Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   		18  
 5'  3'   		19  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctggtcttgcactggttttaaatgatcttatcctatatgtaaacgtttttgtacaagtgcatttcctgaagctttgtgggatgatgatgtatttggcagTTGAAAGGTTTTGAGTTTATAAAAGCAGTTCACCTTGACTCAATTCCATTTGACATGGAACGTGACCTTATCACTCCAACATACAAGAAGAAGAGGCCAC

Basic information

species Glycine max
transcript GLYMA01G43470.2
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G43470.2 (Glycine max), 3'ss of exon 17
lower sequence: GRMZM2G152127_T01 (Zea mays), 3'ss of exon 17
----------------------tctggtcttgcactggttttaaatgatcttatcctatatgtaaacgtttttgtacaagtgcatttcctgaagctttgtgggatgatgatgtatttggcagTTGAAAGGTTTTGAGTTTATAAAAGCAGTTCACCTTGACTCAATTCCATTTGACATGGAACGTGACCTTATCACTCCAACATACAAGAAGAAGAGGCCAC
                        | ||  |  |    |||| |||||| ||   |          | |      |  |    || |   |  | | | |   ||  || || |     ||| | ||||| |||||| | || |  || ||||| || ||| |    || || |||||||| || ||||||||||| || || |||||||||||| ||||||
gtaataagactgaaaccgaaaacgtcgttctctatctattttgaatgattttgctcctcgcagtggcctcagcaaatgatcttatgtatcgtcgttctctta-atcctggtgca----acagCTCAAAGGCTTTGAGCTCATCAGGGCTGTTCATCTGGACCCCGCACCGTTCGACATGGAGCGCGACCTTATCACCCCGACGTACAAGAAGAAGCGGCCAC

upper sequence: GLYMA01G43470.2 (Glycine max), 3'ss of exon 17
lower sequence: AT4G11030.1 (Arabidopsis thaliana), 3'ss of exon 17
tctggtcttgcactggttttaaatgatcttatcctatatgtaaacgtttttgtacaagtgcatttcctgaagctttgtgggatgatgatgtat-ttggcagTTGAAAGGTTTTGAGTTTATAAAAGCAGTTCACCTTGACTCAATTCCATTTGACATGGAACGTGACCTTATCACTCCAACATACAAGAAGAAGAGGCCAC
                            ||    ||| | |      | || |  |  || | ||  ||  | ||||   | | |   |     || | ||||||| ||||||||| | |||||||  ||||| || ||  || |  | || ||||||||||| |||||| | |||||||| ||||| ||||||||||| |
---------------------------gtttctttatttttctcttctcttctttatttggagtttttg--gttttggttgtttaccctccgcgtttgtagTTGAAGGGTTTTGAGATCATAAAAGATGTTCATCTGGAACCAGTGGCGTTCGACATGGAACGAGACCTTCTTACTCCAACCTACAAAAAGAAGAGGCCTC

upper sequence: GLYMA01G43470.2 (Glycine max), 3'ss of exon 17
lower sequence: Vv02s0025g01410.t01 (Vitis vinifera), 3'ss of exon 17
------------------------------------------tctggtcttgcactggttttaaatgatcttatcctatatgtaaacgtttttgtacaagtgcatttcctgaagctttgtgggatgatgat-gtatttggcagTTGAAAGGTTTTGAGTTTATAAAAGCAGTTCACCTTGACTCAATTCCATTTGACATGGAACGTGACCTTATCACTCCAACATACAAGAAGAAGAGGCCAC
                                           |   | || |||       ||  ||    | | |  |   |    ||    |   |  ||   || |     ||||||   |    || ||  ||||||||||||||||||||||||| | |||||||||||||||||| |  | |||||||| |||||||||||||| |||||||||||||| |||||||||||||| |
gttccttttctctaccctttctttattaccatttggctgtgacccattttttcacctccaccaagagaaaa-agcatggaataacttattgacctctgaaagctactcgtctgattttgtgatttttaaattgttcttggcagTTGAAAGGTTTTGAGTTTGTCAAAGCAGTTCACCTTGACCCTGTGCCATTTGATATGGAACGTGACCTGATCACTCCAACATATAAGAAGAAGAGGCCCC

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|254347181|gb|GR856851.1|GR856851
EST:     CAAAAAGTTACATAATTGAAGAGCTCTCAAAGATTGCGAAGGAAAAGAAG                         TTGAAAGGTTTTGAGTTTATAAAAGCAGTTCACCTTGACTCAATTCCATTT
genomic: CAAAAAGTTACATAATTGAAGAGCTCTCAAAGATTGCGAAGGAAAAGAAGgtgttttttt ... tatttggcagTTGAAAGGTTTTGAGTTTATAAAAGCAGTTCACCTTGACTCAATTCCATTT
EST: gi|151396024|gb|EV265901.1|EV265901
EST:     CAAAAAGTTACATAATTGAAGAGCTCTCAAAGATTGCGAAGGAAAAGAAG                         TTGAAAGGTTTTGAGTTTATAAAAGCAGTTCACCTTGACTCAATTCCATTT
genomic: CAAAAAGTTACATAATTGAAGAGCTCTCAAAGATTGCGAAGGAAAAGAAGgtgttttttt ... tatttggcagTTGAAAGGTTTTGAGTTTATAAAAGCAGTTCACCTTGACTCAATTCCATTT
EST: gi|19270925|gb|BM887181.1|BM887181
EST:     CAAAAAGTTACATAATTGAAGAGCTCTCAAAGATTGCGAAGGAAAAGAAG                         TTGAAAGGTTTTGAGTTTATAAAAGCAGTTCACCTTGACTCAATTCCATTT
genomic: CAAAAAGTTACATAATTGAAGAGCTCTCAAAGATTGCGAAGGAAAAGAAGgtgttttttt ... tatttggcagTTGAAAGGTTTTGAGTTTATAAAAGCAGTTCACCTTGACTCAATTCCATTT
EST: gi|23733236|gb|BU764804.1|BU764804
EST:     CAAAAAGTTACATAATTGAAGAGCTCTCAAAGATTGCGAAGGAAAAGAAG                         TTGAAAGGTTTTGAGTTTATAAAAGCAGTTCACCTTGACTCAATTCCATTT
genomic: CAAAAAGTTACATAATTGAAGAGCTCTCAAAGATTGCGAAGGAAAAGAAGgtgttttttt ... tatttggcagTTGAAAGGTTTTGAGTTTATAAAAGCAGTTCACCTTGACTCAATTCCATTT
EST: gi|208119453|gb|GD917386.1|GD917386
EST:     CAAAAAGTTACATAATTGAAGAGCTCTCAAAGATTGCGAAGGAAAAGAAG                         TTGAAAGGTTTTGAGTTTATAAAAGCAGTTCACCTTGACTCAATTCCATTT
genomic: CAAAAAGTTACATAATTGAAGAGCTCTCAAAGATTGCGAAGGAAAAGAAGgtgttttttt ... tatttggcagTTGAAAGGTTTTGAGTTTATAAAAGCAGTTCACCTTGACTCAATTCCATTT
EST: gi|51342594|gb|CO983564.1|CO983564
EST:     CAAAAAGTTACATAATTGAAGAGCTCTCAAAGATTGCGAAGGAAAAGAAG                         TTGAAAGGTTTTGAGTTTATAAAAGCAGTTCACCTTGACTCAATTCCATTT
genomic: CAAAAAGTTACATAATTGAAGAGCTCTCAAAGATTGCGAAGGAAAAGAAGgtgttttttt ... tatttggcagTTGAAAGGTTTTGAGTTTATAAAAGCAGTTCACCTTGACTCAATTCCATTT
EST: gi|11275038|gb|BF325362.1|BF325362
EST:     CAAAAAGTTACATAATTGAAGAGCTCTCAAAGATTGCGAAGGAAAAGAAG                         TTGAAAGGTTTTGAGTTTATAAAAGCAGTTCACCTTGACTCAATTCCATTT
genomic: CAAAAAGTTACATAATTGAAGAGCTCTCAAAGATTGCGAAGGAAAAGAAGgtgttttttt ... tatttggcagTTGAAAGGTTTTGAGTTTATAAAAGCAGTTCACCTTGACTCAATTCCATTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttttgtacaagtgcatttcctgaagctttgtgggatgatgatgtatttggcagTTGAAAGGTTTTGAGTTTATAAAAGCAGTTCACCTTGACTCAATTCCATTTGACATGGAACGTGACCTTATCACTCCAACATACAAGAAGAAGAGGCCAC
                                          atgtattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctggtcttgcactggttttaaatgatcttatcctatatgtaaacgtttttgtacaagtgcatttcctgaagctttgtgggatgatgatgtatttggcagTTGAAAGGTTTTGAGTTTATAAAAGCAGTTCACCTTGACTCAATTCCATTTGACATGGAACGTGACCTTATCACTCCAACATACAAGAAGAAGAGGCCAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG