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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgatttgctttttcagagagatgatattctctttggcctccttgtgctcttctttatttccactggaaagcttgttcacatatcttttgttgtatgtcattcttgctccagAGGTTTGCTGCGTTCTTAGCCCCTTTGACTTCTGGTCGTGTTACTATTGCTGTTAGTGCTGTTTACATATCCAAG

Basic information

species Glycine max
transcript GLYMA06G43840.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G43840.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv12s0028g02660.t01 (Vitis vinifera), 3'ss of exon 5
gtgatttgctttttcagagagatgatattctctttggcctccttgtgctcttctttatttccactggaaagcttgttcacatatcttttgttgtatgtcattcttgctccagAGGTTTGCTGCGTTCTTAGCCCCTTTGACTTCTGGTCGTGTTACTATTGCTGTTAGTGCTGTTTACATATCCAAG
|| ||    |||||| |  ||   ||||  |||   |    |    |    |||   ||||   || |    |  ||  |  | | ||     ||||| ||| ||  | ||||||||||| || ||| ||||||||||||| || ||||||||||| |||||    ||||| ||||||  ||| |||
gtaat--aatttttctggtag-caatatcttct---gatggcaaaagggtctctgactttctgttgaagtagtgattttctaaacctt----atatgtgattatt-tttcagAGGTTTGCGGCCTTCCTAGCCCCTTTGACATCAGGTCGTGTTACCATTGCAACCAGTGCGGTTTACTCATCAAAG
















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|9902565|gb|BE611596.1|BE611596
EST:     ATGTTTCACCAAGTGGTGAATATTTGAGTGCAATAAAGAATGCAGATCAG                         AGGTTTGCTGCGTTCTTAGCCCCTTTGACTTCTGGTCGTGTTACTATTGCT
genomic: ATGTTTCACCAAGTGGTGAATATTTGAGTGCAATAAAGAATGCAGATCAGgtgatttgct ... cttgctccagAGGTTTGCTGCGTTCTTAGCCCCTTTGACTTCTGGTCGTGTTACTATTGCT
EST: gi|33390491|gb|CA853686.1|CA853686
EST:     ATGTTTCACCAAGTGGTGAATATTTGAGTGCAATAAAAAATGCAGATCAG                         AGGTTTGCTGCATTCTTAGCCCCTTTGACTTCTGGTCGTGTTACCATTGCT
genomic: ATGTTTCACCAAGTGGTGAATATTTGAGTGCAATAAAGAATGCAGATCAGgtgatttgct ... cttgctccagAGGTTTGCTGCGTTCTTAGCCCCTTTGACTTCTGGTCGTGTTACTATTGCT
EST: gi|12774606|gb|BG239533.1|BG239533
EST:     GAATATTTGAGTGCAATAAAGAATGCAGATCAG                         AGGTTTGCTGCGTTCTTAGCCCCTTTGACTTCTGGTCGTGTTACTATTGCT
genomic: GAATATTTGAGTGCAATAAAGAATGCAGATCAGgtgatttgct ... cttgctccagAGGTTTGCTGCGTTCTTAGCCCCTTTGACTTCTGGTCGTGTTACTATTGCT
EST: gi|192331590|gb|FK023437.1|FK023437
EST:     ATGTTTCACCAAGTGGTGAATATTTGAGTGCAATAAAGAATGCAGATCAG                         AGGTTTGCTGCGTTCTTAGCCCCTTTGACTTCTGGTCGTGTTACTATTGCT
genomic: ATGTTTCACCAAGTGGTGAATATTTGAGTGCAATAAAGAATGCAGATCAGgtgatttgct ... cttgctccagAGGTTTGCTGCGTTCTTAGCCCCTTTGACTTCTGGTCGTGTTACTATTGCT
EST: gi|7691519|gb|AW759645.1|AW759645
EST:     ATGTTTCACCAAGTGGTGAATATTTGAGTGCAATAAAGAATGCAGATCAG                         AGGTTTGCTGCGTTCTTAGCCCCTTTGACTTCTGGTCGTGTTACTATTGCT
genomic: ATGTTTCACCAAGTGGTGAATATTTGAGTGCAATAAAGAATGCAGATCAGgtgatttgct ... cttgctccagAGGTTTGCTGCGTTCTTAGCCCCTTTGACTTCTGGTCGTGTTACTATTGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttccactggaaagcttgttcacatatcttttgttgtatgtcattcttgctccagAGGTTTGCTGCGTTCTTAGCCCCTTTGACTTCTGGTCGTGTTACTATTGCTGTTAGTGCTGTTTACATATCCAAG
                                           ttcttgctcc  CT-rich tract
                       atatctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgatttgctttttcagagagatgatattctctttggcctccttgtgctcttctttatttccactggaaagcttgttcacatatcttttgttgtatgtcattcttgctccagAGGTTTGCTGCGTTCTTAGCCCCTTTGACTTCTGGTCGTGTTACTATTGCTGTTAGTGCTGTTTACATATCCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT