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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattacatgaatccttgtaaaaaactagtatgcacactcaaatataatatacatttcagatgataggaacttggatgattaggattccaataaaataaatgatttttctcggccttttctagATTCTTCACTTGAAAGGAGACAGAAAGGACTATGACTTTGTGAAGTCAAGTCTTTCAGCAGAAGGCTTCGATGTTGTTTATGATATCAACG

Basic information

species Arabidopsis thaliana
transcript AT1G09340.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G09340.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA19G41540.2 (Glycine max), 3'ss of exon 3
gtattacatgaatccttgtaaaaaactagtatgcacactcaaat-ataatatacatttcagatgataggaacttggatgattaggattccaataaaataaatgatttttctcggcc----------ttttctagATTCTTCACTTGAAAGGAGACAGAAAGGACTATGACTTTGTGAAGTCAAGTCTTTCAGCAGAAGGCTTCGATGTTGTTTATGATATCAACG
||||   |    |   ||||||  || |        ||| |  |  |||   |   |    ||| || ||  ||  ||  ||   | |   ||||    |    ||  |||  |            ||| | ||||  | || |||||||||||||| ||||||| ||||||||| || || ||||| || ||||| || || |||||||||||||| || || |
gtatgttaattgtaaatgtaaactacaaaacattggactaaccttgtaaggcatgatgtgaatg-tatgacttttcatctttgttactattataaccggagcatttactctgtgtagtatttttaatttcccagATCTTGCATTTGAAAGGAGACAGGAAGGACTTTGACTTTGTAAAATCCAGTCTCTCGGCAGAGGGATTTGATGTTGTTTATGACATAAATG

upper sequence: AT1G09340.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA03G38930.1 (Glycine max), 3'ss of exon 3
gtattacatgaatccttgtaaaaaactagta--tgcac--actcaaatataatatacatttcagatgataggaacttggatgattaggattccaata----aaataaatgatttttctcggcctttt------ctagATTCTTCACTTGAAAGGAGACAGAAAGGACTATGACTTTGTGAAGTCAAGTCTTTCAGCAGAAGGCTTCGATGTTGTTTATGATATCAACG
||||   |    |   ||| || |||||  |  || ||  ||     |  |||  |   |    |||  | |   ||  ||  ||   | ||  |||     || |  |  ||  | | |   ||||      | ||||  | || |||||||||||||| |||||||  |||||||| || || ||||| |||||||| || || |||||||||||||| || || |
gtatgctaattgtaaatgtgaacaactaaaaattggactaaccttcttgcaatccatgatgtgaatg-catggcttttcatctttgttactcttatacccggaacatttacttagtgtagtatttttaatttcccagATCTTGCATTTGAAAGGAGACAGGAAGGACTTCGACTTTGTAAAATCCAGTCTCTCAGCAGAGGGATTTGATGTTGTTTATGACATAAATG

upper sequence: AT1G09340.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA19G41540.1 (Glycine max), 3'ss of exon 3
gtattacatgaatccttgtaaaaaactagtatgcacactcaaat-ataatatacatttcagatgataggaacttggatgattaggattccaataaaataaatgatttttctcggcc----------ttttctagATTCTTCACTTGAAAGGAGACAGAAAGGACTATGACTTTGTGAAGTCAAGTCTTTCAGCAGAAGGCTTCGATGTTGTTTATGATATCAACG---------
||||   |    |   ||||||  || |        ||| |  |  |||   |   |    ||| || ||  ||  ||  ||   | |   ||||    |    ||  |||  |            ||| | ||||  | || |||||||||||||| ||||||| ||||||||| || || ||||| || ||||| || || |||||||||||||| || || |         
gtatgttaattgtaaatgtaaactacaaaacattggactaaccttgtaaggcatgatgtgaatg-tatgacttttcatctttgttactattataaccggagcatttactctgtgtagtatttttaatttcccagATCTTGCATTTGAAAGGAGACAGGAAGGACTTTGACTTTGTAAAATCCAGTCTCTCGGCAGAGGGATTTGATGTTGTTTATGACATAAATGGTGTGCAAA

upper sequence: AT1G09340.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv14s0060g00820.t01 (Vitis vinifera), 3'ss of exon 3
gtattacatgaatccttgtaaaaaactagtatgcacactcaaatataatatacatttcagatgataggaacttgg---atgattaggat--tccaataaaataaatgatttttctcggccttttct---------agATTCTTCACTTGAAAGGAGACAGAAAGGACTATGACTTTGTGAAGTCAAGTCTTTCAGCAGAAGGCTTCGATGTTGTTTATGATATCAACG
||||   ||| | ||||||  | |   | | |     ||  |        | ||||     | ||     ||||    ||||  || ||  |||||    || || | | ||||| |   |||| |         || || | || |||||||||||||||||||||| ||| ||||||||  | |||||| |||| |||||||| |||||||| || ||||| || |
gtatattatgta-ccttgtctacatgaattctcactccttcatccccggtttcattagtattcattctctcttgaggaatgaccagcatgttccaagtgcatgaaagttgtttcttgattttttttttctttggtagGTTTTGCATTTGAAAGGAGACAGAAAGGACTTTGAATTTGTGAAAACCAGTCTTGCAGCTGAAGGCTTTGATGTTGTCTACGATATAAATG

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|124861278|gb|EH945715.1|EH945715
EST:     CGGTGAATCTGACCAAGACTTTGCTGATTTCTCTTCTAAG                         ATTCTTCACTTGAAAGGAGACAGAAAGGACTATGACT
genomic: CGGTGAATCTGACCAAGACTTTGCTGATTTCTCTTCTAAGgtattacatg ... ccttttctagATTCTTCACTTGAAAGGAGACAGAAAGGACTATGACT
EST: gi|125299916|gb|EL314001.1|EL314001
EST:     AACAATTGCCCGGTGAATCTGACCAAGACTTTGCTGATTTCTCTTCTAAG                         ATTCTTCACTTGAAAGGAGACAGAAAGGA
genomic: AACAATTGCCCGGTGAATCTGACCAAGACTTTGCTGATTTCTCTTCTAAGgtattacatg ... ccttttctagATTCTTCACTTGAAAGGAGACAGAAAGGA
EST: gi|124935897|gb|EL012846.1|EL012846
EST:     AACAATTGCCCGGTGAATCTGACCAAGACTTTGCTGATTTCTCTTCTAAG                         ATTCTTCACTTGAAAGGAGACAGAAAGGACTATGACTTTGTGAAGTCAAGT
genomic: AACAATTGCCCGGTGAATCTGACCAAGACTTTGCTGATTTCTCTTCTAAGgtattacatg ... ccttttctagATTCTTCACTTGAAAGGAGACAGAAAGGACTATGACTTTGTGAAGTCAAGT
EST: gi|125150468|gb|EL183100.1|EL183100
EST:     CTTTGCTGATTTCTCTTCTAAG                         ATTCTTCACTTGAAAGGAGACAGAAAGGACTATGACTTTGTGAAGTCAAGT
genomic: CTTTGCTGATTTCTCTTCTAAGgtattacatg ... ccttttctagATTCTTCACTTGAAAGGAGACAGAAAGGACTATGACTTTGTGAAGTCAAGT
EST: gi|125115686|gb|EL165543.1|EL165543
EST:     AACAATTGCCCGGTGAATCTGACCAAGACTTTGCTGATTTCTCTTCTAAG                         ATTCTTCACTTGAAAGGAGACAGAAAGGACTA
genomic: AACAATTGCCCGGTGAATCTGACCAAGACTTTGCTGATTTCTCTTCTAAGgtattacatg ... ccttttctagATTCTTCACTTGAAAGGAGACAGAAAGGACTA
EST: gi|125067667|gb|EL134091.1|EL134091
EST:     TTCTCTTCTAAG                         ATTCTTCACTTGAAAGGAGACAGAAAGGACTATGACTTTGTGAAGTCAAGT
genomic: TTCTCTTCTAAGgtattacatg ... ccttttctagATTCTTCACTTGAAAGGAGACAGAAAGGACTATGACTTTGTGAAGTCAAGT
EST: gi|125192000|gb|EL206954.1|EL206954
EST:     AACAATTGCCCGGTGAATCTGACCAAGACTTTGCTGATTTCTCTTCTAAG                         ATTCTTCACTTGAAAGGAGACAGAAAGGACTA
genomic: AACAATTGCCCGGTGAATCTGACCAAGACTTTGCTGATTTCTCTTCTAAGgtattacatg ... ccttttctagATTCTTCACTTGAAAGGAGACAGAAAGGACTA
EST: gi|125092884|gb|EL150679.1|EL150679
EST:     AACAATTGCCCGGTGAATCTGACCAAGACTTTGCTGATTTCTCTTCTAAG                         ATTCTTCACTTGAAAGGA
genomic: AACAATTGCCCGGTGAATCTGACCAAGACTTTGCTGATTTCTCTTCTAAGgtattacatg ... ccttttctagATTCTTCACTTGAAAGGA
EST: gi|125292235|gb|EL306320.1|EL306320
EST:     TTTCTCTTCTAAG                         ATTCTTCACTTGAAAGGAGACAGAAAGGACTATGACTTTGTGAAGTCAAGT
genomic: TTTCTCTTCTAAGgtattacatg ... ccttttctagATTCTTCACTTGAAAGGAGACAGAAAGGACTATGACTTTGTGAAGTCAAGT
EST: gi|124958122|gb|EL032891.1|EL032891
EST:     ACTTTGCTGATTTCTCTTCTAAG                         ATTCTTCACTTGAAAGGAGACAGAAAGGACTATGACTTTGTGAAGTCAAGT
genomic: ACTTTGCTGATTTCTCTTCTAAGgtattacatg ... ccttttctagATTCTTCACTTGAAAGGAGACAGAAAGGACTATGACTTTGTGAAGTCAAGT
EST: gi|116412032|gb|EG454624.1|EG454624
EST:     AACAATTGCCCGGTGAATCTGACCAAGACTTTGCTGATTTCTCTTCTAAG                         ATTCTTCACTTGAAAGGAGACAGAAAGGACTATGACTTTGTGAAGTCAAGT
genomic: AACAATTGCCCGGTGAATCTGACCAAGACTTTGCTGATTTCTCTTCTAAGgtattacatg ... ccttttctagATTCTTCACTTGAAAGGAGACAGAAAGGACTATGACTTTGTGAAGTCAAGT
EST: gi|125320351|gb|EL334436.1|EL334436
EST:     AACAATTGCCCGGTGAATCTGACCAAGACTTTGCTGATTTCTCTTCTAAG                         ATTCTTCACTTGAAAGGAGACAGAAAGGACTA
genomic: AACAATTGCCCGGTGAATCTGACCAAGACTTTGCTGATTTCTCTTCTAAGgtattacatg ... ccttttctagATTCTTCACTTGAAAGGAGACAGAAAGGACTA
EST: gi|124881240|gb|EH960142.1|EH960142
EST:     AACAATTGCCCGGTGAATCTGACCAAGACTTTGCTGATTTCTCTTCTAAG                         ATTCTTCACTTGAAAGGAGACAGAA
genomic: AACAATTGCCCGGTGAATCTGACCAAGACTTTGCTGATTTCTCTTCTAAGgtattacatg ... ccttttctagATTCTTCACTTGAAAGGAGACAGAA
EST: gi|124739950|gb|EH831112.1|EH831112
EST:     TTTCTCTTCTAAG                         ATTCTTCACTTGAAAGGAGACAGAAAGGACTATGACTTTGTGAAGTCAAGT
genomic: TTTCTCTTCTAAGgtattacatg ... ccttttctagATTCTTCACTTGAAAGGAGACAGAAAGGACTATGACTTTGTGAAGTCAAGT
EST: gi|124946121|gb|EL022070.1|EL022070
EST:     TCTGACCAAGACTTTGCTGATTTCTCTTCTAAG                         ATTCTTCACTTGAAAGGAGACAGAAAGGACTATGACTTTGTGAAGTCAAGT
genomic: TCTGACCAAGACTTTGCTGATTTCTCTTCTAAGgtattacatg ... ccttttctagATTCTTCACTTGAAAGGAGACAGAAAGGACTATGACTTTGTGAAGTCAAGT
EST: gi|116412031|gb|EG454623.1|EG454623
EST:     AACAATTGCCCGGTGAATCTGACCAAGACTTTGCTGATTTCTCTTCTAAG                         ATTCTTCACTTGAAAGGAGACAGAAAGGACTATGACTTTGTGAAGTCAAGT
genomic: AACAATTGCCCGGTGAATCTGACCAAGACTTTGCTGATTTCTCTTCTAAGgtattacatg ... ccttttctagATTCTTCACTTGAAAGGAGACAGAAAGGACTATGACTTTGTGAAGTCAAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacttggatgattaggattccaataaaataaatgatttttctcggccttttctagATTCTTCACTTGAAAGGAGACAGAAAGGACTATGACTTTGTGAAGTCAAGTCTTTCAGCAGAAGGCTTCGATGTTGTTTATGATATCAACG
                                   tttttctcggcctttt  CT-rich tract
                attccaataaaataaa  TA-rich tract