Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagctatagttattctctgttattggtttggttaataaaaaaatctcgagattaacattttcgtttggtgctaattcccgatatgcagGTTGCGAAAGAGAATGCTGATGTGATCATAATGGACGATAACTTCAAAACAATAGTAAATGTGGCTAGATGGGGACGTGCTGTATATATAAACATTCAGA

Basic information

species Arabidopsis thaliana
transcript AT2G41560.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G41560.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os05g41580.1 (Oryza sativa), 3'ss of exon 4
-gtaagctatagttattctctgttattggtttggttaataaaaaaatctcgagattaacattttcgtt---------tggtgctaattcc--cgatatgcagGTTGCGAAAGAGAATGCTGATGTGATCATAATGGACGATAACTTCAAAACAATAGTAAATGTGGCTAGATGGGGACGTGCTGTATATATAAACATTCAGA
  |  ||| ||    |  ||  | |||| ||| || |      |  |  || |  | | || |  ||          || ||| | ||    |  | |||||||||| |||||||  |||||||| || |||||||| || || ||| |||| || |||||||| ||||||||||| ||||| || ||  ||||||| ||||
ccttggctgtaacagtattc-atcattg-tttagtgacatttgattttccgtgtatgatatatctgtggacaagttgtgatgcaagttttatctgtttgcagGTTGCAAAAGAGAGCGCTGATGTTATAATAATGGATGACAATTTCGAAACCATTGTAAATGTTGCTAGATGGGGCCGTGCAGTTTACTTAAACATCCAGA

upper sequence: AT2G41560.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G305159_T02 (Zea mays), 3'ss of exon 5
---------gtaagctatagttattctctgttattgg--tttggttaataaaaaaatctcgagattaacattttcgtttggtgctaattcccgatatgcagGTTGCGAAAGAGAATGCTGATGTGATCATAATGGACGATAACTTCAAAACAATAGTAAATGTGGCTAGATGGGGACGTGCTGTATATATAAACATTCAGA
         |   |   | |||||||  |   | | |  |||  || || | | ||  |     |  | ||||  | | |    |  ||  |   |||||||| || ||||| ||||| ||||| || |||||||| ||||| ||||  || || |||||||| ||||||||||| ||||| || ||  | ||||||||||
cttagctgagattgtatttgttattccattcaactaggcttttctttatgatacaaattgttagtgtagatttatgat-gcaaatgtttggctggatgcagGTCGCAAAAGAAAATGCCGATGTTATAATAATGGATGATAATTTCAGTACCATTGTAAATGTTGCTAGATGGGGTCGTGCGGTTTACTTGAACATTCAGA

upper sequence: AT2G41560.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA10G15800.1 (Glycine max), 3'ss of exon 4
------------gtaagct---atagttattctctgttattggtttggttaataaaaaaatctcgagattaacattttcgtttggtgctaattcccgatatgcagGTTGCGAAAGAGAATGCTGATGTGATCATAATGGACGATAACTTCAAAACAATAGTAAATGTGGCTAGATGGGGACGTGCTGTATATATAAACATTCAGA
             |  | |   ||   |||| | | |||||| | ||||| |    |  | |   | | ||   ||    |||     | || ||   | | |||||||| ||||| ||||||||||| || |||||||| ||||||||||  || || || |||||||| ||||||||||| ||  |||| ||||||||||| |
aattcttgtcatatttgtttcgatgtctattttatattattg-tctggttgacgttatcacc--aatactatttttccttttttaaaattatacct--tttacagGTTGCCAAAGAAAATGCTGATGTCATTATAATGGATGATAACTTCACTACTATTGTCAATGTGGCCAGATGGGGACGGGCCATATACATAAACATTCAAA

upper sequence: AT2G41560.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA02G32780.1 (Glycine max), 3'ss of exon 4
------------gtaagct---atagttattctctgttattggtttggttaataaaaaaatctcgagattaacattttcgtttggtgctaattcccgatatgcagGTTGCGAAAGAGAATGCTGATGTGATCATAATGGACGATAACTTCAAAACAATAGTAAATGTGGCTAGATGGGGACGTGCTGTATATATAAACATTCAGA
             |  | |   ||   |||| | | |||||    ||||| ||   |  |     | ||||   ||    ||| |   | || ||   | | |||||||| ||||| ||||||||||| || |||||||| ||||||||||  || || || |||||||| || |||||||| ||  |||| ||||||||||| |
aatccttgtcctatttgtttcgatgtctattttatattatta-cctggttgatgttatcact--aatattatttttccttttttgaaattatacct--tttacagGTTGCCAAAGAAAATGCTGATGTCATTATAATGGATGATAACTTCACTACTATTGTCAATGTGGCCAGGTGGGGACGGGCCATATACATAAACATTCAAA

upper sequence: AT2G41560.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA03G29010.1 (Glycine max), 3'ss of exon 5
----------gtaagctat--agttattctctgttattggtttggttaataaaaaaatctcgagattaacattttcgtttggtgctaatt--cccgatatgcagGTTGCGAAAGAGAATGCTGATGTGATCATAATGGACGATAACTTCAAAACAATAGTAAATGTGGCTAGATGGGGACGTGCTGTATATATAAACATTCAGA
           | |  |||  |   | ||| |  | ||   || | |   |   | | ||    |||||||||||   |   |  |||||      || | ||||| || ||||| ||||||||||| || |||||||| ||||||||||  || || || ||||| |  | |||||||||||| ||||||||||||||||| |
tagtagttacatcatttatttaccgactctttaatttttcctttgctgccattgatacct----attaacattttttgtccttcataattaatttcatttacagGTCGCTAAAGAAAATGCTGATGTCATTATAATGGATGATAACTTCACGACTATTGTCAATGTTGTCAAATGGGGACGTGCAGTATATATAAACATTCAAA

upper sequence: AT2G41560.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA19G31770.1 (Glycine max), 3'ss of exon 2
------gtaagctatagttattctctgt-tattggt-----ttggttaataaaaaaatctcgagattaacattttcgtttggtgctaattcccgatatgcagGTTGCGAAAGAGAATGCTGATGTGATCATAATGGACGATAACTTCAAAACAATAGTAAATGTGGCTAGATGGGGACGTGCTGTATATATAAACATTCAGA
      |     | |  ||  ||| | | ||||  |     || | ||  |   | |||| |     |   |||  | ||| |  | | | || || | |||||||| ||||| ||||| ||||| || |||||||| ||||||||||  || || || ||||| |  | |||||||||||| ||||| ||||||||||| |
tacgtggcggtttctttttcctctttttatattaatgactctttgctaccattcatatctagtagc-attttttgtgcttgataattaatacc-atttacagGTTGCCAAAGAAAATGCCGATGTCATTATAATGGATGATAACTTCACGACTATTGTCAATGTTGTCAAATGGGGACGTGCAGTATACATAAACATTCAAA

upper sequence: AT2G41560.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv08s0007g08960.t01 (Vitis vinifera), 3'ss of exon 4
----gtaagctatagttattctctgttattggtttggttaataaaaaaatctcgagatta-------acattttcgtttggtgctaattcccgatatgcagGTTGCGAAAGAGAATGCTGATGTGATCATAATGGACGATAACTTCAAAACAATAGTAAATGTGGCTAGATGGGGACGTGCTGTATATATAAACATTCAGA
    ||| | |  |     || ||| || |  ||    |  ||        |    ||||       || |   | | |     |  |     || |  ||||||| ||||| ||||||||||| ||||||||||||||||| ||    || ||||||||||| || | |||||| ||||| ||||||||||||||||| |
acttgtaggatgcaacctgtc-ctgctacttattccagtgctattcctgcttttgcattattcttgaacttacccatatatacatggtatgttatctatagGTTGCCAAAGAAAATGCTGATGTCATCATAATGGACGATAATTTTGCCACTATAGTAAATGTAGCCAAATGGGGCCGTGCAGTATATATAAACATTCAAA

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|125028833|gb|EL101102.1|EL101102
EST:     GGCAGACATTGGACTAGCAATGGGAATAGCTGGAACAGAG                         GTTGCGAAAGAGAATGCTGATGTGATCATAATGGA
genomic: GGCAGACATTGGACTAGCAATGGGAATAGCTGGAACAGAGgtaagctata ... cgatatgcagGTTGCGAAAGAGAATGCTGATGTGATCATAATGGA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aataaaaaaatctcgagattaacattttcgtttggtgctaattcccgatatgcagGTTGCGAAAGAGAATGCTGATGTGATCATAATGGACGATAACTTCAAAACAATAGTAAATGTGGCTAGATGGGGACGTGCTGTATATATAAACATTCAGA
                                   tgctaat  putative branch site (score: 2)
                                         ttccc  CT-rich tract
                 attaacatttt  TA-rich tract