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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttttgagtaatatgctgtttacgagttagtaatcagcagctgatagtagattctgtgtgtacatataataagctttacttttattgtttgttgtgcagACACAGTTAATGGTTTCTCATTCCATCCATTTCTACCCCATGCTGTATCATCCTCAGGCCACCGAAGATTTGTAATTCCAGATGATGGCAATGAAGAATT

Basic information

species Glycine max
transcript GLYMA07G30960.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G30960.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv00s0181g00120.t01 (Vitis vinifera), 3'ss of exon 12
--ttttttgagtaatatgctgtttac--gagttagtaatcagcagct-gatagtagattctgtgtgtacatataataagctttacttt---tattgtttgttgtgcagACACAGTTAATGGTTTCTCATTCCATCCATTTCTACCCCATGCTGTATCATCCTCAGGCCACCGAAGATTTGTAATTCCAGATGATGGCAATGAAGAATT---
   |   |   | | ||| | ||| |  ||  | |  || |  |  |  ||  |  ||    | ||    | | |     ||||  ||   | |||| |  | | |||||||  ||||||||||||| |||||||||||||| ||    ||||  ||||| |||||||||||  |||||| ||||||   |||   |||||| || ||   
gtatgactagttgacatgttatttgctagaaattgccatgataaatttaattttgcatctattctgggtttcttacctattttaaattggtttttgtcttatatacagACACCATTAATGGTTTCTCTTTCCATCCATTTCTGCCAATGGCTGCCTCATCATCAGGCCACCGGCGATTTGGAATTCC---TGAATCCAATGAGGATTTGAG
















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|31306634|gb|CD391837.1|CD391837
EST:     CAAGTTTCGAGGCTGCTTTAG                         ACACAGTTAATGGTTTCTCATTCCATCCATTTCTACCCCATGCTGTATCAT
genomic: CAAGTTTCGAGGCTGCTTTAGgtacttaagt ... tgttgtgcagACACAGTTAATGGTTTCTCATTCCATCCATTTCTACCCCATGCTGTATCAT
EST: gi|51335098|gb|CO978964.1|CO978964
EST:     ATATAATCTCCAAACTGGGCAGTGGGTGTCAAGTTTCGAGGCTGCTTTAG                         ACACAGTTAATGGTTTCTCATTCCATCCATTTCTACCCCATGCTGTATCAT
genomic: ATATAATCTCCAAACTGGGCAGTGGGTGTCAAGTTTCGAGGCTGCTTTAGgtacttaagt ... tgttgtgcagACACAGTTAATGGTTTCTCATTCCATCCATTTCTACCCCATGCTGTATCAT
EST: gi|209724272|gb|BW666614.1|BW666614
EST:     ATATAATCTCCAAACTGGGCAGTGGGTGTCAAGTTTCGAGGCTGCTTTAG                         ACACAGTTAATGGTTTCTCATTCCATCCATTTCTACCCCATGCTGTATCAT
genomic: ATATAATCTCCAAACTGGGCAGTGGGTGTCAAGTTTCGAGGCTGCTTTAGgtacttaagt ... tgttgtgcagACACAGTTAATGGTTTCTCATTCCATCCATTTCTACCCCATGCTGTATCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagtagattctgtgtgtacatataataagctttacttttattgtttgttgtgcagACACAGTTAATGGTTTCTCATTCCATCCATTTCTACCCCATGCTGTATCATCCTCAGGCCACCGAAGATTTGTAATTCCAGATGATGGCAATGAAGAATT
                   atataataagctttac  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttttgagtaatatgctgtttacgagttagtaatcagcagctgatagtagattctgtgtgtacatataataagctttacttttattgtttgttgtgcagACACAGTTAATGGTTTCTCATTCCATCCATTTCTACCCCATGCTGTATCATCCTCAGGCCACCGAAGATTTGTAATTCCAGATGATGGCAATGAAGAATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - tgctgtt
- - - - - - - - - - - - - - - - - - - cagctga
- - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtgtgt