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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttacttttaggtttcgcagccaacaaattacgattcctttttttttttttgaattggtttttgagagtttttgttgtcgagtagAACATATGAGATTATTCCGCCGGTGAATTGGGGGATTCGGATTGTGCCGGAGAAGAAGGCGTTTGTGATTGAGCGATTCGGGAAGTACGTCAAGACTCTT

Basic information

species Glycine max
transcript GLYMA06G14340.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G14340.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os08g06200.1 (Oryza sativa), 3'ss of exon 1
gttacttttaggtttcgcagccaacaaattacgattcctttttttttttttgaattggtttttgagagtttttgttgtcgagtagAACATATGAGA---TTATTCCGCCGGTGAATTGGGGGATTCGGATTGTGCCGGAGAAGAAGGCGTTTGTGATTGAGCGATTCGGGAAGTACGTCAAGACTCTT
|| |          ||    ||  |   ||  | ||    ||||  |||| |||  |||  ||||    |  || ||  | || | |  || |||    | |   |||||||||| |||||| |  | || |||||||||||||||||||| ||| | ||||| ||||| |||||||||||||| || 
gtcagcgccccaactcct--cctcctcgttttggttttggttttggttttggaag-ggtggttgatgtgtggtggtggtg-gttgcagGTACGAGGCGCTGAGCACGCCGGTGAACTGGGGGGTGAGCATCGTGCCGGAGAAGAAGGCGTTCGTGGTGGAGCGGTTCGGCAAGTACGTCAAGACGCTC

upper sequence: GLYMA06G14340.1 (Glycine max), 3'ss of exon 1
lower sequence: AT4G27585.1 (Arabidopsis thaliana), 3'ss of exon 1
gttacttttaggtttcgcagccaacaaatt-acgattcctttttttttttttgaattggtttttgagagttt----ttg--ttgtcga-----gtagAACATATGAGATTATTCCGCCGGTGAATTGGGGGATTCGGATTGTGCCGGAGAAGAAGGCGTTTGTGATTGAGCGATTCGGGAAGTACGTCAAGACTCTT---
|   | |||| ||||| || |  || | ||     ||      |||  ||||  ||| |  |     |  ||    |||  || | ||     || | |  | | |  | |  ||||||  ||||||||| || ||||| || ||||||| ||||||||||||||||||||||||||| || ||||  | |||  |    
gaatcatttatgtttctcaccttacgatttcgtttttgaagcatttggttttagattagagtagagaaccttaggattgatttatggatgttcgttgtagTTTTCAATTGACGCCGCCGACGAATTGGGGAATCCGGATAGTTCCGGAGAGGAAGGCGTTTGTGATTGAGCGATTCGGTAAATACGCTACGACGTTGCCG
















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|17021681|gb|BM092715.1|BM092715
EST:     CATTTCTCCTCCGTCCGTTACCTCCGCACCGGTCGCGATCCCAGCTCAAG                         AACATATGAGATTATTCCGCCGGTGAATTGGGGGATTCGGATTGTGCCGGA
genomic: CATTTCTCCTCCGTCCGTTACCTCCGCACCGGTCGCGATCCCAGCTCAAGgttactttta ... tgtcgagtagAACATATGAGATTATTCCGCCGGTGAATTGGGGGATTCGGATTGTGCCGGA
EST: gi|298192577|gb|HO036659.1|HO036659
EST:     CATTTCTCCTCCGTCCGTTACCTCCGCACCGGTCGCGATCCCAGCTCAAG                         AACATATGAGATTATTCCGCTGGTGAATTGGGGGATTCGGATTGTGCCGGA
genomic: CATTTCTCCTCCGTCCGTTACCTCCGCACCGGTCGCGATCCCAGCTCAAGgttactttta ... tgtcgagtagAACATATGAGATTATTCCGCCGGTGAATTGGGGGATTCGGATTGTGCCGGA
EST: gi|192328054|gb|FK021800.1|FK021800
EST:     CATTTCTCCTCCGTCCGTTACCTCCGCACCGGTCGCGATCCCAGCTCAAG                         AACATATGAGATTATTCCGCCGGTGAATTGGGGGATTCGGATTGTGCCGGA
genomic: CATTTCTCCTCCGTCCGTTACCTCCGCACCGGTCGCGATCCCAGCTCAAGgttactttta ... tgtcgagtagAACATATGAGATTATTCCGCCGGTGAATTGGGGGATTCGGATTGTGCCGGA
EST: gi|193305921|gb|FK269598.1|FK269598
EST:     CATTTCTCCTCCGTCCGTTACCTCCGCACCGGTCGCGATCCCAGCTCAAG                         AACATATGAGATTATTCCGCCGGTGAATTGGGGGATTCGGATTGTGCCGGA
genomic: CATTTCTCCTCCGTCCGTTACCTCCGCACCGGTCGCGATCCCAGCTCAAGgttactttta ... tgtcgagtagAACATATGAGATTATTCCGCCGGTGAATTGGGGGATTCGGATTGTGCCGGA
EST: gi|208085246|gb|GD881808.1|GD881808
EST:     GCGATCCCAGCTCAAG                         AACATATGAGATTATTCCGCCGGTGAATTGGGGGATTCGGATTGTGCCGGA
genomic: GCGATCCCAGCTCAAGgttactttta ... tgtcgagtagAACATATGAGATTATTCCGCCGGTGAATTGGGGGATTCGGATTGTGCCGGA
EST: gi|11687700|gb|BF595376.1|BF595376
EST:     CATTTCTCCTCCGTCCGTTACCTCCGCACCGGTCGCGATCCCAGCTCAAG                         AACATATGAGATTATTCCGCCGGTGAATTGGGGGATTCGGATTGTGCCGGA
genomic: CATTTCTCCTCCGTCCGTTACCTCCGCACCGGTCGCGATCCCAGCTCAAGgttactttta ... tgtcgagtagAACATATGAGATTATTCCGCCGGTGAATTGGGGGATTCGGATTGTGCCGGA
EST: gi|209700740|gb|BW670488.1|BW670488
EST:     CATTTCTCCTCCGTCCGTTACCTCCGCACCGGTCGCGATCCCAGCTCAAG                         AACATATGAGATTATTCCGCCGGTGAATTGGGGGATTCGGATTGTGCCGGA
genomic: CATTTCTCCTCCGTCCGTTACCTCCGCACCGGTCGCGATCCCAGCTCAAGgttactttta ... tgtcgagtagAACATATGAGATTATTCCGCCGGTGAATTGGGGGATTCGGATTGTGCCGGA
EST: gi|208029931|gb|GD827003.1|GD827003
EST:     CATTTCTCCTCCGTCCGTTACCTCCGCACCGGTCGCGATCCCAGCTCAAG                         AACATATGAGATTATTCCGCCGGTGAATTGGGGGATTCGGATTGTGCCGGA
genomic: CATTTCTCCTCCGTCCGTTACCTCCGCACCGGTCGCGATCCCAGCTCAAGgttactttta ... tgtcgagtagAACATATGAGATTATTCCGCCGGTGAATTGGGGGATTCGGATTGTGCCGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acgattcctttttttttttttgaattggtttttgagagtttttgttgtcgagtagAACATATGAGATTATTCCGCCGGTGAATTGGGGGATTCGGATTGTGCCGGAGAAGAAGGCGTTTGTGATTGAGCGATTCGGGAAGTACGTCAAGACTCTT
                                      tttttgtt  CT-rich tract
        tttttttttttttgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttacttttaggtttcgcagccaacaaattacgattcctttttttttttttgaattggtttttgagagtttttgttgtcgagtagAACATATGAGATTATTCCGCCGGTGAATTGGGGGATTCGGATTGTGCCGGAGAAGAAGGCGTTTGTGATTGAGCGATTCGGGAAGTACGTCAAGACTCTT

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