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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tattgtttctgtgatgaacacgttatgcaaaatagtacatctagtccttgaatatattgattcttgttttgctgatttgcgtttaattatccttgtgtagGATGTTAAGTCTGCAGACAGGATCTCAGATGCTGCTCTAGAATCTGCGGTTCTGCAATTTATCCCATGCATCCGTTCTGGTAGTTTTGCTGACATTGGGC

Basic information

species Glycine max
transcript GLYMA10G01270.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G01270.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv07s0005g02110.t01 (Vitis vinifera), 3'ss of exon 1
------tattgtttctgtgatgaacacgttatgcaaaatagtacatctagtccttgaatatattgattcttgttttgctgatttgcgtttaattatccttgtgtagGATGTTAAGTCTGCAGACAGGATCTCAGATGCTGCTCTAGAATCTGCGGTTCTGCAATTTATCCCATGCATCCGTTCTGGTAGTTTTGCTGACATTGGGC
       ||  | |  ||||| | ||| |   |    |||     |  | |   |||    |   |  ||||   |  |||||  | |||  || |  |    |||||| | || ||| | || |  |   |||| ||| |||| ||||||||  || |||||||| |||| |||||||| |||||||| |||||||||||||| |
tgatctgatcatctgagtgat-agcacttgtggttttataaatagtagattttctgagggaa--aacacttgacata-tgattccccttt--tttttttgtcctagGATATAAAATCTCCTGAGAAAAATCCAGACGCTACTCTTGAATCTGCTATTGTGCAATTTGTCCCTTGCATCCGATCTGGTAGCTTTGCTGACATTGGAC
















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|209722665|gb|BW654672.1|BW654672
EST:     GAGTTCGTGCCACTGAGTCGGTCTCCGCCGAGTTACTCACTTCACAAGAA                         GATGTTAAGTCTGCAGACAGGATCTCAGATGCTGCTCTAGAATCTGCGGTT
genomic: GAGTTCGTGCCACTGAGTCGGTCTCCGCCGAGTTACTCACTTCACAAGAAgtcagttttt ... ccttgtgtagGATGTTAAGTCTGCAGACAGGATCTCAGATGCTGCTCTAGAATCTGCGGTT
EST: gi|9204306|gb|BE330530.1|BE330530
EST:     GAGTTCGTGCCACTGAGTCGGTCTCCGCCGAGTTACTCACTTCACAAGAA                         GATGTTAAGTCTGCAGACAGGATCTCAGATGCTGCTCTAGAATCTGCGGTT
genomic: GAGTTCGTGCCACTGAGTCGGTCTCCGCCGAGTTACTCACTTCACAAGAAgtcagttttt ... ccttgtgtagGATGTTAAGTCTGCAGACAGGATCTCAGATGCTGCTCTAGAATCTGCGGTT
EST: gi|6567337|gb|AW234948.1|AW234948
EST:     GAGTTCGTGCCACTGAGTCGGTCTCCGCCGAGTTACTCACTTCACAAGAA                         GATGTTAAGTCTGCAGACAGGATCTCAGATGCTGCTCTAGAATCTG
genomic: GAGTTCGTGCCACTGAGTCGGTCTCCGCCGAGTTACTCACTTCACAAGAAgtcagttttt ... ccttgtgtagGATGTTAAGTCTGCAGACAGGATCTCAGATGCTGCTCTAGAATCTG
EST: gi|298187561|gb|HO034710.1|HO034710
EST:     GAGTTCGTGCCACTGAGTCGGTCTCCGCCGAGTTACTCACTTCACAAGAA                         GATGTTAAGTCTGCAGACAGGATCTCAGATGCTGCTCTAGAATCTGCGGTT
genomic: GAGTTCGTGCCACTGAGTCGGTCTCCGCCGAGTTACTCACTTCACAAGAAgtcagttttt ... ccttgtgtagGATGTTAAGTCTGCAGACAGGATCTCAGATGCTGCTCTAGAATCTGCGGTT
EST: gi|254331465|gb|GR845937.1|GR845937
EST:     GAGTTCGTGCCACTGAGTCGGTCTCCGCCGAGTTACTCACTTCACAAGAA                         GATGTTAAGTCTGCAGACAGGATCTCAGATGCTGCTCTAGAATCTGCGGTT
genomic: GAGTTCGTGCCACTGAGTCGGTCTCCGCCGAGTTACTCACTTCACAAGAAgtcagttttt ... ccttgtgtagGATGTTAAGTCTGCAGACAGGATCTCAGATGCTGCTCTAGAATCTGCGGTT
EST: gi|192296589|gb|FG991651.1|FG991651
EST:     GAGTTCGTGTCACTGAGTCGGTCTCCGCCGAGTTACTCACTTCACAAGAA                         GATGTTAAGTCTGCAGACAGGATCTCAGATGCTGCTCTAGAATCTGCGGTT
genomic: GAGTTCGTGCCACTGAGTCGGTCTCCGCCGAGTTACTCACTTCACAAGAAgtcagttttt ... ccttgtgtagGATGTTAAGTCTGCAGACAGGATCTCAGATGCTGCTCTAGAATCTGCGGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccttgaatatattgattcttgttttgctgatttgcgtttaattatccttgtgtagGATGTTAAGTCTGCAGACAGGATCTCAGATGCTGCTCTAGAATCTGCGGTTCTGCAATTTATCCCATGCATCCGTTCTGGTAGTTTTGCTGACATTGGGC
                                         ttatcctt  CT-rich tract
     aatatattgattctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tattgtttctgtgatgaacacgttatgcaaaatagtacatctagtccttgaatatattgattcttgttttgctgatttgcgtttaattatccttgtgtagGATGTTAAGTCTGCAGACAGGATCTCAGATGCTGCTCTAGAATCTGCGGTTCTGCAATTTATCCCATGCATCCGTTCTGGTAGTTTTGCTGACATTGGGC

- - gtttctg
- - - - - - - - - - - -tatgcaa
- - - - - - - - - - - - - - - - - - - - - - -ccttgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gctgatt