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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgttaaatctttactttctcctccttcccgcattcattgatcgcatatttagtgtttctaaacgtaaatggttttacttgtgtacaacagGCTTGTGCTTTCAGAGACTCTTATGAGAAATTCAAGAAAGCTGGTGCAGAGGTCATTGGCATTAGTGGAGATGACTCTGCTTCTCACAAG

Basic information

species Arabidopsis thaliana
transcript AT3G26060.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G26060.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA17G05150.1 (Glycine max), 3'ss of exon 2
----gttgttaaatctttactttctcctccttcccgcattcattgatcgcatatttagtgtttctaaac---gtaaatggtt--ttacttgtgtacaacagGCTTGTGCTTTCAGAGACTCTTATGAGAAATTCAAGAAAGCTGGTGCAGAGGTCATTGGCATTAGTGGAGATGACTCTGCTTCTCACAAG
         |||||  || || |     | |      | |||| |  |  || |||| | | | | ||     ||| |  ||  ||| || | ||   |||||||| |||||||| || || || ||||| ||||||||||| || |||| |||  |||| || ||||| |||||  |||| |||||||||
aacaaacaataaatgattgctattgtaccatcgatatagtcatggggcctat-tttactatctattaattaattaattaattaattaattttttattgcagGCTTGCGCTTTCAGGGATTCATACGAGAAGTTCAAGAAAGCAGGAGCAGTGGTTGTTGGGATAAGTGGTGATGATGCTGCCTCTCACAAG

upper sequence: AT3G26060.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA13G17350.1 (Glycine max), 3'ss of exon 2
----gttgttaaatctttactttctcctccttcccgcattcattgatcgcatatttagtgtttctaaacgta-aatgg---ttttacttgtgtacaacagGCTTGTGCTTTCAGAGACTCTTATGAGAAATTCAAGAAAGCTGGTGCAGAGGTCATTGGCATTAGTGGAGATGACTCTGCTTCTCACAAG
    ||  |        ||   | |   |     | || | | | || ||   | ||   ||  || |   |   |||   |||||||  | ||   |||||||| |||||||| || || |||||||| ||||||||||| || || | |||  |||| || ||||| |||||  |||| |||||||||
tactgtgctggtggtggtagaatatatgcaagaacacaataaatcattgctattgtaccattgatacagtcatggtggctattttactattttattgcagGCTTGCGCTTTCAGGGATTCATATGAGAAGTTCAAGAAAGCAGGAGCGGTGGTTGTTGGGATAAGTGGTGATGATGCTGCCTCTCACAAG

upper sequence: AT3G26060.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv11s0016g00560.t01 (Vitis vinifera), 3'ss of exon 2
gttgttaaatctt-tactttctcctccttcccgcattcattgatcgcatattta-gtgtttctaaacgtaaatggtt--ttacttgtgta----caacagGCTTGTGCTTTCAGAGACTCTTATGAGAAATTCAAGAAAGCTGGTGCAGAGGTCATTGGCATTAGTGGAGATGACTCTGCTTCTCACAAG
||| ||| ||    |  ||    | |  |||   | |   |  | | |   | | | |||||      |  |    |    | |  |||        ||||| ||||||||||| |||||||||||||||||||||||||| || ||  ||||  | ||||||||||| |||||| |  | || ||||||
gtttttacatgaaatggttaaaacccaatccaagaattggtattagaaccgtcatgggtttcagggaatggaaaactaacaattgatgtggccttggcagGCATGTGCTTTCAGGGACTCTTATGAGAAATTCAAGAAAGCAGGAGCCCAGGTTGTGGGCATTAGTGGTGATGACCCATCATCACACAAG

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|125135746|gb|EL175898.1|EL175898
EST:     ATGAAACCCCTGGCTGCACCAAGCAG                         GCTTGTGCTTTCAGAGACTCTTATGAGAAATTCAAGAAAGCTGGTGCAGAG
genomic: ATGAAACCCCTGGCTGCACCAAGCAGgttgttaaat ... tgtacaacagGCTTGTGCTTTCAGAGACTCTTATGAGAAATTCAAGAAAGCTGGTGCAGAG
EST: gi|125016918|gb|EL089187.1|EL089187
EST:     TTGTTCTCTACTTCCACCCTGCAGATGAAACCCCTGGCTGCACCAAGCAG                         GCTTGTGCTTTCAGAGACTCTTATGAGAAATTCAAGAAAG
genomic: TTGTTCTCTACTTCTACCCTGCAGATGAAACCCCTGGCTGCACCAAGCAGgttgttaaat ... tgtacaacagGCTTGTGCTTTCAGAGACTCTTATGAGAAATTCAAGAAAG
EST: gi|124863151|gb|EH947588.1|EH947588
EST:     TTGTTCTCTACTTCTACCCTGCAGATGAAACCCCTGGCTGCACCAAGCAG                         GCTTGTGCTTT
genomic: TTGTTCTCTACTTCTACCCTGCAGATGAAACCCCTGGCTGCACCAAGCAGgttgttaaat ... tgtacaacagGCTTGTGCTTT
EST: gi|125316083|gb|EL330168.1|EL330168
EST:     CTACTTCTACCCTGCAGATGAAACCCCTGGCTGCACCAAGCAG                         GCTTGTGCTTTCAGAGACTCTTATGAGAAATTCAAGAAAGCTGGTGCAGAG
genomic: CTACTTCTACCCTGCAGATGAAACCCCTGGCTGCACCAAGCAGgttgttaaat ... tgtacaacagGCTTGTGCTTTCAGAGACTCTTATGAGAAATTCAAGAAAGCTGGTGCAGAG
EST: gi|125031330|gb|EL103599.1|EL103599
EST:     TGTTCTCTACTTCTACCCTGTCAGATGAAACCCCTGGCTGCACCAAGCAG                         GCTTGTGCTTTCAGAGACTCTTATGAGAAATTCAAGAAA
genomic: TGTTCTCTACTTCTACCCTG-CAGATGAAACCCCTGGCTGCACCAAGCAGgttgttaaat ... tgtacaacagGCTTGTGCTTTCAGAGACTCTTATGAGAAATTCAAGAAA
EST: gi|124736053|gb|EH827455.1|EH827455
EST:     TGTTCTCTACTTCTACCCTGCAGATGAAACCCCTGGCTGCACCAAGCAG                         GCTTGTGCTTTCAGAGACTCTTATGAGAAATTCAAGAAAG
genomic: TGTTCTCTACTTCTACCCTGCAGATGAAACCCCTGGCTGCACCAAGCAGgttgttaaat ... tgtacaacagGCTTGTGCTTTCAGAGACTCTTATGAGAAATTCAAGAAAG
EST: gi|125025354|gb|EL097623.1|EL097623
EST:     CCCTGGCTGCACCAAGCAG                         GCTTGTGCTTTCAGAGACTCTTATGAGAAATTCAAGAAAGCTGGTGCAGAG
genomic: CCCTGGCTGCACCAAGCAGgttgttaaat ... tgtacaacagGCTTGTGCTTTCAGAGACTCTTATGAGAAATTCAAGAAAGCTGGTGCAGAG
EST: gi|124888832|gb|EH967734.1|EH967734
EST:     ACCCTGCAGATGAAACCCCTGGCTGCACCAAGCAG                         GCTTGTGCTTTCAGAGACTCTTATGAGAAATTCAAGACAGCTGGTGCAGAG
genomic: ACCCTGCAGATGAAACCCCTGGCTGCACCAAGCAGgttgttaaat ... tgtacaacagGCTTGTGCTTTCAGAGACTCTTATGAGAAATTCAAGAAAGCTGGTGCAGAG
EST: gi|116447992|gb|EG490584.1|EG490584
EST:     TTGTTCTCTACTTCTACCCTGCAGATGAAACCCCTGGCTGCACCAAGCAG                         GCTTGTGCTTTCAGAGA
genomic: TTGTTCTCTACTTCTACCCTGCAGATGAAACCCCTGGCTGCACCAAGCAGgttgttaaat ... tgtacaacagGCTTGTGCTTTCAGAGA
EST: gi|125245195|gb|EL259280.1|EL259280
EST:     CTGGCTGCACCAAGCAG                         GCTTGTGCTTTCAGAGACTCTTATGAGAAATTCAAGAAAGCTGGTGCAGAG
genomic: CTGGCTGCACCAAGCAGgttgttaaat ... tgtacaacagGCTTGTGCTTTCAGAGACTCTTATGAGAAATTCAAGAAAGCTGGTGCAGAG
EST: gi|125295011|gb|EL309096.1|EL309096
EST:     TTGTTCTCTACTTCTACCCTGCAGATGAAACCCCTGGCTGCACCAAGCAG                         GCTTGTGCTTTCAGAGACTCTT
genomic: TTGTTCTCTACTTCTACCCTGCAGATGAAACCCCTGGCTGCACCAAGCAGgttgttaaat ... tgtacaacagGCTTGTGCTTTCAGAGACTCTT
EST: gi|124993897|gb|EL066166.1|EL066166
EST:     TGTTCTCTACTTCTACCCTGCTAGATGAAACCCCTGGCTGCACCAAGCAG                         GCTTGTGCTTTCAGAGACTCTTATGAGAAATTCAAGAAAGC
genomic: TGTTCTCTACTTCTACCCTGC-AGATGAAACCCCTGGCTGCACCAAGCAGgttgttaaat ... tgtacaacagGCTTGTGCTTTCAGAGACTCTTATGAGAAATTCAAGAAAGC
EST: gi|125071086|gb|EL136263.1|EL136263
EST:     TTGTCCTCTACTTCTACCCTGCAGATGAAACCCCTGGCTGCACCAAGCAA                         GCTTGTGCTTTCAGAGACTCTTATGAGAAATTCAAGAAAG
genomic: TTGTTCTCTACTTCTACCCTGCAGATGAAACCCCTGGCTGCACCAAGCAGgttgttaaat ... tgtacaacagGCTTGTGCTTTCAGAGACTCTTATGAGAAATTCAAGAAAG
EST: gi|125186926|gb|EL201880.1|EL201880
EST:     TTGTTCTCTACTTCTACCCTGCAGATGAAACCCCTGGCTGCACCAAGCAG                         GCTTGTGCTTTCAGAGACTCTTATGAGAAATTCAAG
genomic: TTGTTCTCTACTTCTACCCTGCAGATGAAACCCCTGGCTGCACCAAGCAGgttgttaaat ... tgtacaacagGCTTGTGCTTTCAGAGACTCTTATGAGAAATTCAAG
EST: gi|125270560|gb|EL284645.1|EL284645
EST:     TTGTTCTCTACTTCTACCCTGCAGATGAAACCCCTGGCTGCACCAAGCAG                         GCTTGTGCTTTCAGAGACT
genomic: TTGTTCTCTACTTCTACCCTGCAGATGAAACCCCTGGCTGCACCAAGCAGgttgttaaat ... tgtacaacagGCTTGTGCTTTCAGAGACT
EST: gi|125252891|gb|EL266976.1|EL266976
EST:     TTGTTCTCTACTTCTACCCTGCAGATGAAACCCCTGGCTGCACCAAGCAG                         GCTTGTGCTTTCAGAGACT
genomic: TTGTTCTCTACTTCTACCCTGCAGATGAAACCCCTGGCTGCACCAAGCAGgttgttaaat ... tgtacaacagGCTTGTGCTTTCAGAGACT
EST: gi|124774045|gb|EH864174.1|EH864174
EST:     ATGAAACCCCTGGCTGCACCAAGCAG                         GCTTGTGCTTTCAGAGACTCTTATGAGAAATTCAAGAAAGCTGGTGCAGAG
genomic: ATGAAACCCCTGGCTGCACCAAGCAGgttgttaaat ... tgtacaacagGCTTGTGCTTTCAGAGACTCTTATGAGAAATTCAAGAAAGCTGGTGCAGAG
EST: gi|125034975|gb|EL107244.1|EL107244
EST:     TGTTACTCTACTTCTACCCTGCAGATGAAACCCCTGGCTGCACCAAGCAG                         GCTTGTGCTTTCAGAG
genomic: TGTT-CTCTACTTCTACCCTGCAGATGAAACCCCTGGCTGCACCAAGCAGgttgttaaat ... tgtacaacagGCTTGTGCTTTCAGAG
EST: gi|124764466|gb|EH854596.1|EH854596
EST:     TTGTTCTCTACTTCTACCCTGCAGATGAAACCCCTGGCTGCACCAAGCAG                         GCTTGTGCTTTCAGAGACTCTTATGAGAAATT
genomic: TTGTTCTCTACTTCTACCCTGCAGATGAAACCCCTGGCTGCACCAAGCAGgttgttaaat ... tgtacaacagGCTTGTGCTTTCAGAGACTCTTATGAGAAATT
EST: gi|86080940|gb|DR376697.1|DR376697
EST:     TTGTTCTCTACTTCTACCCTGCAGATGAAACCCCTGGCTGCACCAAGCAG                         GCTTGTGCTTTCAGAGACTCTTATGAGAAATTCAAGAAAGCTGGTGCAGAG
genomic: TTGTTCTCTACTTCTACCCTGCAGATGAAACCCCTGGCTGCACCAAGCAGgttgttaaat ... tgtacaacagGCTTGTGCTTTCAGAGACTCTTATGAGAAATTCAAGAAAGCTGGTGCAGAG
EST: gi|124934696|gb|EL011745.1|EL011745
EST:     GGCTGCACCAAGCAG                         GCTTGTGCTTTCAGAGACTCTTATGAGAAATTCAAGAAAGCTGGTGCAGAG
genomic: GGCTGCACCAAGCAGgttgttaaat ... tgtacaacagGCTTGTGCTTTCAGAGACTCTTATGAGAAATTCAAGAAAGCTGGTGCAGAG
EST: gi|124935149|gb|EL012158.1|EL012158
EST:     ATGAAACCCCTGGCTGCACCAAGCAG                         GCTTGTGCTTTCAGAGACTCTTATGAGAAATTCAAAAAAGCTGGTGCAGAG
genomic: ATGAAACCCCTGGCTGCACCAAGCAGgttgttaaat ... tgtacaacagGCTTGTGCTTTCAGAGACTCTTATGAGAAATTCAAGAAAGCTGGTGCAGAG
EST: gi|124810065|gb|EH895321.1|EH895321
EST:     TTGTTCTCTACTTCTACCCTGCAGATGAAACCCCTGGCTGCACCAAGCAG                         GCTTGTGCTTTCAGAGACTCTT
genomic: TTGTTCTCTACTTCTACCCTGCAGATGAAACCCCTGGCTGCACCAAGCAGgttgttaaat ... tgtacaacagGCTTGTGCTTTCAGAGACTCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgatcgcatatttagtgtttctaaacgtaaatggttttacttgtgtacaacagGCTTGTGCTTTCAGAGACTCTTATGAGAAATTCAAGAAAGCTGGTGCAGAGGTCATTGGCATTAGTGGAGATGACTCTGCTTCTCACAAG
                    ttctaaa  putative branch site (score: 2)
         atatttagt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgttaaatctttactttctcctccttcccgcattcattgatcgcatatttagtgtttctaaacgtaaatggttttacttgtgtacaacagGCTTGTGCTTTCAGAGACTCTTATGAGAAATTCAAGAAAGCTGGTGCAGAGGTCATTGGCATTAGTGGAGATGACTCTGCTTCTCACAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG