Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtattgttgtgaacaaaagtattaaatttgctacccttcaaaatcagatggtgttgtctttaggtaatttatcatactaagtattttggcatttattagGTCATGGTGGTTGATGCTGAGGCATACACATATGATGACGAGGTGCTTAAGAAAGCAGAAGCTATGGGCAAGCCTGGGCTTGTAGAAATCATTGCGAGGC

Basic information

species Glycine max
transcript GLYMA20G02360.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G02360.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os09g02284.1 (Oryza sativa), 3'ss of exon 2
----tgtattgttgtgaac-aaaagtattaaatttgctaccctt-caaaatcagatggtgttgtctttaggtaatttatcatactaagtattttggcatttattagGTCATGGTGGTTGATGCTGAGGCATACACATATGATGACGAGGTGCTTAAGAAAGCAGAAGCTATGGGCAAGCCTGGGCTTGTAGAAATCATTGCGAGGC
      ||| | |||   | || || || | |||    |   ||     ||  ||     |  |  ||       | |     |||| | | |  |  ||||  ||||  | || |  ||||| |||||||| ||||||||||| |||||  | ||||||||||| || ||||| ||||| ||  |  |||| |||| ||| | | 
gctgattatagctgtactctaacagcataagattcttcatatttgttgtattggaacaaatcatgattg------tcacagagctaattttctgtgactttaccagGTGGTAGTTGAGGATGCAGAGGCATATACATATGATGATGAGGTCATCAAGAAAGCAGATGCCATGGGAAAGCCCGGATTGATAGAGATCAATGCCAAGG

upper sequence: GLYMA20G02360.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv03s0180g00050.t01 (Vitis vinifera), 3'ss of exon 2
tgtattgttgtgaacaaaagtattaaatttgctacccttcaaaatcagatggtgttgtctttaggtaatttatcatactaagtattt----tggcatttattagGTCATGGTGGTTGATGCTGAGGCATACACATATGATGACGAGGTGCTTAAGAAAGCAGAAGCTATGGGCAAGCCTGGGCTTGTAGAAATCATTGCGAGGC
|  | ||| |||   |  |  | | || || |  ||| ||     | ||  |||||  ||| || ||||  |||||     || |||    ||   ||| | ||||  | |||| |||||||||||||||||| |||||||| || ||||| |||||||||||||||||||| ||||| |||||||| || |||  ||| |   
ttgaatgt-gtggggaggaaaactcaacttccagcccatctg---ctgaatgtgtttccttcagataatgcatcatgggttgtctttcatatgctctttttcagGTTGTTGTGGCTGATGCTGAGGCATACACTTATGATGATGAAGTGCTCAAGAAAGCAGAAGCTATGGGGAAGCCAGGGCTTGTGGAGATCTATGCCAAAG

upper sequence: GLYMA20G02360.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S79_74V6.1 (Physcomitrella patens), 3'ss of exon 3
-------------------tgtattgttgtgaacaaaagtattaaattt--gctacccttcaaaatcagatggtgttgtctttaggtaatttatc--atactaagtattttgg--catttatt--------------------agGTCATGGTGGTTGATGCTGAGGCATACACATATGATGACGAGGTGCTTAAGAAAGCAGAAGCTATGGGCAAGCCTGGGCTTGTAGAAATC-ATTGCGAGGC
                     | || |||      | |   ||||||||    |   ||  |   |||||   | || |    | |||||  | |  |||    | |||||    ||  | ||                    ||||  ||||||| ||  |||| |||||||| ||||| || || ||||| |||||||||||||| ||||| ||||| ||  | || |||||  |  || ||| 
gtagcatattcatttaactcatcttattgcagtttacaaccttaaatttcgattcgtctcgacgttcagagtattttctgagcaagtaatcgaccctatatgcggcattttaaatcacgtgttgctgcgtataaacatgctgcagGTGGTGGTGGTGGACCCTGAAGCATACACCTATGACGAAGAAGTGCTGAAGAAAGCAGAAGCCATGGGTAAGCCAGGTTTAGTGGAAATTTACAGCAAGG-

upper sequence: GLYMA20G02360.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ38153 (Selaginella moellendorffii), 3'ss of exon 3
tgtattgttgtgaacaaaagtattaaatttgctacccttcaaaatcagatggtgttgtctttaggtaatttatcata-ctaagtattttggcatttattagGTCATGGTGGTTGATGCTGAGGCATACACATATGATGACGAGGTGCTTAAGAAAGCAGAAGCTATGGGCAAGCCTGGGCTTGTAGAAATC-ATTGCGAGGC
                                          |  |||  |   ||    || | |||   |  | | || |    ||||   ||   |||||    ||| | ||  | ||||||||||| ||||||||||| ||| | |||||||| ||||| ||||| |||||||| ||||| || ||| || || ||| 
---------------------------------------gtcagccagtcgagcttagagtttgataagaaactaaagctcaaagctttg---ttccatagGTGGAAGTGATCGACCCAGAGGCATACACTTATGATGACGAAGTGATCAAGAAAGCCGAAGCCATGGGAAAGCCTGGCCTTGTGGAGATCTATGGCAAGG-

upper sequence: GLYMA20G02360.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ15766 (Selaginella moellendorffii), 3'ss of exon 3
tgtattgttgtgaacaaaagtattaaatttgctacccttcaaaatcagatggtgttgtctttaggtaatttatcata-ctaagtattttggcatttattagGTCATGGTGGTTGATGCTGAGGCATACACATATGATGACGAGGTGCTTAAGAAAGCAGAAGCTATGGGCAAGCCTGGGCTTGTAGAAATC-ATTGCGAGGC
                                          |  |||  |   ||    || | |||   |  | | || |    ||||   ||   |||||    ||||| ||  | ||||||||||| ||||||||||| ||| | |||||||| ||||| ||||| |||||||| ||||| || ||| || || ||| 
---------------------------------------gtcagccagtcgagcttagagtttgataagaaactaaagctcaaagctttg---ttccatagGTGGAAGTGGTCGACCCAGAGGCATACACTTATGATGACGAAGTGATCAAGAAAGCGGAAGCCATGGGAAAGCCTGGCCTTGTGGAGATCTATGGCAAGG-

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|193707865|gb|FK647661.1|FK647661
EST:     TTGATCCAGTGACACAACAG                         GTCATGGTGGTTGATGCTGAGGCATACACATATGATGACGAGGTGCTTAAG
genomic: TTGATCCAGTGACACAACAGgttcggtttt ... catttattagGTCATGGTGGTTGATGCTGAGGCATACACATATGATGACGAGGTGCTTAAG
EST: gi|13790386|gb|BG652977.1|BG652977
EST:     TTGACAGTAGTCCAACCCGTGTCTTTGAAATTGATCCAGTGACACAACAG                         GTCATGGTGGTTGATGCTGAGGCATACACATATG
genomic: TTGACAGTAGTCCAACCCGTGTCTTTGAAATTGATCCAGTGACACAACAGgttcggtttt ... catttattagGTCATGGTGGTTGATGCTGAGGCATACACATATG
EST: gi|208332035|gb|GE127698.1|GE127698
EST:     TTGACAGTAGTCCAACCCGTGTCTTTGAAATTGATCCAGTGACACAACAG                         GTCATGGTGGTTGATGCTGAGGCATACACATATGATGACGAGGTGCTTAAG
genomic: TTGACAGTAGTCCAACCCGTGTCTTTGAAATTGATCCAGTGACACAACAGgttcggtttt ... catttattagGTCATGGTGGTTGATGCTGAGGCATACACATATGATGACGAGGTGCTTAAG
EST: gi|208153490|gb|GD945723.1|GD945723
EST:     TTGACAGTAGTCCAACCCGTGTCTTTGAAATTGATCCAGTGACACAACAG                         GTCATGGTGGTTGATGCTGAGG
genomic: TTGACAGTAGTCCAACCCGTGTCTTTGAAATTGATCCAGTGACACAACAGgttcggtttt ... catttattagGTCATGGTGGTTGATGCTGAGG
EST: gi|193623900|gb|FK573822.1|FK573822
EST:     TAGTCCAACCCGTGTCTTTGAAATTGATCCAGTGACACAACAG                         GTCATGGTGGTTGATGCTGAGGCATACACATATGATGACGAGGTGCTTAAG
genomic: TAGTCCAACCCGTGTCTTTGAAATTGATCCAGTGACACAACAGgttcggtttt ... catttattagGTCATGGTGGTTGATGCTGAGGCATACACATATGATGACGAGGTGCTTAAG
EST: gi|120531834|gb|EH259967.1|EH259967
EST:     TTGACAGTAGTCCAACCCGTGTCTTTGAAATTGATCCAGTGACACAACAG                         GTCATGGTGGTTGATGCTGAG
genomic: TTGACAGTAGTCCAACCCGTGTCTTTGAAATTGATCCAGTGACACAACAGgttcggtttt ... catttattagGTCATGGTGGTTGATGCTGAG
EST: gi|208250412|gb|GE044649.1|GE044649
EST:     TTGACAGTAGTCCAACCCGTGTCTTTGAAATTGATCCAGTGACACAACAG                         GTCATGGTGGTTGATGCTGAGGCATACACATAT
genomic: TTGACAGTAGTCCAACCCGTGTCTTTGAAATTGATCCAGTGACACAACAGgttcggtttt ... catttattagGTCATGGTGGTTGATGCTGAGGCATACACATAT
EST: gi|208321527|gb|GE120784.1|GE120784
EST:     TTGACAGTAGTCCAACCCGTGTCTTTGAAATTGTTCCAGTGACACAACAG                         GTCATGGTGGTTGATGCTGAGGCATACACATATGATGACGAGGTGCTTAAA
genomic: TTGACAGTAGTCCAACCCGTGTCTTTGAAATTGATCCAGTGACACAACAGgttcggtttt ... catttattagGTCATGGTGGTTGATGCTGAGGCATACACATATGATGACGAGGTGCTTAA-
EST: gi|120531458|gb|EH259591.1|EH259591
EST:     TTGACAGTAGTCCAACCCGTGTCTTTGAAATTGATCCAGTGACACAACAG                         GTCATGGTGGTTGATGCTGAGGCATACACATATGATGACGAGGTGCTTAAG
genomic: TTGACAGTAGTCCAACCCGTGTCTTTGAAATTGATCCAGTGACACAACAGgttcggtttt ... catttattagGTCATGGTGGTTGATGCTGAGGCATACACATATGATGACGAGGTGCTTAAG
EST: gi|254315328|gb|GR825137.1|GR825137
EST:     TGTCTTTGAAATTGATCCCAGTGACACAAACAG                         GTCATGGTGGTTGATGCTGAGGCATACACATATGATGACGAGGTGCTTAA
genomic: TGTCTTTGAAATTGAT-CCAGTGACAC-AACAGgttcggtttt ... catttattagGTCATGGTGGTTGATGCTGAGGCATACACATATGATGACGAGGTGCTTAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagatggtgttgtctttaggtaatttatcatactaagtattttggcatttattagGTCATGGTGGTTGATGCTGAGGCATACACATATGATGACGAGGTGCTTAAGAAAGCAGAAGCTATGGGCAAGCCTGGGCTTGTAGAAATCATTGCGAGGC
                    taatttatcatactaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtattgttgtgaacaaaagtattaaatttgctacccttcaaaatcagatggtgttgtctttaggtaatttatcatactaagtattttggcatttattagGTCATGGTGGTTGATGCTGAGGCATACACATATGATGACGAGGTGCTTAAGAAAGCAGAAGCTATGGGCAAGCCTGGGCTTGTAGAAATCATTGCGAGGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - -tgttgtg
- - - - - - aacaaaa
- - - - - - - - - - - - - - - - - cccttca
- - - - - - - - - - - - - - - - - - - - - - - -gatggtg