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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agatctgcttagtttgagccgtgcatatctgtaaaaataaaagttaaaaataatttacatacatagttgctgcagctaatattcctttttggcttttcagCATACATGCTTGAGAGGCTCCGTTGATCCTTTGCTAGAGGAAGCTGATATTGACAAAGATGGAAAAATAAGCCTACCAGAGTTTCGGAGACTTCTTAGAA

Basic information

species Glycine max
transcript GLYMA16G23870.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G23870.2 (Glycine max), 3'ss of exon 13
lower sequence: LOC_Os07g22710.4 (Oryza sativa), 3'ss of exon 8
-------------------------------------------------------agatctgcttagtttgagccgtgcatatctg-taaaaataaaagttaaaa--ataatttacatacatagttgctgcagctaatat-----tcctttttggcttttcagCATACATGCTTGAGAGGCTCCGTTGATCCTTTGCTAGAGGAAGCTGATATTGACAAAGATGGAAAAATAAGCCTACCAGAGTTTCGGAGACTTCTTAGAA
                                                        ||| |  ||  | | ||      ||   |  |      | |   ||| |   |||||||   |   ||||  |||  || ||||     | |||      | | ||||| ||| |  ||| ||| ||  |||||||  | || ||||| ||||| ||||||| |||||||||||||||||||   || ||||| || || || | ||
gtacacctcttcaaatacctgtgaaacattactcttttcctattcacgtgagaattgatttatttcctataagattccaatccttaattggtgcatagcataagatcgtaatttattcaaccagttcatgcttctcatatatgtattcttacattgtctgcagCAAACAGGACTGAAAGGTTCTATTGATCCCCTCCTGGAGGAGGCTGACATTGACAGAGATGGAAAAATAAGCCTAGATGAATTTCGCAGGCTCCTGAAAA

upper sequence: GLYMA16G23870.2 (Glycine max), 3'ss of exon 13
lower sequence: Vv04s0023g03420.t01 (Vitis vinifera), 3'ss of exon 11
--agatctgcttagtttgagccgtgcatatctgtaaaaataaaagttaaaaataatttacatacatagttgctgcagctaatattcctttttggcttttcagCATACATGCTTGAGAGGCTCCGTTGATCCTTTGCTAGAGGAAGCTGATATTGACAAAGATGGAAAAATAAGCCTACCAGAGTTTCGGAGACTTCTTAGAA
     | |    || || |   |||| |   | |    ||   | |      | |  || | |||  |      |||  | |  | | |||| ||| |  |||| ||  |||| ||||||||  |||| ||  ||||||||||||||||||||||||||||||| |  |||||| |  |||| || || || ||||| ||||
tttcctgtagacagcttca--tgtgcttggtttttgtgatcttattattttttgacataaagacacggcctgaccagagattgcttcatttttgctgtgtagCACACGGGCTTAAGAGGCTCAATTGACCCACTGCTAGAGGAAGCTGATATTGACAAAGATGGGAGGATAAGCTTGGCAGAATTCCGAAGGCTTCTAAGAA
















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|193718866|gb|FK655244.1|FK655244
EST:     AATTTGACCTAGATAAAGATGGCTATATTACTCCGGAAGAACTTAGAATG                         CATACATGCTTGAGAGGCTCCGTTGATCCTTTG
genomic: AATTTGACCTAGATAAAGATGGCTATATTACTCCGGAAGAACTTAGAATGgttggtctca ... ggcttttcagCATACATGCTTGAGAGGCTCCGTTGATCCTTTG
EST: gi|207815878|gb|GD788763.1|GD788763
EST:     CCTAGATAAAGATGGCTATATTACTCCGGAAGAACTTAGAATG                         CATACATGCTTGAGAGGCTCCGTTGATCCTTTGCTAGAGGAAGCTGATATT
genomic: CCTAGATAAAGATGGCTATATTACTCCGGAAGAACTTAGAATGgttggtctca ... ggcttttcagCATACATGCTTGAGAGGCTCCGTTGATCCTTTGCTAGAGGAAGCTGATATT
EST: gi|22931966|gb|BU549105.1|BU549105
EST:     AATTTGACCTAGATAAAGATGGCTATATTACTCCGGAAGAACTTAGAATG                         CATACATGCTTGAGAGGCTCCGTTGATCCTTTGCTAGAGGAAGCTGATATT
genomic: AATTTGACCTAGATAAAGATGGCTATATTACTCCGGAAGAACTTAGAATGgttggtctca ... ggcttttcagCATACATGCTTGAGAGGCTCCGTTGATCCTTTGCTAGAGGAAGCTGATATT
EST: gi|207717904|gb|GD697376.1|GD697376
EST:     AATTTGACCTAGATAAAGATGGCTATATTACTCCGGAAGAACTTAGAATG                         CATACATGCTTGAGAGGCTCCGTTGATCCTTTGCTAGAGGAAGCTGATATT
genomic: AATTTGACCTAGATAAAGATGGCTATATTACTCCGGAAGAACTTAGAATGgttggtctca ... ggcttttcagCATACATGCTTGAGAGGCTCCGTTGATCCTTTGCTAGAGGAAGCTGATATT
EST: gi|16348882|gb|BI974477.1|BI974477
EST:     AATTTGACCTAGATAAAGATGGCTATATTACTCCGGAAGAACTTAGAATG                         CATACATGCTTGAGAGGCTCCGTTGATCCTTTGCTAGAGGAAGCTGATATT
genomic: AATTTGACCTAGATAAAGATGGCTATATTACTCCGGAAGAACTTAGAATGgttggtctca ... ggcttttcagCATACATGCTTGAGAGGCTCCGTTGATCCTTTGCTAGAGGAAGCTGATATT
EST: gi|193527749|gb|FK485939.1|FK485939
EST:     AATTTGACCTAGATAAAGATGGCTATATTACTCCGGAAGAACTTAGAATG                         CATACATGCTTGAGAGGCTCCGTTGATCCTTTG
genomic: AATTTGACCTAGATAAAGATGGCTATATTACTCCGGAAGAACTTAGAATGgttggtctca ... ggcttttcagCATACATGCTTGAGAGGCTCCGTTGATCCTTTG
EST: gi|207725902|gb|GD701386.1|GD701386
EST:     CCTAGATAAAGATGGCTATATTACTCCGGAAGAACTTAGAATG                         CATACATGCTTGAGAGGCTCCGTTGATCCTTTGCTAGAGGAAGCTGATATT
genomic: CCTAGATAAAGATGGCTATATTACTCCGGAAGAACTTAGAATGgttggtctca ... ggcttttcagCATACATGCTTGAGAGGCTCCGTTGATCCTTTGCTAGAGGAAGCTGATATT
EST: gi|9204567|gb|BE330791.1|BE330791
EST:     AATTTGACCTAGATAAAGATGGCTATATTACTCCGGAAGAACTTAGAATG                         CATACATGCTTGAGAGGCTCCGTTGATCCTTTGCTAGAGGAAGCTGATATT
genomic: AATTTGACCTAGATAAAGATGGCTATATTACTCCGGAAGAACTTAGAATGgttggtctca ... ggcttttcagCATACATGCTTGAGAGGCTCCGTTGATCCTTTGCTAGAGGAAGCTGATATT
EST: gi|11274128|gb|BF324496.1|BF324496
EST:     AATTTGACCTAGATAAAGATGGCTATATTACTCCGGAAGAACTTAGAATG                         CATACATGCTTGAGAGGCTCCGTTGATCCTTTGCTAGAGGAAGCTGATATT
genomic: AATTTGACCTAGATAAAGATGGCTATATTACTCCGGAAGAACTTAGAATGgttggtctca ... ggcttttcagCATACATGCTTGAGAGGCTCCGTTGATCCTTTGCTAGAGGAAGCTGATATT
EST: gi|207782295|gb|GD753278.1|GD753278
EST:     AGAACTTAGAATG                         CATACATGCTTGAGAGGCTCCGTTGATCCTTTGCTAGAGGAAGCTGATATT
genomic: AGAACTTAGAATGgttggtctca ... ggcttttcagCATACATGCTTGAGAGGCTCCGTTGATCCTTTGCTAGAGGAAGCTGATATT
EST: gi|193630006|gb|FK573298.1|FK573298
EST:     AGTTTGACCTAGATAAAGATGGCTATATTACTCCGGAAGAACTTAGAATG                         CATACATGCTTGAGCGGCTCCGTTGATCCTTTGCTAGAGGAAG
genomic: AATTTGACCTAGATAAAGATGGCTATATTACTCCGGAAGAACTTAGAATGgttggtctca ... ggcttttcagCATACATGCTTGAGAGGCTCCGTTGATCCTTTGCTAGAGGAAG
EST: gi|193490437|gb|FK453364.1|FK453364
EST:     AGTTTGACCTAGATAAAGATGGCTATATTACTCCGGAAGAACTTAGAATG                         CATACATGCTTGAGACGGCTCCGTTGATCCTTTGCTAGAGGAAG
genomic: AATTTGACCTAGATAAAGATGGCTATATTACTCCGGAAGAACTTAGAATGgttggtctca ... ggcttttcagCATACATGCTTGAGA-GGCTCCGTTGATCCTTTGCTAGAGGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaaataatttacatacatagttgctgcagctaatattcctttttggcttttcagCATACATGCTTGAGAGGCTCCGTTGATCCTTTGCTAGAGGAAGCTGATATTGACAAAGATGGAAAAATAAGCCTACCAGAGTTTCGGAGACTTCTTAGAA
                            agctaat  putative branch site (score: 3)
                                    ttcctttttggctttt  CT-rich tract
     taatttacatacata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agatctgcttagtttgagccgtgcatatctgtaaaaataaaagttaaaaataatttacatacatagttgctgcagctaatattcctttttggcttttcagCATACATGCTTGAGAGGCTCCGTTGATCCTTTGCTAGAGGAAGCTGATATTGACAAAGATGGAAAAATAAGCCTACCAGAGTTTCGGAGACTTCTTAGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- -tctgctt
- - - - - - - - - - -tgcatat
- - - - - - - - - - - - - - - - -aaaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -catacat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttgctgc