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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtggaaatttgttttgtaaatttgtaatatatgaaatatgacatattccattatgtttggaatgaatttgctttataactttgcatgctacatatttgcagAAAATCAAGAACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGATAACCCAG

Basic information

species Glycine max
transcript GLYMA20G23080.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G23080.2 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os07g14270.3 (Oryza sativa), 3'ss of exon 7
gtttgtggaaatttgttttgtaaatttgtaatatatgaaata-tgacatattccattatgtttggaatgaatttgctttataactttgcatgctacatatttgcagAAAATCAAGAACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGATAACCCAG
   |||| | || |||||  | |    |    |  ||||| | |  |||||| | |  | | ||  || ||  || ||  |                  ||| ||||||||||||||||| |||||  |||| ||||||||||||||  |||| || |||||||
--gtgtgaatatctgtttactgatgcagatgcacttgaaacacttgcatatttc-tggtttctgacataaacatgtttctt------------------tttccagAAAATCAAGAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGACAACCCAG

upper sequence: GLYMA20G23080.2 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G358059_T01 (Zea mays), 3'ss of exon 7
gtttgtggaaatttgttttgtaaatttgtaatatatgaaatatgacatattccattatgtttggaatgaatttgctttataactttgcatgctacatatttgcagAAAATCAAGAACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGATAACCCAG
   | ||| | ||  ||||   ||  | |||  |   |   ||  |||||||    || | ||  |  |  ||| || |     ||||              ||||||||||||||||| |||||  | || ||||||||||||||  ||||||| |||||||
--gtatggcagttcctttt---aacctataaactgacagcaatt-catattctg--atatctgacagcatgttgtttcac----ttgc--------------cagAAAATCAAGAACCCGAACTACCAGGGTAAATGGAAGGCACCTATGATTGACAACCCAG

upper sequence: GLYMA20G23080.2 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G074687_T01 (Zea mays), 3'ss of exon 7
gtttgtggaaatttgttttgtaaat--ttgtaatatatgaaatatgacatattccattatgtttggaatgaatttgctttataactttgcatgctacatatttgcagAAAATCAAGAACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGATAACCCAG
              || | | |  |  ||| | | |||  ||  ||||||      | || ||  ||       |   | | |     ||||| | ||  ||  ||||||||||||||||| |||||  | || ||||||||||||||  ||||||| |||||||
--------------gtatggcagttccttgaactgtatacaaactgacatcaat--tcatattctga-------tatctgaca-----gcatgtttcac-ttgccagAAAATCAAGAACCCTAACTACCAGGGTAAATGGAAGGCACCTATGATTGACAACCCAG

upper sequence: GLYMA20G23080.2 (Glycine max), 3'ss of exon 7
lower sequence: AT1G09210.1 (Arabidopsis thaliana), 3'ss of exon 6
gtttgtggaaatttgttttgtaaatttgtaatatatgaaatatgacatattccattatgtttggaatgaatttgctttataactttgcatgctacatatttgcagAAAATCAAGAACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGATAACCCAG
                ||||| ||||| || |  |  || |||       |  ||  || |     |   | | | |   ||   ||      | || |||| || ||||||||||||||||||| || || || ||| |||| ||||||||||| ||||| |
---------------gtttgtcaatttctattccaaaaagtat------ctatatcctggtcaacgtttttcttcctctcaaggctgtcaa--atatttttgtagCAAATCAAGAACCCCAACTACAAGGGCAAGTGGGAGGCTCCATTGATTGACAACCCTG

upper sequence: GLYMA20G23080.2 (Glycine max), 3'ss of exon 7
lower sequence: Vv07s0005g01390.t01 (Vitis vinifera), 3'ss of exon 7
gtttgtggaaatttgttttgtaaatttgtaatatatgaaatatgacatattccattatgtttggaatgaatttgctttataactttgcatgctacatatttgcagAAAATCAAGAACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGATAACCCAG
           || | |    |||| | || ||  | | ||     || ||     || || | | |  |         ||| | | | ||  |   ||| |||| |||| || ||||||||||| || |||||||||||||||||  ||||||| |||||||
----------gttcgct---gaaatgtttattagttaagatg----atgttatggaattttggaagttgacggttcacttaattgttcttg--aaccattggcagCAAATAAAAAACCCCAACTACAAGGGAAAATGGAAGGCACCTATGATTGACAACCCAG

upper sequence: GLYMA20G23080.2 (Glycine max), 3'ss of exon 7
lower sequence: Vv14s0060g01290.t01 (Vitis vinifera), 3'ss of exon 7
gtttgtggaaatttgttttgtaaatttgtaatatatgaaatatgacatattccattatgtttggaatgaatttgctttataactttgcatgctacatatttgcagAAAATCAAGAACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGATAACCCAG
                |||||    | ||  ||  | || | ||| | |||  ||| || | | ||   | |||  | ||||  || |   |||  | || ||||||||| ||||| |||||||| || |||||||||||||||||| ||||||| |||||||
---------------gtttgtggcatggttttagtttaagt-tgaaacatttaattttgctggtaaaagagttg--tcataa--ttcctctctatctcttggcagAAAATTAAGAATCCCAACTACAAGGGAAAATGGAAGGCACCAATGATTGACAACCCAG

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|208273375|gb|GE070619.1|GE070619
EST:     ACCCCCTACCATTGCCAACCCTGATTACAAGGGCCCATGGAAGGCAAAAG                         AAAATCAAGAACCCCAACTATAAA
genomic: ACCCCCTACCATTGCCAACCCTGATTACAAGGGCCCATGGAAGGCAAA-Ggtttgtggaa ... atatttgcagAAAATCAAGAACCCCAACTATAAA
EST: gi|298193745|gb|HO040393.1|HO040393
EST:     CACCCCCTACCATTGCCAACCCTGATTACAAGGGCCCATGGAAGGCAAAG                         AAAATCAAGAACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGAT
genomic: CACCCCCTACCATTGCCAACCCTGATTACAAGGGCCCATGGAAGGCAAAGgtttgtggaa ... atatttgcagAAAATCAAGAACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGAT
EST: gi|13790097|gb|BG652688.1|BG652688
EST:     CACCCCCTACCATTGCCAACCCTGATTACAAGGGCCCATGGAAGGCAAAG                         AAAATCAAGAACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGAT
genomic: CACCCCCTACCATTGCCAACCCTGATTACAAGGGCCCATGGAAGGCAAAGgtttgtggaa ... atatttgcagAAAATCAAGAACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGAT
EST: gi|7147510|gb|AW509432.1|AW509432
EST:     CACCCCCTACCATTGCCAACCCTGATTACAAGGGCCCATGGAAGGCAAAG                         AAAATCAAGAACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGAT
genomic: CACCCCCTACCATTGCCAACCCTGATTACAAGGGCCCATGGAAGGCAAAGgtttgtggaa ... atatttgcagAAAATCAAGAACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGAT
EST: gi|22521717|gb|BU080528.1|BU080528
EST:     CACCCCCTACCATTGCCAACCCTGATTACAAGGGCCCATGGAAGGCAAAG                         AAAATCAAGAACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGAT
genomic: CACCCCCTACCATTGCCAACCCTGATTACAAGGGCCCATGGAAGGCAAAGgtttgtggaa ... atatttgcagAAAATCAAGAACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGAT
EST: gi|24136456|gb|BU926966.1|BU926966
EST:     CACCCCCTACCATTGCCAACCCTGATTACAAGGGCCCATGGAAGGCAAAG                         AAAATCAAGAACCCCAAGTATAAAGGAAAATGGAAGGCACCATTGATTGAT
genomic: CACCCCCTACCATTGCCAACCCTGATTACAAGGGCCCATGGAAGGCAAAGgtttgtggaa ... atatttgcagAAAATCAAGAACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGAT
EST: gi|208317285|gb|GE117494.1|GE117494
EST:     CACCCCCTACCATTGCCAACCCTGATTACAAGGGCCCATGGAAGGCAAAG                         AAAATCAAGAACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGAT
genomic: CACCCCCTACCATTGCCAACCCTGATTACAAGGGCCCATGGAAGGCAAAGgtttgtggaa ... atatttgcagAAAATCAAGAACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGAT
EST: gi|208091443|gb|GD886338.1|GD886338
EST:     CCTACCATTGCCAACCCTGATTACAAGGGCCCATGGAAGGCAAAG                         AAAATCAAGAGCCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGAT
genomic: CCTACCATTGCCAACCCTGATTACAAGGGCCCATGGAAGGCAAAGgtttgtggaa ... atatttgcagAAAATCAAGAACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGAT
EST: gi|207707986|gb|GD689865.1|GD689865
EST:     CACCCC-TACCATTGCCAACCCTGATTACAAGGGCCCATGGAGGGCAAAG                         AAAATCAAGAACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGAT
genomic: CACCCCCTACCATTGCCAACCCTGATTACAAGGGCCCATGGAAGGCAAAGgtttgtggaa ... atatttgcagAAAATCAAGAACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGAT
EST: gi|26045988|gb|CA783372.1|CA783372
EST:     CACCCCCTACCATTGCCAACCCTGATTACAAGGGCCCATGGAAGGCAAAG                         AAAATCAAGAACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGAT
genomic: CACCCCCTACCATTGCCAACCCTGATTACAAGGGCCCATGGAAGGCAAAGgtttgtggaa ... atatttgcagAAAATCAAGAACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGAT
EST: gi|208268672|gb|GE072089.1|GE072089
EST:     CACCCCCTACCATTGCCAACCCTGATTACAAGGGCCCATGGAAGGCAAAG                         AAAATCAAGAACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGAT
genomic: CACCCCCTACCATTGCCAACCCTGATTACAAGGGCCCATGGAAGGCAAAGgtttgtggaa ... atatttgcagAAAATCAAGAACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGAT
EST: gi|22524331|gb|BU083142.1|BU083142
EST:     CACCCCCTACCATTGCCAACCCTGATTACAAGGGCCCATGGAAGGCAAAG                         AAAATCAAGAACCCCAACTATAAAGGAAAATGGAAAGCACCATTGATTGAT
genomic: CACCCCCTACCATTGCCAACCCTGATTACAAGGGCCCATGGAAGGCAAAGgtttgtggaa ... atatttgcagAAAATCAAGAACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccattatgtttggaatgaatttgctttataactttgcatgctacatatttgcagAAAATCAAGAACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGATAACCCAG
                          ttataac  putative branch site (score: 2)
                  aatttgctttataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtggaaatttgttttgtaaatttgtaatatatgaaatatgacatattccattatgtttggaatgaatttgctttataactttgcatgctacatatttgcagAAAATCAAGAACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGATAACCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG