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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagccccttgtatattatttagtgtgcatcttttaattgtatggtagtgatgctttgcagtatattgatgtttactttgtcttttgcctttattatgtagGCAAAGTGCTTGGAGACAGGGGAAACTGTGGCTATAAAGAAGGTTCTTCAAGACAAGAGGTACAAGAACCGGGAATTGCAAACCATGCGTCTTCTGGATC

Basic information

species Glycine max
transcript GLYMA02G01220.3
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G01220.3 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os05g04340.2 (Oryza sativa), 3'ss of exon 4
gttagccccttg-tatatt-atttagtgtgcatcttttaattgtatggtagtg-atgctttgcagtatattgatgtttactttgtcttttgcctt-tattatgtagGCAAAGTGCTTGGAGACAGGGGAAACTGTGGCTATAAAGAAGGTTCTTCAAGACAAGAGGTACAAGAACCGGGAATTGCAAACCATGCGTCTTCTGGATC
||| | |  | |  | ||  |||||   ||||  | || | ||| |     ||  || | ||  |   |||||||    |||  | | |||  |  | || | ||||| |||||| |||| || || || ||||||||||||||||||||||||||||||||||| || |||||||| ||  ||||||| |||||  |||| || |
gtttgtctttagacagatcgatttatgttgcacttgttcagtgtgttaatttgtgtgttctggtggcgattgatgaacccttcatttcttgaatgatcttgtatagGCCAAGTGCCTGGAAACCGGTGAGACTGTGGCTATAAAGAAGGTTCTTCAAGACAAGAGATATAAGAACCGTGAGCTGCAAACAATGCGAGTTCTTGACC

upper sequence: GLYMA02G01220.3 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G155836_T01 (Zea mays), 3'ss of exon 4
gttagcccct-tgtatattatttagtg--tgcatcttttaattgt-atggtagtgatgctttgcagtat--attgatgtttactttgtcttttgcctt--------------tattatgtagGCAAAGTGCTTGGAGACAGGGGAAACTGTGGCTATAAAGAAGGTTCTTCAAGACAAGAGGTACAAGAACCGGGAATTGCAAACCATGCGTCTTCTGGATC
||| |   || |  | || | |  |    || ||  | |  || | || |||||  | |  |   |||   | | ||   | |||   || ||   ||              | || |  |||| |||||  | || || || || || || |||||||| |||||||||||||||||||| |||||||| || ||  |||||||||||||  | || || |
gtttgttactatacaaatcagtatgaaactgaattatctggtttttattgtagtatttcacttaggtagtaactaatagctccttcccctctttttttataaaaataaatgatcttgtacagGCCAAGTGTCTTGAAACTGGTGAGACCGTAGCTATAAAAAAGGTTCTTCAAGACAAGAGATACAAGAATCGTGAGCTGCAAACCATGCGAGTGCTTGACC

upper sequence: GLYMA02G01220.3 (Glycine max), 3'ss of exon 4
lower sequence: Vv07s0005g02100.t01 (Vitis vinifera), 3'ss of exon 4
gttagccccttgtatattatttagtgtgcatcttt-taattgtatggtagtgatgctttgcagtatattgatgttt--actttgtct------------tttgcctttattatgtagGCAAAGTGCTTGGAGACAGGGGAAACTGTGGCTATAAAGAAGGTTCTTCAAGACAAGAGGTACAAGAACCGGGAATTGCAAACCATGCGTCTTCTGGATC
|| ||    | ||  | |   || || | ||||   |||  |  ||   ||  ||  |   |  |  || |||| |  | || |||             | ||| | | ||||| ||||||||||||| ||||| || ||||| || || || || || ||||||||||||||||| ||||||||| | || || || || |||||||||||||| |
gtaagagtttggtg-agtgggtaatgggtatctgagtaacggcctgtgtgttctggctgaaacaaattttatgtcttgatttggtcaaataaggatatatatgcttcttttatgcagGCAAAGTGCTTAGAGACTGGTGAAACAGTTGCAATTAAAAAAGTTCTTCAAGACAAGAGATACAAGAACAGAGAGTTACAGACTATGCGTCTTCTGGACC

upper sequence: GLYMA02G01220.3 (Glycine max), 3'ss of exon 4
lower sequence: PP1S52_55V6.1 (Physcomitrella patens), 3'ss of exon 4
gttagccccttgta-tattatttagtgtgcatcttttaattgtatggtagtgatgctttgcagtatattgatgtttactttgtcttttgcctttattatgtagGCAAAGTGCTTGGAGACAGGGGAAACTGTGGCTATAAAGAAGGTTCTTCAAGACAAGAGGTACAAGAACCGGGAATTGCAAACCATGCGTCTTCTGGATC
  |   |  | ||  |   |  | |  | ||||| ||  | | |   |  || || |       |||   ||  | |      |  |  |   | || |  |||| || ||| | ||||  ||||| || ||||| ||||||||||| || ||||||||||| |||||||| || ||  | || | |||| | ||  ||||||
--tgtactgtagtggtgaaacatgggatacatctgtttgtgggacactcatggtgatagaactaatacatattctcatgactgcggtgactcctgttgt-cagGCTAAATGCATTGAGAGCGGGGAGACGGTGGCCATAAAGAAGGTGCTCCAAGACAAGAGATACAAGAATCGAGAGCTCCAGATCATGAGGCTATTGGATC

upper sequence: GLYMA02G01220.3 (Glycine max), 3'ss of exon 4
lower sequence: PP1S74_168V6.1 (Physcomitrella patens), 3'ss of exon 3
gttagcccc--ttgtatattatttagtgtgcatcttttaattgtatggtagtgatgctttgcagtatattgatgtttactttgtcttt-tgcctttattatgtagGCAAAGTGCTTGGAGACAGGGGAAACTGTGGCTATAAAGAAGGTTCTTCAAGACAAGAGGTACAAGAACCGGGAATTGCAAACCATGCGTCTTCTGGATC
  || |  |  | |      |  | | |   |||| |  ||   | | |   | || |    |       ||||||    | |      |   ||| || |  ||||||| ||| | ||||  || |||||||||||||| |||||||| ||||| |||||||| ||||||||||| ||| | || | |||||| || ||||| |
--taacttcactggagccagacatggggctgatctgtccatgtgacgttcaaggtggt--agaactaggggatgttctgatcgcgagggtaattttgttgt-cagGCAAAATGCATAGAGAGCGGAGAAACTGTGGCTATTAAGAAGGTGCTTCAGGACAAGAGATACAAGAACCGAGAACTTCAGATCATGCGGCTGCTGGAGC

upper sequence: GLYMA02G01220.3 (Glycine max), 3'ss of exon 4
lower sequence: EFJ07216 (Selaginella moellendorffii), 3'ss of exon 4
gttagccccttgtatattatttagtgtgcatcttttaattgtatggtagtgatgctttgcagtatattgatgtttactttgtcttttgcctttattatgtagGCAAAGTGCTTGGAGACAGGGGAAACTGTGGCTATAAAGAAGGTTCTTCAAGACAAGAGGTACAAGAACCGGGAATTGCAAACCATGCGTCTTCTGGATC
                           | ||   |       |  || |  |        || |   |  |  |   ||  |||||  | ||    ||| |||| ||||||||||| || || ||||| |||||||| || ||||| || ||||||||| ||||||||||||| ||  | || |  ||||| || || || |
---------------------------gtattgctagtccaaacagt-gcaaca----aaagcaggct--ttatcgtttcttctttctctttgggaatgcagGCCAAGTGCTTGGAAACCGGAGAAACCGTGGCTATCAAAAAGGTCCTCCAAGACAAGCGGTACAAGAACCGAGAGCTCCAGATAATGCGCCTCCTCGACC

upper sequence: GLYMA02G01220.3 (Glycine max), 3'ss of exon 4
lower sequence: EFJ07923 (Selaginella moellendorffii), 3'ss of exon 4
gttagccccttgtatattatttagtgtgcatcttttaattgtatggtagtgatgctttgcagtatattgatgtttactttgtcttttgcctttattatgtagGCAAAGTGCTTGGAGACAGGGGAAACTGTGGCTATAAAGAAGGTTCTTCAAGACAAGAGGTACAAGAACCGGGAATTGCAAACCATGCGTCTTCTGGATC
                           | ||   |       |  || |  |      ||||  | ||   ||||      |||||  | ||    ||| |||| ||||||||||| || || ||||| |||||||| || ||||| || ||||||||| | ||||||||||| ||  | || |  ||||| || || || |
---------------------------gtattgctagtccaaacagt-gcaacaaaa-gcaggcttttatcgtttct----tctttctctttgggaatgcagGCCAAGTGCTTGGAAACCGGAGAAACCGTGGCTATCAAAAAGGTCCTCCAAGACAAGCGCTACAAGAACCGAGAGCTCCAGATAATGCGCCTCCTCGACC

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|193637987|gb|FK586223.1|FK586223
EST:     ACATGGCTGAGCGAGTTGTTGGAAATGGATCATTTGGTGTAGTTTTCCAG                         GCAAAGTGCTTGGAGACAGGGGAAACTGTGGCTATAAAGAAGGTTCTTCAA
genomic: ACATGGCTGAGCGAGTTGTTGGAAATGGATCATTTGGTGTAGTTTTCCAGgttagcccct ... tattatgtagGCAAAGTGCTTGGAGACAGGGGAAACTGTGGCTATAAAGAAGGTTCTTCAA
EST: gi|120532325|gb|EH260458.1|EH260458
EST:     ACATGGCTGAGCGAGTTGTTGGAAATGGATCATTTGGTGTAGTTTTCCAG                         GCAAAGTGCTTGGAGACAGGGGAAACTGTGGCTATAAAGAAGGTTCTTCAA
genomic: ACATGGCTGAGCGAGTTGTTGGAAATGGATCATTTGGTGTAGTTTTCCAGgttagcccct ... tattatgtagGCAAAGTGCTTGGAGACAGGGGAAACTGTGGCTATAAAGAAGGTTCTTCAA
EST: gi|207819740|gb|GD790444.1|GD790444
EST:     ACATGGCTGAGCGAGTTGTTGGAAATGGATCATTTGGTGTAGTTTTCCAG                         GCAAAGTGCTTGGAGACAGGGGAAACTGTGGCTATAAAGAAGGTTCTTCAA
genomic: ACATGGCTGAGCGAGTTGTTGGAAATGGATCATTTGGTGTAGTTTTCCAGgttagcccct ... tattatgtagGCAAAGTGCTTGGAGACAGGGGAAACTGTGGCTATAAAGAAGGTTCTTCAA
EST: gi|193551204|gb|FK507989.1|FK507989
EST:     ACATGGCTGAGCGAGTTGTTGGAAATGGATCATTTGGTGTAG-TTTCCAG                         GCAAAGTGCTTGGAGACAGGGGAAACTGTGGCTATAAAGAAGGTTCTTCAA
genomic: ACATGGCTGAGCGAGTTGTTGGAAATGGATCATTTGGTGTAGTTTTCCAGgttagcccct ... tattatgtagGCAAAGTGCTTGGAGACAGGGGAAACTGTGGCTATAAAGAAGGTTCTTCAA
EST: gi|193379170|gb|FK343944.1|FK343944
EST:     CTGAGCGAGTTTGTTGGAAATGGATCATTTGGTGTAGTTTTCCAG                         GCAAAGTGCTTGGAGACAGGGGAAACTGTGGCTATAAAGAAGGTTCTTCAA
genomic: CTGAGCGAG-TTGTTGGAAATGGATCATTTGGTGTAGTTTTCCAGgttagcccct ... tattatgtagGCAAAGTGCTTGGAGACAGGGGAAACTGTGGCTATAAAGAAGGTTCTTCAA
EST: gi|207809238|gb|GD782208.1|GD782208
EST:     GGTGTAGTTTTCCAG                         GCAAAGTGCTTGGAGACAGGGGAAACTGTGGCTATAAAGAAGGTTCTTCAA
genomic: GGTGTAGTTTTCCAGgttagcccct ... tattatgtagGCAAAGTGCTTGGAGACAGGGGAAACTGTGGCTATAAAGAAGGTTCTTCAA
EST: gi|4396096|gb|AI495093.1|AI495093
EST:     ACATGGCTGAGCGAGTTGTTGGAAATGGATCATTTGGTGTAGTTTTCCAG                         GCAAAGTGCTTGGAGACAGGGGAAACTGTGGCTATAAAGAAGGTTCTTCAA
genomic: ACATGGCTGAGCGAGTTGTTGGAAATGGATCATTTGGTGTAGTTTTCCAGgttagcccct ... tattatgtagGCAAAGTGCTTGGAGACAGGGGAAACTGTGGCTATAAAGAAGGTTCTTCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtgatgctttgcagtatattgatgtttactttgtcttttgcctttattatgtagGCAAAGTGCTTGGAGACAGGGGAAACTGTGGCTATAAAGAAGGTTCTTCAAGACAAGAGGTACAAGAACCGGGAATTGCAAACCATGCGTCTTCTGGATC
                 tattgat  putative branch site (score: 3)
                         tttactttgtcttttg  CT-rich tract
               tatattgatgttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagccccttgtatattatttagtgtgcatcttttaattgtatggtagtgatgctttgcagtatattgatgtttactttgtcttttgcctttattatgtagGCAAAGTGCTTGGAGACAGGGGAAACTGTGGCTATAAAGAAGGTTCTTCAAGACAAGAGGTACAAGAACCGGGAATTGCAAACCATGCGTCTTCTGGATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC