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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtaatatgtatgttgtttatcttgtactacttttacacattcagctcttaactccatcatcatcatcatcatcatcatttgtaattgtagCACTTTTTCGGTGGAGCAATGGGCGTTTTCACAACTCAAACCCTCTTGAGTTCTGTTGGCGTCTCTAGAAACAGAGCTGCTCCTGGGGCTGTCGCCATCA

Basic information

species Glycine max
transcript GLYMA17G00580.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G00580.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv12s0035g01870.t01 (Vitis vinifera), 3'ss of exon 2
-----------------------------------------------------------------------------gtatgtaatatgtatgttgtttatctt-----gtactacttttacacattcagctcttaactccatcatc--atcatcatcatcatcatttgtaattgtagCACTTTTTCGGTGGAGCAATGGGCGTTTTCACAACTCAAACCCTCTTGAGTTCTGTTGGCGTCTCTAGAAACAGAGCTGCTCCTGGGGCTGTCGCCATCA
                                                                                  || |||| || ||    | | |     ||   | || |    | |  | |     | | |  ||   ||  | || |   |||| | | |||||||||||| || || ||||||||||| ||||||||||| ||||| ||  ||| ||| ||||| || ||||||||| || |||||||||||||||| || ||||
gtattctcttacgtttggtgctataccataaaggcgggcttttttaggaaatgagagccatctcatatttggagaacacggatattatgaatattacaaaacattctacgtctaatttatgtgaagtggggttgctgccctaaaatacaatactgatgaatttcatgt-tcattgtagCACTTCTTTGGCGGAGCAATGGGTGTTTTCACAACACAAACACTTCTGAATTCAGTTGGAGTTTCTAGAAACCGATCTGCTCCTGGGGCTGTTGCTATCA
















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|213600078|gb|DB970224.1|DB970224
EST:     ATAGTGTTATTCCTTCCTATGTCCCCTACATGACATGGAGGGCTCTTAAG                         CACTTTTTCGGTGGAGCAATGGGCGTTTTCACAACTCAAACCCTCTTGAGT
genomic: ATAGTGTTATTCCTTCCTATGTCCCCTACATGACATGGAGGGCTCTTAAGgtatgtaata ... gtaattgtagCACTTTTTCGGTGGAGCAATGGGCGTTTTCACAACTCAAACCCTCTTGAGT
EST: gi|9259952|gb|BE348099.1|BE348099
EST:     ATAGTGTTATTCCTTCCTATGTCCCCTACATGACATGGAGGGCTCTTAAG                         CACTTTTTCGGTGGAGCAATGGGCGTTTTCACAACTCAAACCCTCTTGAGT
genomic: ATAGTGTTATTCCTTCCTATGTCCCCTACATGACATGGAGGGCTCTTAAGgtatgtaata ... gtaattgtagCACTTTTTCGGTGGAGCAATGGGCGTTTTCACAACTCAAACCCTCTTGAGT
EST: gi|20075889|gb|BQ094672.1|BQ094672
EST:     ATAGTGTTATTCCTTCCTATGTCCCCTACATGACATGGAGGGCTCTTAAG                         CACTTTTTCGGTGGAGCAATGGGCGTTTTCACAACTCAAACCCTCTTGAGT
genomic: ATAGTGTTATTCCTTCCTATGTCCCCTACATGACATGGAGGGCTCTTAAGgtatgtaata ... gtaattgtagCACTTTTTCGGTGGAGCAATGGGCGTTTTCACAACTCAAACCCTCTTGAGT
EST: gi|213589361|gb|DB961694.1|DB961694
EST:     ATAGTGTTATTCCTTCCTATGTCCCCTACATGACATGGAGGGCTCTTAAG                         CACTTTTTCGGTGGAGCAATGGGCGTTTTCACAACTCAAACCCTCTTGAGT
genomic: ATAGTGTTATTCCTTCCTATGTCCCCTACATGACATGGAGGGCTCTTAAGgtatgtaata ... gtaattgtagCACTTTTTCGGTGGAGCAATGGGCGTTTTCACAACTCAAACCCTCTTGAGT
EST: gi|24136013|gb|BU926523.1|BU926523
EST:     ATAGTGTTATTCCTTCCTATGTCCCCTACATGACATGGAGGGCTCTTAAG                         CACTTTTTCGGTGGAGCAATGGGCGTTTTCACAACTCAAACCCTCTTGAGT
genomic: ATAGTGTTATTCCTTCCTATGTCCCCTACATGACATGGAGGGCTCTTAAGgtatgtaata ... gtaattgtagCACTTTTTCGGTGGAGCAATGGGCGTTTTCACAACTCAAACCCTCTTGAGT
EST: gi|6070425|gb|AW099812.1|AW099812
EST:     ATAGTGTTATTCCTTCCTATGTCCCCTACATGACATGGAGGGCTCTTAAG                         CACTTTTTCGGTGGAGCAATGGGCGTTTTCACAACTCAAACCCTCTTGAGT
genomic: ATAGTGTTATTCCTTCCTATGTCCCCTACATGACATGGAGGGCTCTTAAGgtatgtaata ... gtaattgtagCACTTTTTCGGTGGAGCAATGGGCGTTTTCACAACTCAAACCCTCTTGAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacattcagctcttaactccatcatcatcatcatcatcatcatttgtaattgtagCACTTTTTCGGTGGAGCAATGGGCGTTTTCACAACTCAAACCCTCTTGAGTTCTGTTGGCGTCTCTAGAAACAGAGCTGCTCCTGGGGCTGTCGCCATCA
          tcttaac  putative branch site (score: 2)
                                         atttgtaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtaatatgtatgttgtttatcttgtactacttttacacattcagctcttaactccatcatcatcatcatcatcatcatttgtaattgtagCACTTTTTCGGTGGAGCAATGGGCGTTTTCACAACTCAAACCCTCTTGAGTTCTGTTGGCGTCTCTAGAAACAGAGCTGCTCCTGGGGCTGTCGCCATCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT