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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacacatattatagatagatatatggtagtatggtacaatagtaatttatgaaagataagggttggagaattgattaaatttgcagTGTGGAAAGAGCTAGCGAAAGAGAACAAAGAGTTCTTCGAGGCATACGAGAGAAGACGAGAAGAAATACCGACCGAGAAAGAGACAGCTCGAAGAATCCG

Basic information

species Arabidopsis thaliana
transcript AT5G02580.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G02580.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G108723_T01 (Zea mays), 3'ss of exon 2
---------------------------------------------------------------------------------------gtacacatattatagatagatatatggtagtatggtaca--------atagtaatttatgaaag-ataagggttggagaattg-attaaat--ttgcagTGTGGAAAGAGCTAGCGAAAGAGAACAAAGAGTTCTTCGAGGCATACGAGAGAAGACGAGAAGAAATACCGACCGAGAAAGAGACAGCTCGAAGAATCCG
                                                                                         |  |||| |||   |  |||   | |  ||   || |         |  || | ||| |    ||  ||  || | ||    |  | ||   |||||||||||| ||||||| |||||||||||| |||||||||||| | ||| | |     || || ||      |   |||   |||||        | |||  
gtaccggccgtactaccgtgcatatatactggacacgcgcacgcgttatgctttccttcccccgttcaaccatttctcgtttaccttccatgcataatatgcttcaataatcgatcatagattatattgttgttgttctattctatcatttcatgtggtctgaaaaagcacaccacatgcatgcagTGTGGAAGGAGCTAGAGAAAGAGAACAAGGAGTTCTTCGAGACGTACAACAAGGACCGCGAGGAGCGGAAGGTGGAGGCGGAGACGATGGCGCGGATCGA

upper sequence: AT5G02580.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA19G35810.1 (Glycine max), 3'ss of exon 2
-----------gtacacatattatagatagata-tatggtagtatggtacaatagta-atttatgaaagataagggttggagaat-tgattaaatttgcagTGTGGAAAGAGCTAGCGAAAGAGAACAAAGAGTTCTTCGAGGCATACGAGAGAAGACGAGAAGAAATACCGACCGAGAAAGAGACAGCTCGAAGAATCCG
           ||| |  | || |  ||   |  | |     | |  |    || |  || | |||| || |   ||    | || ||||       ||||| ||||| ||| ||| ||| |||||||| ||||||||||||||||||  ||| ||  ||| ||| | | |  | |||| |||||||   | ||| |||| 
atgttgttaaagta-atgtgttgtcaatgttttctctctctctctctttttttattctatctgtgaatgacacacgtgcatgcatgtgatcgcgcgagcagTTTGGAAGGAGTTAGAGAAGGAGAACAAGGAGTTCTTCGAGGCATACACGAGGAGCAGAGCAGAGAGAGCTTCGGAGAGAGAGACAAGGCAAAGGATCCA

upper sequence: AT5G02580.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA03G33110.1 (Glycine max), 3'ss of exon 2
---------gtacacatattatagatagatatatggtagtatg-----gtacaatagta-atttatgaaagataagggttggagaattgattaaatttgcagTGTGGAAAGAGCTAGCGAAAGAGAACAAAGAGTTCTTCGAGGCATACGAGAGAAGACGAGAAGAAATACCGACCGAGAAAGAGACAGCTCGAAGAATCCG
         ||     | || |   |   | |   |||   |       || |   ||   | | |||| || |   ||    | ||   | |  |  ||||| ||||| ||| ||| ||| |||||||| ||||||||||||||||||  ||| ||  ||| ||| | | |  | |||| |||||||   | ||| |||| 
taatatgttgtcattgttttctcttttttttttctgtaacctatatatatatatgtgtgtgtgtgtgaatgacacacgtgcatgcat--gtgatgtgcgcagTTTGGAAGGAGTTAGAGAAGGAGAACAAGGAGTTCTTCGAGGCATACACGAGGAGCAGAGTAGAGAAAGCTTCGGAGAGAGAGACAAGGCAAAGGATCCA

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|86029377|gb|DR325130.1|DR325130
EST:     GGATGCTCTGTTCAAGCATGCTAATATTAAGCCTATCATCACTTCCACAG                         TGT-GAAAGAGCTAGCGAAAGAGAACAAAGAGTTCTTCGAGGCATACGAGA
genomic: GGATGCTCTGTTCAAGCATGCTAATATTAAGCCTATCATCACTTCCACAGgtacacatat ... aaatttgcagTGTGGAAAGAGCTAGCGAAAGAGAACAAAGAGTTCTTCGAGGCATACGAGA
EST: gi|86029380|gb|DR325133.1|DR325133
EST:     GGATGCTCTGTTCAAGCATACTAATATTAAGCCTATCATCACTTCCACAG                         TGTG-AAAGAGCTAGCGAAAGAGAACAAAGAGTTCTTCGAGGCATACGAGA
genomic: GGATGCTCTGTTCAAGCATGCTAATATTAAGCCTATCATCACTTCCACAGgtacacatat ... aaatttgcagTGTGGAAAGAGCTAGCGAAAGAGAACAAAGAGTTCTTCGAGGCATACGAGA
EST: gi|86029379|gb|DR325132.1|DR325132
EST:     GGATGCTCTGTTCAAGCATGCTAATATTAAGCCTATCATCACTTCCACAG                         TGTG-AAAGAGCTAGCGAAAGAGAACAAAGAGTTCTTCGAGGCATACGAGA
genomic: GGATGCTCTGTTCAAGCATGCTAATATTAAGCCTATCATCACTTCCACAGgtacacatat ... aaatttgcagTGTGGAAAGAGCTAGCGAAAGAGAACAAAGAGTTCTTCGAGGCATACGAGA
EST: gi|86076807|gb|DR372564.1|DR372564
EST:     GGATGCTCTGTTCAAGCATACTAATATTAAGCCTATCATCACTTCCACAG                         TGTGGAAAGAGCTAGCGAAAGAGAACAAAGAGTTCTTCGAGGCATACGAGA
genomic: GGATGCTCTGTTCAAGCATGCTAATATTAAGCCTATCATCACTTCCACAGgtacacatat ... aaatttgcagTGTGGAAAGAGCTAGCGAAAGAGAACAAAGAGTTCTTCGAGGCATACGAGA
EST: gi|86029378|gb|DR325131.1|DR325131
EST:     GGATGCTCTGTTCAAGCATGCTAATATTAAGCCTATCATCACTTCCACAG                         TGTG-AAAGAGCTAGCGAAAGAGAACAAAGAGTWMTTCGAGGCATACGAGA
genomic: GGATGCTCTGTTCAAGCATGCTAATATTAAGCCTATCATCACTTCCACAGgtacacatat ... aaatttgcagTGTGGAAAGAGCTAGCGAAAGAGAACAAAGAGTTCTTCGAGGCATACGAGA
EST: gi|19874569|gb|AU235400.1|AU235400
EST:     GGATGCTCTGTTCAAGCATGCTAATATTAAGCCTATCATCACTTCCACAG                         TGTGGAAAGAGCTAGCGAAAGAGAACAAAGAGTTCTTCGAGGCATACGAGA
genomic: GGATGCTCTGTTCAAGCATGCTAATATTAAGCCTATCATCACTTCCACAGgtacacatat ... aaatttgcagTGTGGAAAGAGCTAGCGAAAGAGAACAAAGAGTTCTTCGAGGCATACGAGA
EST: gi|86029381|gb|DR325134.1|DR325134
EST:     GGATGCTCTGTTCAAGCATGCTAATATTAAGCCTATCATCACTTCCACAG                         TGTGGAAAGAGCTAGCGAAAGAGAACAAAGAGTTCTTCGAGGCATACGAGA
genomic: GGATGCTCTGTTCAAGCATGCTAATATTAAGCCTATCATCACTTCCACAGgtacacatat ... aaatttgcagTGTGGAAAGAGCTAGCGAAAGAGAACAAAGAGTTCTTCGAGGCATACGAGA
EST: gi|86029382|gb|DR325135.1|DR325135
EST:     GGATGCTCTGTTCAAGCATGCTAATATTAAGCCTATCATCACTTCCACAG                         TGTG-AAAGAGCTAGCGAAAGAGAACAAAGAGTTCTTCGAGGCATACGAGA
genomic: GGATGCTCTGTTCAAGCATGCTAATATTAAGCCTATCATCACTTCCACAGgtacacatat ... aaatttgcagTGTGGAAAGAGCTAGCGAAAGAGAACAAAGAGTTCTTCGAGGCATACGAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggtacaatagtaatttatgaaagataagggttggagaattgattaaatttgcagTGTGGAAAGAGCTAGCGAAAGAGAACAAAGAGTTCTTCGAGGCATACGAGAGAAGACGAGAAGAAATACCGACCGAGAAAGAGACAGCTCGAAGAATCCG
                                     aattgat  putative branch site (score: 4)
      aatagtaatttatgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacacatattatagatagatatatggtagtatggtacaatagtaatttatgaaagataagggttggagaattgattaaatttgcagTGTGGAAAGAGCTAGCGAAAGAGAACAAAGAGTTCTTCGAGGCATACGAGAGAAGACGAGAAGAAATACCGACCGAGAAAGAGACAGCTCGAAGAATCCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA