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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtgtcatccgttattgctgtttcattactatgccaatggagtgttagttgatggaatcattcatttaaatactaacttagacagaactcaattttcacagCTACCATTACCACACCTTAAAGTTGGATATTTAACTGCACCTCCTGTGGGGGCATCGATTGCACCTCATAATGACTGGAAACGATCAGAATTCCTTTTGG

Basic information

species Glycine max
transcript GLYMA20G35990.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G35990.1 (Glycine max), 3'ss of exon 11
lower sequence: AT5G41950.1 (Arabidopsis thaliana), 3'ss of exon 11
gtgtcatccgttattgctgtttcattactatgccaatggagtgttagttgatggaatcattcatttaaatactaacttagacagaactcaattttcacagCTACCATTACCACACCTTAAAGTTGGATATTTAACTGCACCTCCTGTGGGGGCATCGATTGCACCTCATAATGACTGGAAACGATCAGAATTCCTTTTGG
           ||       |||| |  ||  | |      ||||   |  |||||     ||    || | ||| ||  |      |   ||||  ||||||||  | || || ||||||||||||||| |||||||||| ||||||||    ||  |||| ||||| | ||| ||||||||  |||| ||     |  
----------gtacattccattcact-ttaaacaatcaagttgttttcttgtggaaatgacca----aaaaataaattgaa------tttgttttggcagCTACCTCTCCCGCATCTTAAAGTTGGATATCTAACTGCACCACCTGTGGGCAACTCACTTGCTCCTCACAGTGATTGGAAACGCACAGAGTTTGAACTCA
















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|14205428|gb|BG839106.1|BG839106
EST:     GTTTATAGCAGTGCCTTGCGGTTGGTGCGTTCTATG                         CTACCATTACCACACCTTAAAGTTGGATATTTAACTGCACCTCCTGTGGGG
genomic: GTTTATAGCAGTGCCTTGCGGTTGGTGCGTTCTATGgtgagtacac ... attttcacagCTACCATTACCACACCTTAAAGTTGGATATTTAACTGCACCTCCTGTGGGG
EST: gi|12773285|gb|BG238212.1|BG238212
EST:     GTTTATAGCAGTGCCTTGCGGTTGGTGCGTTCTATG                         CTACCATTACCACACCTTAAAGTTGGATATTTAACTGCACCTCCTGTGGGG
genomic: GTTTATAGCAGTGCCTTGCGGTTGGTGCGTTCTATGgtgagtacac ... attttcacagCTACCATTACCACACCTTAAAGTTGGATATTTAACTGCACCTCCTGTGGGG
EST: gi|22932072|gb|BU549211.1|BU549211
EST:     GTTTATAGCAGTGCCTTGCGGTTGGTGCGTTCTATG                         CTACCATTACCACACCTTAAAGNNNGATATTTAACTGCACCTCCTGTGGGG
genomic: GTTTATAGCAGTGCCTTGCGGTTGGTGCGTTCTATGgtgagtacac ... attttcacagCTACCATTACCACACCTTAAAGTTGGATATTTAACTGCACCTCCTGTGGGG
EST: gi|298173874|gb|HO017210.1|HO017210
EST:     GTTTATAGCAGTGCCTTGCGGTTGGTGCGTTCTATG                         CTACCATTACCACACCTTAAAGTTGGATATTTAACTGCACCTCCTGTGGGG
genomic: GTTTATAGCAGTGCCTTGCGGTTGGTGCGTTCTATGgtgagtacac ... attttcacagCTACCATTACCACACCTTAAAGTTGGATATTTAACTGCACCTCCTGTGGGG
EST: gi|254324005|gb|GR836237.1|GR836237
EST:     GTTTATAGCAGTGCCTTGCGGTTGGTGCGTTCTATG                         CTACCATTACCACACCTTAAAGTTGGATATTTAACTGCACCTCCTGTGGGG
genomic: GTTTATAGCAGTGCCTTGCGGTTGGTGCGTTCTATGgtgagtacac ... attttcacagCTACCATTACCACACCTTAAAGTTGGATATTTAACTGCACCTCCTGTGGGG
EST: gi|16347758|gb|BI973353.1|BI973353
EST:     GTTTATAGCAGTGCCTTGCGGTTGGTGCGTTCTATG                         CTACCATTACCACACCTTAAAGTTGGATATTTAACTGCACCTCCTGTGGGG
genomic: GTTTATAGCAGTGCCTTGCGGTTGGTGCGTTCTATGgtgagtacac ... attttcacagCTACCATTACCACACCTTAAAGTTGGATATTTAACTGCACCTCCTGTGGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttgatggaatcattcatttaaatactaacttagacagaactcaattttcacagCTACCATTACCACACCTTAAAGTTGGATATTTAACTGCACCTCCTGTGGGGGCATCGATTGCACCTCATAATGACTGGAAACGATCAGAATTCCTTTTGG
                        tactaac  putative branch site (score: 0)
                                              ttttcac  putative PPT
         aatcattcatttaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtcatccgttattgctgtttcattactatgccaatggagtgttagttgatggaatcattcatttaaatactaacttagacagaactcaattttcacagCTACCATTACCACACCTTAAAGTTGGATATTTAACTGCACCTCCTGTGGGGGCATCGATTGCACCTCATAATGACTGGAAACGATCAGAATTCCTTTTGG

-tgtcatc
- - - - - - - tgctgtt
- - - - - - - - - - - - - -ctatgcc
- - - - - - - - - - - - - - - - - - - gagtgtt
- - - - - - - - - - - - - - - - - - - - - - - gttgatg