAAGTTGATAGAgtaagttgtgttttagtcttgtgcattaatgtatgacccaaggaaatgaatcagtaactactgtgaaatctttcctcaatgaaatgtttgaaaataaaat...

Basic information

species Glycine max
transcript GLYMA13G20970.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G20970.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv08s0007g04740.t01 (Vitis vinifera), 5'ss of exon 4
CACCTTCACAAACTTATCTTTAGTGTGGTCTAAAGAAGTGGAACTCTATTCAACTAATCAGAATTGCGTGAAGATGCTAGTTGGAAATAAAGTTGATAGAgtaagttgtgt----tttagtcttgtgcattaatgtatgacccaaggaaatgaatcagtaactactgtgaaatctttcctcaatgaaa-tgtttgaaaataaaat
 | ||| |||||||| ||    |||||| |||||||||| || || || || ||||||||| | || ||||||||||| |||||||||||||||||||||||||||| |||    | |  |    ||| | ||     || || || | | |||| | ||| |  | |    |  |   |  |      || || |         
GAGCTTTACAAACTTGTCCGATGTGTGGGCTAAAGAAGTAGAGCTTTACTCGACTAATCAGGACTGTGTGAAGATGCTTGTTGGAAATAAAGTTGATAGAgtaagttttgtgatctctgcttccatgcttaaaaactggatcccagaagaagaattattaaatggtttatggttatgggtgtacatgcctgctttatgtc-----
















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|209720225|gb|BW674565.1|BW674565
EST:     CAGAATTGCGTGAAGATGCTAGTTGGAAATAAAGTTGATAGA                         GATTCTGAAAGGGTTGTGAGCAAAGAAGAGGGTTTAGCACTTGCCGAGGAG
genomic: CAGAATTGCGTGAAGATGCTAGTTGGAAATAAAGTTGATAGAgtaagttgtg ... ctattcttagGATTCTGAAAGGGTTGTGAGCAAAGAAGAGGGTTTAGCACTTGCCGAGGAG
EST: gi|298176712|gb|HO026833.1|HO026833
EST:     CAACTAATCAGAATTGCGTGAAGATGCTAGTTGGAAATAAAGTTGATAGA                         GATTCTGAAAGGGTTGTGAGCAAAGAAGAGGGTTTAGCACTTGCCGAGGAG
genomic: CAACTAATCAGAATTGCGTGAAGATGCTAGTTGGAAATAAAGTTGATAGAgtaagttgtg ... ctattcttagGATTCTGAAAGGGTTGTGAGCAAAGAAGAGGGTTTAGCACTTGCCGAGGAG
EST: gi|15201651|gb|BI424985.1|BI424985
EST:     CAACTAATCAGAATTGCGTGAAGATGCTAGTTGGAAATAAAGTTGATAGA                         GATTCTGAAAGGGTTGTGAGCAAAGAAGAGGGTTTAGCACTTGCCGAGGAG
genomic: CAACTAATCAGAATTGCGTGAAGATGCTAGTTGGAAATAAAGTTGATAGAgtaagttgtg ... ctattcttagGATTCTGAAAGGGTTGTGAGCAAAGAAGAGGGTTTAGCACTTGCCGAGGAG
EST: gi|192303747|gb|FG998673.1|FG998673
EST:     CAACTAATCAGAATTGCGTGAAGATGCTAGTTGGAAATAAAGTTGATAGA                         GATTCTGAAAGGGTTGTGAGCAAAGAAGAGGGTTTAGCACTTGCCGAGGAG
genomic: CAACTAATCAGAATTGCGTGAAGATGCTAGTTGGAAATAAAGTTGATAGAgtaagttgtg ... ctattcttagGATTCTGAAAGGGTTGTGAGCAAAGAAGAGGGTTTAGCACTTGCCGAGGAG
EST: gi|192303748|gb|FG998674.1|FG998674
EST:     GATGCTAGTTGGAAATAAAGTTGATAGA                         GATTCTGAAAGGGTTGTGAGCAAAGAAGAGGGTTTAGCACTTGCCGAGGAG
genomic: GATGCTAGTTGGAAATAAAGTTGATAGAgtaagttgtg ... ctattcttagGATTCTGAAAGGGTTGTGAGCAAAGAAGAGGGTTTAGCACTTGCCGAGGAG
EST: gi|13563363|gb|BG551583.1|BG551583
EST:     CAACTAATCAGAATTGCGTGAAGATGCTAGTTGGAAATAAAGTTGATAGA                         GATTCTGAAAGGGTTGTGAGCAAAGAAGAGGGTTTAGCACTT
genomic: CAACTAATCAGAATTGCGTGAAGATGCTAGTTGGAAATAAAGTTGATAGAgtaagttgtg ... ctattcttagGATTCTGAAAGGGTTGTGAGCAAAGAAGAGGGTTTAGCACTT
EST: gi|58018762|gb|CX705504.1|CX705504
EST:     CAACTAATCAGAATTGCGTGAAGATGTTAGTTGGAAATAAAGTTGATAGA                         GATTCTGAAAGGGTTGTGAGCAAAGAAGAGGGTTTAGCACTTGCCGAGGAG
genomic: CAACTAATCAGAATTGCGTGAAGATGCTAGTTGGAAATAAAGTTGATAGAgtaagttgtg ... ctattcttagGATTCTGAAAGGGTTGTGAGCAAAGAAGAGGGTTTAGCACTTGCCGAGGAG

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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CACCTTCACAAACTTATCTTTAGTGTGGTCTAAAGAAGTGGAACTCTATTCAACTAATCAGAATTGCGTGAAGATGCTAGTTGGAAATAAAGTTGATAGAgtaagttgtgttttagtcttgtgcattaatgtatgacccaaggaaatgaatcagtaactactgtgaaatctttcctcaatgaaatgtttgaaaataaaat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaataaa