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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttaaatctgttattcaacttgccattttttgttttcaatttcaaacatgatttgcacatgaaaacactgttaggactaagttttcatgtttttatgtagGTCTTCATCATCGGACCGGTGAAGGAGGTGAGGAAAGCCGAGGCCATGATTCGGGGTAGAATCTTGGATATATAGTTAAGAAATGTGTTACTTCTCTTTG

Basic information

species Glycine max
transcript GLYMA14G10520.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G10520.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G081924_T01 (Zea mays), 3'ss of exon 9
cttaaatctgttattcaacttgccattttttgttttcaatttcaaacatgatttgcacatgaaaacactgttag-gactaagttttcatgttttt-----atgtagGTCTTCATCATCGGACCGGTGAAGGAGGTGAGGAAAGCCGAGGCCATGATTCGGGGTAGAATCTTGGATATATAGTTAAGAAATGTGTTACTTCTCTTTG
      |  |||| |  |     || |  ||||    ||  |  | |   ||   || ||   |    |||||  ||    |||||  | | | |     |||||||| |||||||| ||| | ||||| || || |||||||||||||||||  |  | ||  ||||  ||||  | |||  | |  |    || |  | | |  
-----tttagttaatataagcaacaatcgttgtgcagaaact-gatctgaatgaacatatttcagttttgttactgatcctgtttttttttgtgtgctaaatgtagGTTTTCATCATTGGATCAGTGAATGAAGTCAGGAAAGCCGAGGCCATCTTCAGAGGCCGAATGCTGGAGTTCTAGAGATGTTACCCTTTGCGCCCCATGT

upper sequence: GLYMA14G10520.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv04s0008g00650.t01 (Vitis vinifera), 3'ss of exon 9
cttaaatctgttattcaacttgccattttttgttttcaatttcaaacatgat--ttgcacatgaaaacactgt-taggactaagttttcatgtttttatgtagGTCTTCATCATCGGACCGGTGAAGGAGGTGAGGAAAGCCGAGGCCATGATTCGGGGTAGAATCTTGGATATATAGTTAAGAAATGTGTTACTTCTCTTTG
   |||| | | | |   | ||          ||  |||||| | |  | |   || ||   | ||   ||   ||||  | |  | | |||||    || |||| ||||||||||||||||||||| ||||||||||||| || |||||  |  ||||  ||||  |||| || || | | ||||    |    |   | ||
-gcaaatttttgagttcccatgtgtcccaactttcccaatttgacatctaacccttccattcgtaattcctaaataggcattatatattatgtt--ggtgcagGTGTTCATCATCGGACCGGTGAAGCAGGTGAGGAAAGCAGAAGCCATATTAAGGGGACGAATGCTGGAAATGTATTGAGGAAAAACTTGTAGTGCTTGTG
















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|11688550|gb|BF596226.1|BF596226
EST:     TGCCGAAATTCTCACGGGAGGTCCCAAGGGCCCACCTGACAAG                         GTCTTCATCATCGGACCGGTGAAGGAGGTGAGGAAAGCCGAGGCCATGATT
genomic: TGCCGAAATTCTCACGGGAGGTCCCAAGGGCCCACCTGACAAGgttcgtatgt ... ttttatgtagGTCTTCATCATCGGACCGGTGAAGGAGGTGAGGAAAGCCGAGGCCATGATT
EST: gi|193632285|gb|FK581869.1|FK581869
EST:     TGCCGAAATTCTCACGGGAGGTCCCAAGGGCCCACCTGACAAG                         GTCTTCATCATCGGACCGGTGAAGGAGGTGAGGAAAGCCGAGGCCATGATT
genomic: TGCCGAAATTCTCACGGGAGGTCCCAAGGGCCCACCTGACAAGgttcgtatgt ... ttttatgtagGTCTTCATCATCGGACCGGTGAAGGAGGTGAGGAAAGCCGAGGCCATGATT
EST: gi|193581283|gb|FK535510.1|FK535510
EST:     TGCCGAAATTCTCACGGGAGGTCCCAAGGGCCCACCTGACAAG                         GTCTTCATCATCGGACCGGTGAAGGAGGTGAGGAAAGCCGAGGCCAT
genomic: TGCCGAAATTCTCACGGGAGGTCCCAAGGGCCCACCTGACAAGgttcgtatgt ... ttttatgtagGTCTTCATCATCGGACCGGTGAAGGAGGTGAGGAAAGCCGAGGCCAT
EST: gi|10843821|gb|BF067074.1|BF067074
EST:     TGCCGAAATTCTCACGGGAGGTCCCAAGGGCCCACCTGACAAG                         GTCTTCATCATCG
genomic: TGCCGAAATTCTCACGGGAGGTCCCAAGGGCCCACCTGACAAGgttcgtatgt ... ttttatgtagGTCTTCATCATCG
EST: gi|15287707|gb|BI471598.1|BI471598
EST:     TGCCGAAATTCTCACGGGAGGTCCCAAGGGCCCACCTGACAAG                         GTCTTCATCATCGGACCGGTGAAGGAGGTGAGGAAAGCCGAGGCCATGATT
genomic: TGCCGAAATTCTCACGGGAGGTCCCAAGGGCCCACCTGACAAGgttcgtatgt ... ttttatgtagGTCTTCATCATCGGACCGGTGAAGGAGGTGAGGAAAGCCGAGGCCATGATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acatgatttgcacatgaaaacactgttaggactaagttttcatgtttttatgtagGTCTTCATCATCGGACCGGTGAAGGAGGTGAGGAAAGCCGAGGCCATGATTCGGGGTAGAATCTTGGATATATAGTTAAGAAATGTGTTACTTCTCTTTG
                                          tgttttt  CT-rich tract
                                    ttttcatgtttttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttaaatctgttattcaacttgccattttttgttttcaatttcaaacatgatttgcacatgaaaacactgttaggactaagttttcatgtttttatgtagGTCTTCATCATCGGACCGGTGAAGGAGGTGAGGAAAGCCGAGGCCATGATTCGGGGTAGAATCTTGGATATATAGTTAAGAAATGTGTTACTTCTCTTTG

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