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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atttgctttgcacatatcacttgctttataattaaactgtctagtgtaattggtgaatgtttttgcttattggaatgatttgtgcatgtatgttttttagTTTGCTACTGAGGACCTTGTCAAAGAGGTTGAGAATTCCATTGCTGAATTCAAACGTCAAAACCAAGAATATGATGAGGAACGGGTGAAGGGACAG

Basic information

species Glycine max
transcript GLYMA02G46430.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G46430.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv19s0090g01210.t01 (Vitis vinifera), 3'ss of exon 11
------------------------------------------------------atttgctttgcac-atatcacttgctttataattaaactg--tctagtgtaattggtgaatgtttttgcttattggaatgatttgtgcatgtatgttttttagTTTGCTACTGAGGACCTTGTCAAAGAGGTTGAGAATTCCATTGCTGAATTCAAACGTCAAAACCAAGAATATGATGAGGAACGGGTGAAGGGACAG
                                                         |||||   |   | |   || | ||  |  | ||| |  |||  | ||   | |     | |      | || || ||| |||     | ||| ||  ||||| | || ||||| |||||||||||||| ||||| |||||| | |||||||||||||| || |||||||| ||||| || ||  | |  | ||||
gtcagctttcctttgtaaatatacccactagtctctgctcaatgctcatcagtgggctgcttcatattgtgttgtttccatttaagatgaacaggatctcatttacaagttacccatatacaaacaatg-aaggatatgtttgc-tctgtgttgcagTTTCCAACAGAGGAGCTTGTCAAAGAGGTGGAGAACTCCATTTCAGAATTCAAACGTCATAAACAAGAATACGATGAAGAGCGTATTAGAGAACAG
















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|13479488|gb|BG508831.1|BG508831
EST:     TAAAACAGAGTCTGGCAGTTGGTGATATTTATAAGCGTGAAAATCTGCAG                         TTTGCTACTGAGGACCTTGTCAAAGAGGTTGAGAATTCCATTGCTGAATTC
genomic: TAAAACAGAGTCTGGCAGTTGGTGATATTTATAAGCGTGAAAATCTGCAGgtagtgagtt ... tgttttttagTTTGCTACTGAGGACCTTGTCAAAGAGGTTGAGAATTCCATTGCTGAATTC
EST: gi|31461278|gb|CD403306.1|CD403306
EST:     TAAAACAGAGTCTGGCAGTTGGTGATATTTATAAGCGTGAAAATCTGCAG                         TTTGCTACTGAGGGCCTTGGTCAGAGAGGTTGAGAATTCCATTGCTGAATT
genomic: TAAAACAGAGTCTGGCAGTTGGTGATATTTATAAGCGTGAAAATCTGCAGgtagtgagtt ... tgttttttagTTTGCTACTGAGGACCTT-GTCAAAGAGGTTGAGAATTCCATTGCTGAATT
EST: gi|13481810|gb|BG511153.1|BG511153
EST:     TAAAACAGAGTCTGGCAGTTGGTGATATATATAGGCGTGAAAATCTGCAG                         TTTGCTACTGAGGACCTTGTCAAAGAGGTTGAGAATTCCATTGCTGAATTC
genomic: TAAAACAGAGTCTGGCAGTTGGTGATATTTATAAGCGTGAAAATCTGCAGgtagtgagtt ... tgttttttagTTTGCTACTGAGGACCTTGTCAAAGAGGTTGAGAATTCCATTGCTGAATTC
EST: gi|31464295|gb|CD406323.1|CD406323
EST:     TTTATAAGCGTGAAAATCTGCAG                         TTTGCTACTGAGGACCTTGTCAAAGAGGTTGAGAATTCCATTGCTGAATTC
genomic: TTTATAAGCGTGAAAATCTGCAGgtagtgagtt ... tgttttttagTTTGCTACTGAGGACCTTGTCAAAGAGGTTGAGAATTCCATTGCTGAATTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaattggtgaatgtttttgcttattggaatgatttgtgcatgtatgttttttagTTTGCTACTGAGGACCTTGTCAAAGAGGTTGAGAATTCCATTGCTGAATTCAAACGTCAAAACCAAGAATATGATGAGGAACGGGTGAAGGGACAG
                                             tgtttttt  CT-rich tract
                                        atgtatgtttttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atttgctttgcacatatcacttgctttataattaaactgtctagtgtaattggtgaatgtttttgcttattggaatgatttgtgcatgtatgttttttagTTTGCTACTGAGGACCTTGTCAAAGAGGTTGAGAATTCCATTGCTGAATTCAAACGTCAAAACCAAGAATATGATGAGGAACGGGTGAAGGGACAG

- - - - tgcacat
- - - - - - - - -cacttgc
- - - - - - - - - - - - - - - - - - ctgtcta
- - - - - - - - - - - - - - - - - - - - - - - - attggtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggaatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcatgta