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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagattttgtgcatttggctattaaatctcctggaaattttcttcccttgttaacccctgcaatttgataaataattaacagGTGGAGACATTTGGTGCTATGGCAAAAACTGAGAAAATTGCATTTATCCTTGAACAA

Basic information

species Arabidopsis thaliana
transcript AT5G09900.3
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G09900.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA04G39520.1 (Glycine max), 3'ss of exon 4
----------------------------gtaagattttgtgcatttggctattaaatctc-----ctggaaattttcttcccttgttaacccctgcaatttgataaataattaacagGTGGAGACATTTGGTGCTATGGCAAAAACTGAGAAAATTGCATTTATCCTTGAACAA
                             |   ||| ||  | ||||| | ||  || ||      | |  |  ||      ||||| ||       |||   |   |  |||||||||||| || |||||||| ||||| |||||||||||||| ||||| || |||||||||
gtcagtgtgaattttaaacgtgtgatggattttattatgcacctttggtttttgtatgtcactagttagtgaaattagctgtttgttgacttacatgattgatt---tccttaacagGTGGAAACTTTTGGTGCCATGGCTAAAACTGAGAAAATCGCATTCATTCTTGAACAA

upper sequence: AT5G09900.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA06G15330.1 (Glycine max), 3'ss of exon 4
----------------------------gtaagattttgtgcatttggctattaaatctc-ctggaaatt----ttcttcccttgttaacccctgcaatttgataaataattaacagGTGGAGACATTTGGTGCTATGGCAAAAACTGAGAAAATTGCATTTATCCTTGAACAA
                             |   ||| ||| | ||||| | ||  || || || | ||||    ||        ||| ||       ||| | |   |  |||||||||||| || ||||| || ||||| |||||||||||||| ||||| || |||||||||
gtccgtgtgaattttaaatgtgtgatggattttattatgtacctttggtttttgtatgtctctagtaattgaaattagctatcagttgacttacatgattggtt---tccttaacagGTGGAAACTTTTGGCGCCATGGCTAAAACTGAGAAAATCGCATTCATTCTTGAACAA

upper sequence: AT5G09900.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA05G32030.2 (Glycine max), 3'ss of exon 4
----------------gtaagattttgtgcatttggctattaaatctcctggaaattttcttcccttgttaacccctgcaatttgataaataat--taacagGTGGAGACATTTGGTGCTATGGCAAAAACTGAGAAAATTGCATTTATCCTTGAACAA
                 | |  ||||||    ||   || |   | |  ||||  |          | || |        ||   ||   ||||  ||||||||||| || |||||||| ||||| || ||||||||||||||||| || || ||||||
gtcagtgtgaacgtgtctcatgttttgttggcttctatactttgttttttggacttaactgataagtattcagtttacttatggaatgggtaatcttaacagGTGGAAACTTTTGGTGCCATGGCCAAGACTGAGAAAATTGCATTCATTCTCGAACAA

upper sequence: AT5G09900.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA08G15340.1 (Glycine max), 3'ss of exon 4
--------------gtaagat--tttgtgcatttggctattaaatctcctggaaattttcttcccttgttaacccctgcaatttgataaataatt--aacagGTGGAGACATTTGGTGCTATGGCAAAAACTGAGAAAATTGCATTTATCCTTGAACAA
              || | ||  |||||    |||  || |   | |  ||||  |          | || |        ||   ||   ||||   |||||||||| ||||| ||||| ||||| || |||||||||||||| || || |||||||||
gtcagtgtgaatgtgtcacatgttttgttggcttgtatactttgttttttggatgtaactaattagtattcagtttacttatggaatgggtaatctgaacagGTGGAAACATTCGGTGCCATGGCCAAGACTGAGAAAATTGCGTTCATTCTTGAACAA

upper sequence: AT5G09900.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv07s0031g01970.t01 (Vitis vinifera), 3'ss of exon 4
----------------------gtaagattttgtgcatttggctattaaatctcctggaaattttcttcccttgt---taacccctgcaatttgataaataat------taacagGTGGAGACATTTGGTGCTATGGCAAAAACTGAGAAAATTGCATTTATCCTTGAACAA
                       |  | |||| |   |||||   |  ||    ||       || ||   || |   | || |  ||| |||| |  ||  |      | ||||||||| ||||||||||| |||||||||||||| ||||||||||| || |||||||||
gtcagttaaaaatagagttaccatgggctttt-tatttttggtattagaaaacactaaccccgttgtttgtttttatattacacgagcactttggttgatgttacttaatcacagGTGGAAACATTTGGTGCAATGGCAAAAACTGAAAAAATTGCATTCATTCTTGAACAA

upper sequence: AT5G09900.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S58_256V6.1 (Physcomitrella patens), 3'ss of exon 4
-----------------------------------------------------------------------------------gtaagattttgtgcatttggctattaaatctcctggaaattttcttcccttgttaacc----cctgcaatttgataaataattaac--agGTGGAGACATTTGGTGCTATGGCAAAAACTGAGAAAATTGCATTTATCCTTGAACAA
                                                                                   ||   ||   |||| |    |  |  | |   ||    |  ||  |   |  |  |||    |    ||| |   ||      ||   |||||||||| || |||||||||||||| || ||||||||||| || || || || || 
gtatgatccctaatcttccactttttttgaaacttatatttaggagcaagaaatttcgtttttgatctcgaagtcggtgtgaagtggtatgcggtgcctgaaccagtagattggtctacgcagctttctaattgatgcacctgatctaataatgttgcaatactccaatgaagGTGGAGACCTTCGGTGCTATGGCAAAGACAGAGAAAATTGCTTTCATTCTAGAGCAG

upper sequence: AT5G09900.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S257_89V6.2 (Physcomitrella patens), 3'ss of exon 4
----------------------------------------------------------gtaagattttgtgcatttggctatta----aatctcctggaaattttcttcccttgttaacccctg---caatttgataaataattaacagGTGGAGACATTTGGTGCTATGGCAAAAACTGAGAAAATTGCATTTATCCTTGAACAA
                                                           |    |      ||||| | |  ||    | |   | ||    | | ||   |  |  | |||||   |   | |     |  |   |||||||| || |||||||| ||||||||||||||||| ||||| || || |||||||||
gtatgtgatattgcttcgtgctgttgatcaattcaacggttagtaacatgtaatgttcatggtgtggaagacattttggtgctactagagtgcacagggtggtgtattgaatattggagccctgattcgtatcggcgtttggtcttcagGTGGAAACTTTTGGTGCCATGGCAAAAACTGAGAAGATTGCTTTCATTCTTGAACAA

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|125313119|gb|EL327204.1|EL327204
EST:     CAGATCTTATGCAAGAAGTTGCT                         GTGGAGACATTTGGTGCTATGGCAAAAACTGAGAAAATTGCATTTATCCTT
genomic: CAGATCTTATGCAAGAAGTTGCTgtaagatttt ... taattaacagGTGGAGACATTTGGTGCTATGGCAAAAACTGAGAAAATTGCATTTATCCTT
EST: gi|116434451|gb|EG477043.1|EG477043
EST:     AAGAACAGGGTCAGATAGCTGAAGCTGCAGATCTTATGCAAGAAGTTGCT                         GTGGAGACATTTGGTGCTATGGCAAAAACTGAGAAAATTGCATTTATCCTT
genomic: AAGAACAGGGTCAGATAGCTGAAGCTGCAGATCTTATGCAAGAAGTTGCTgtaagatttt ... taattaacagGTGGAGACATTTGGTGCTATGGCAAAAACTGAGAAAATTGCATTTATCCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcctggaaattttcttcccttgttaacccctgcaatttgataaataattaacagGTGGAGACATTTGGTGCTATGGCAAAAACTGAGAAAATTGCATTTATCCTTGAACAA
                                  aatttgataaataatt  TA-rich tract