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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacagttctttttcccctgcttttgtgtgtctgtgtgttgcttgcacttccgtttcacatgcttctttagtttctttcttcccttttaaagtttaaatgtgcagCCTTGGACAGTGATGATCTACTTTATCTCAAAGAGCAAATGGAAGCCGAGGAGGATGCAGAACGCCTCCTGCGTCGCACTGAAAAACGGGCATTTGCTGC

Basic information

species Glycine max
transcript GLYMA09G28980.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G28980.2 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os02g42540.1 (Oryza sativa), 3'ss of exon 3
gtacagttctttttcccctgcttttgtgtgtctgtgtgttgcttgcacttccgtttcacatgcttctttagtttctttcttcccttttaaagtttaaatgtgcagCCTTGGACAGTGATGATCTACTTTATCTCAAAGAGCAAATGGAAGCCGAGGAGGATGCAGAACGCCTCCTGCGTCGCACTGAAAAACGGGCATTTGCTGC
           | |  | |||| |  ||| | | ||| |     | |  |  ||   |  | | || |||  ||  || ||   | |  | ||||     | |||| ||||||||||||||| |||| || || ||||| ||||||||||| ||||| || ||||| || || || || || ||||| || || |||||||||||
----------gtatttcatgctctc-tgtttttttgtat-----gaatctgtgt---aggttcctcattaactttgtt-ttatgtgtcgatgtttt----ttcagCATTGGACAGTGATGATTTACTGTACCTAAAAGAACAAATGGAAGCTGAGGAAGACGCAGAGCGTCTTCTTCGCCGTACTGAGAAGCGTGCATTTGCTGC

upper sequence: GLYMA09G28980.2 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G146786_T01 (Zea mays), 3'ss of exon 3
gtacagttctttttcccctgcttttgtgtgtctgtgtgttgcttgcacttccgtttcacatgcttctttagtttctttcttcccttttaaagtttaaatgtgcagCCTTGGACAGTGATGATCTACTTTATCTCAAAGAGCAAATGGAAGCCGAGGAGGATGCAGAACGCCTCCTGCGTCGCACTGAAAAACGGGCATTTGCTGC
                                   || || | |||   |    |    |  |  || ||   | | |    || ||   |   |   | | |||| |||||||| |||||| | ||||| || ||||||||||||||||| || || |||||||| ||||| || ||||  ||||| || ||||||||||||||
-----------------------------------gtatttcatgcttcttttataggaagacccctgtaaagtttgtagctcccttgttaaccttgttcttcagCATTGGACAGCGATGATTTGCTTTACCTGAAAGAGCAAATGGAAGCTGAAGAAGATGCAGAGCGCCTTCTTCGTCATACTGAGAAGCGGGCATTTGCTGC

upper sequence: GLYMA09G28980.2 (Glycine max), 3'ss of exon 3
lower sequence: AT1G73350.2 (Arabidopsis thaliana), 3'ss of exon 3
gtacagttctttttcccctgcttttgtgtgtctgtgtgttgcttgcacttccgtttcacatgcttctttagtttctttcttcccttttaaagtttaaatgtgcagCCTTGGACAGTGATGATCTACTTTATCTCAAAGAGCAAATGGAAGCCGAGGAGGATGCAGAACGCCTCCTGCGTCGCACTGAAAAACGGGCATTTGCTGC
||||   ||| | || |   ||||| |         ||||  | |  ||||  ||  |  ||  || |     |  |||||         |||||     || ||| || || || || ||| |||||||||| ||||| || |||||||| ||||| ||||||||||| || ||| | || ||||| |||||||| ||||||||
gtaccaatctctctctctctctttttt---------tgtttttcgttcttcttttgtagttgtgtcatggccataattctt--------gagttt---cttgtagCTTTAGATAGCGACGATTTACTTTATCTGAAAGAACAGATGGAAGCAGAGGAAGATGCAGAACGTCTTCTGAGACGAACTGAGAAACGGGCTTTTGCTGC

upper sequence: GLYMA09G28980.2 (Glycine max), 3'ss of exon 3
lower sequence: AT1G73350.1 (Arabidopsis thaliana), 3'ss of exon 3
gtacagttctttttcccctgcttttgtgtgtctgtgtgttgcttgcacttccgtttcacatgcttctttagtttctttcttcccttttaaagtttaaatgtgcagCCTTGGACAGTGATGATCTACTTTATCTCAAAGAGCAAATGGAAGCCGAGGAGGATGCAGAACGCCTCCTGCGTCGCACTGAAAAACGGGCATTTGCTGC------
||||   ||| | || |   ||||| |         ||||  | |  ||||  ||  |  ||  || |     |  |||||         |||||     || ||| || || || || ||| |||||||||| ||||| || |||||||| ||||| ||||||||||| || ||| | || ||||| |||||||| ||||||||      
gtaccaatctctctctctctctttttt---------tgtttttcgttcttcttttgtagttgtgtcatggccataattctt--------gagttt---cttgtagctttagATAGCGACGATTTACTTTATCTGAAAGAACAGATGGAAGCAGAGGAAGATGCAGAACGTCTTCTGAGACGAACTGAGAAACGGGCTTTTGCTGCCTTTAA

upper sequence: GLYMA09G28980.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv16s0039g00280.t01 (Vitis vinifera), 3'ss of exon 3
gtacagttctttttcccctgcttttgtgtgtctg---tgtgttgcttgcacttccgtttcacatgcttctttagtttctttcttcccttt--taaagtttaaatgtgcagCCTTGGACAGTGATGATCTACTTTATCTCAAAGAGCAAATGGAAGCCGAGGAGGATGCAGAACGCCTCCTGCGTCGCACTGAAAAACGGGCATTTGCTGC
|||| ||   |    | ||     || || | ||     | || | | || |          |   || ||| |||| ||| |    |||  | |||||| ||| |||||| |||||||||||||||||||| |||||||| ||||| ||||| || ||||||||||||||||||||  | || ||||| || || || || ||||||||
gtactgtctctgcctctctctggctgggtttttggttcctttttccttcaatatatacctttagtttttttttgtttttttttgaattttggttaagtttgaatatgcagCATTGGACAGTGATGATCTACTCTATCTCAAGGAGCAGATGGAGGCTGAGGAGGATGCAGAACGCCTTTTACGCCGCACAGAGAAGCGTGCCTTTGCTGC

upper sequence: GLYMA09G28980.2 (Glycine max), 3'ss of exon 3
lower sequence: PP1S402_46V6.1 (Physcomitrella patens), 3'ss of exon 3
------------------------gtacagttctttttcccctgcttttgtgtgtctgtgtgttgcttgcact------tccgtt----tcacatgcttctttagtttc--tttcttcccttttaaagt------ttaaatgtgcagCCTTGGACAGTGATGATCTACTTTATCTCAAAGAGCAAATGGAAGCCGAGGAGGATGCAGAACGCCTCCTGCGTCGCACTGAAAAACGGGCATTTGCTGC
                        | ||| |  | |      | ||    ||    ||| || ||| |||| |      ||| ||    |  |    |   ||| ||    || ||  ||| |||| |       | |||||  |||| ||||| ||||||||| | |||||  | ||||||||||||||||| ||||||||||| || ||  | | ||| || ||||| |||||||| || ||   
gtacagctcaaaacgctatttttagcacattgatatcctatgtactgc-atgctgatgtttgatgcatgcagtgaagactccattgtgatggcggagtgtgttaattatcattgctgacctcttaatgcaattcatgaaatgcacagCATTGGATAGTGATGATTTGCTTTACTTAAAAGAGCAAATGGAAGCTGAGGAGGATGCGGAGCGGTTGCGGCGACGAACTGAGAAACGGGCGTTCGCA--

upper sequence: GLYMA09G28980.2 (Glycine max), 3'ss of exon 3
lower sequence: EFJ15111 (Selaginella moellendorffii), 3'ss of exon 3
gtacagttctttttcccctgcttttgtgtgtctgtgtgttgcttgcacttccgtttcacatgcttctttagtttctttcttcccttttaaagtttaaatgtgcagCCTTGGACAGTGATGATCTACTTTATCTCAAAGAGCAAATGGAAGCCGAGGAGGATGCAGAACGCCTCCTGCGTCGCACTGAAAAACGGGCATTTGCTGC
|||| ||||||    |   | |||||  | ||  ||  || ||         | |     |  |||||   |||||  | |     |   || ||   | ||||||  | ||||| |||||||| || || |||||||| || |||||||||||||||||||| ||  |                                    
gtactgttcttca--cttagtttttgaat-tccttgcatttctctaggaaaagctcgttttttttcttggttttctcacgttttcctgggaggttc--tttgcagCTCTTGACAGCGATGATCTTCTCTACCTCAAAGAACAGATGGAAGCCGAGGAGGATGCCGAGAGG-----------------------------------

upper sequence: GLYMA09G28980.2 (Glycine max), 3'ss of exon 3
lower sequence: EFJ16082 (Selaginella moellendorffii), 3'ss of exon 3
gtacagttctttttcccctgcttttgtgtgtctgtgtgttgcttgcacttccgtttcacatgcttctttagtttctttcttcccttttaaagtttaaatgtgcagCCTTGGACAGTGATGATCTACTTTATCTCAAAGAGCAAATGGAAGCCGAGGAGGATGCAGAACGCCTCCTGCGTCGCACTGAAAAACGGGCATTTGCTGC
|||| ||||||    |   | |||||  | ||  ||  || ||   |        ||   |  |||||   |||||  | |     |   ||  |   | ||||||  | ||||| |||||||| || || |||||||| || |||||||||||||||||||| ||  |                                    
gtactgttcttca--cttagtttttgaat-tccttgcatttctc-taggaaaagctcgtttttttcttggttttctcacgttttcctgggagggtc--tttgcagCTCTTGACAGCGATGATCTTCTCTACCTCAAAGAACAGATGGAAGCCGAGGAGGATGCCGAGAGG-----------------------------------

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|51335221|gb|CO979087.1|CO979087
EST:     GATGCAAGAGGTTGCTGGGGAGCGCGGAGGTTACCTTCATGGACGAGGCG                         CCTTGGACAGTGATGATCTACTTTATCTCAAAGAGCAAATGGAAGCCGAGG
genomic: GATGCAAGAGGTTGCTGGGGAGCGCGGAGGTTACCTTCATGGACGAGGCGgtacagttct ... aaatgtgcagCCTTGGACAGTGATGATCTACTTTATCTCAAAGAGCAAATGGAAGCCGAGG
EST: gi|120532801|gb|EH260934.1|EH260934
EST:     ATGGACGAGGCG                         CCTTGGACAGTGATGATCTACTTTATTCTCAAAGAGCAAATGGAAGCCGAG
genomic: ATGGACGAGGCGgtacagttct ... aaatgtgcagCCTTGGACAGTGATGATCTACTTTA-TCTCAAAGAGCAAATGGAAGCCGAG
EST: gi|18040197|gb|BM308491.1|BM308491
EST:     GATGCAAGAGGTTGCTGGGGAGCGCGGAGGTTACCTTCATGGACGAGGCG                         CCTTGGACAGTGATGATCTACTTTATCTCAAAGAGCAAATGGAAGCCGAGG
genomic: GATGCAAGAGGTTGCTGGGGAGCGCGGAGGTTACCTTCATGGACGAGGCGgtacagttct ... aaatgtgcagCCTTGGACAGTGATGATCTACTTTATCTCAAAGAGCAAATGGAAGCCGAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccgtttcacatgcttctttagtttctttcttcccttttaaagtttaaatgtgcagCCTTGGACAGTGATGATCTACTTTATCTCAAAGAGCAAATGGAAGCCGAGGAGGATGCAGAACGCCTCCTGCGTCGCACTGAAAAACGGGCATTTGCTGC
                                  ttttaaagtttaaatg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacagttctttttcccctgcttttgtgtgtctgtgtgttgcttgcacttccgtttcacatgcttctttagtttctttcttcccttttaaagtttaaatgtgcagCCTTGGACAGTGATGATCTACTTTATCTCAAAGAGCAAATGGAAGCCGAGGAGGATGCAGAACGCCTCCTGCGTCGCACTGAAAAACGGGCATTTGCTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC