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

gtctgtcttttaagtcttgttcatattttggttctggttttttaaagagcaatcttatattcagtgatcttacattgagttcttaaattgtgcagTTTGGGTACATTGTTCTTACGACCTCGGCTGGTATTATGGACCACGAAGAAGCCAGGAGAAAGAATGTTGGTGGCAAGGTTCTTGGCTTCTTTTACTGAA

Basic information

species Arabidopsis thaliana
transcript AT5G59850.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G59850.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G018228_T02 (Zea mays), 3'ss of exon 2
gtctgtctt--ttaagtcttgttcatattttggttctggttttttaaagagcaatcttatattcagtgatcttacattgagttcttaaattgtgcagTTTGGGTACATTGTTCTTACGACCTCGGCTGGTATTATGGACCACGAAGAAGCCAGGAGAAAGAATGTTGGTGGCAAGGTTCTTGGCTTCTTTTACTGAA
||  |||     |      | | || | | || ||   |||| |    |  || | | |    |||||  || ||  ||  |  || | | ||| ||||||| ||||| || || || || || ||||| ||||||||||| || || ||| |  | ||||||||||||||||||||||| || |||||||| ||||
gttagtccaggctgctgtctctacaaaatctgattagagtttgtct--gtacactttgac-cccagtg--ctaactgtgcctctttgactggtgtagTTTGGCTACATCGTCCTAACAACTTCTGCTGGAATTATGGACCATGAGGAGGCCCGCCGTAAGAATGTTGGTGGCAAGGTTCTAGGTTTCTTTTATTGAA

upper sequence: AT5G59850.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G059624_T01 (Zea mays), 3'ss of exon 2
----gtctgtcttttaagt-cttgttcatattt-tggttct-ggttttttaaagagcaatcttatattcag--tgatcttacattg----------agttct-----taaattgtgcagTTTGGGTACATTGTTCTTACGACCTCGGCTGGTATTATGGACCACGAAGAAGCCAGGAGAAAGAATGTTGGTGGCAAGGTTCTTGGCTTCTTTTACTGAA
    ||| ||   ||   | |   ||| | ||| |   | | | | |   |  ||| | |  || || |||  ||||  || |||           || | |     |  |||||||| ||||| |  |||||  | || ||||||||||| || ||||| ||| ||||||||| ||| |||||||||||||| || || || || || || |||    
gtacgtccgttccttcgctacacattcttgtttctaactatagatctagcattgagtatttgtacatgcagtttgattctatattataatttaactagctttccctgtccattgtGCAATTTGGTTTTATTGTCTTGACCACCTCGGCTGGCATCATGGATCACAAAGAAGCCACGAGGAAGAATGTTGGTGGAAATGTGCTAGGTTTTTTCTAC----

upper sequence: AT5G59850.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G328578_T01 (Zea mays), 3'ss of exon 3
gtctgtcttttaagtcttgttcatatt--ttggttctggttttttaaagagcaatcttatattcagtgatcttacattgagttcttaaat--tgtgcagTTTGGGTACATTGTTCTTACGACCTCGGCTGGTATTATGGACCACGAAGAAGCCAGGAGAAAGAATGTTGGTGGCAAGGTTCTTGGCTTCTTTTACTGAA
||  |||   |  |   | |  |||     || ||   ||| | |  | |  |    |  |  |||||  || ||  ||  |  || | |  |||| ||||||| ||||| || || || || || ||||| ||||||||||| || || || ||  | ||||||||||||| ||||| ||| || |||||||||||||
gttagtccaatccgctgtctctataaaagctgattagagttgtctgtacaata----tgaaaccagtg--ctaactgtgcctctttgactggtgtgtagTTTGGCTACATCGTCCTAACAACTTCTGCTGGAATTATGGACCATGAGGAGGCTAGCCGTAAGAATGTTGGTGCCAAGGCTCTAGGTTTCTTTTACTGAA

upper sequence: AT5G59850.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S115_101V6.1 (Physcomitrella patens), 3'ss of exon 2
gtctgtcttttaagtcttgttcatattttggttctggttttttaaagagcaatctta---tattcagtgatcttacattga-gttcttaaattgt--gcagTTTGGGTACATTGTTCTTACGACCTCGGCTGGTATTATGGACCACGAAGAAGCCAGGAGAAAGAATGTTGGTGGCAAGGTTCTTGGCTTCTTTTACTGAA
   |   ||   |||  |||    | ||| ||  ||  | ||      | | |||||   ||||  ||    ||    ||| | || |   ||||  | ||||||| ||||||||| | || || || ||||| |||||||||||||| || |||||||||||||| || || || ||||||||||| |||||||||||| 
acttaagttgacagtagtgtggggaatttcgtagtgagtattgcctttg-actcttagggtatttggttccattctgctgatgctcgtttcttgtttgtagTTTGGATACATTGTTTTGACAACATCTGCTGGAATTATGGACCACGACGAGGCCAGGAGAAAGAACGTAGGAGGAAAGGTTCTTGGTTTCTTTTACTGAT

upper sequence: AT5G59850.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S426_18V6.1 (Physcomitrella patens), 3'ss of exon 2
gtctgtctttta-agtcttgttcatattttggtt-ctggttttttaaagagcaatcttatattcagtgatcttacattgagttcttaaattgt----gcagTTTGGGTACATTGTTCTTACGACCTCGGCTGGTATTATGGACCACGAAGAAGCCAGGAGAAAGAATGTTGGTGGCAAGGTTCTTGGCTTCTTTTACTGAA
 ||||| |||   | ||   ||  | | ||||   |  ||   | ||    | |  |   |     |    |  ||| || || | |  || |    |||||| || ||||||||  | |||||||| |||||||||||||| ||||| || |||||| | ||||| || || ||||| || || || ||||| || ||| 
-tctgtatttggcattcacattattgtcttggcaacaagtcaatgaacccacgaattggaagagcatatcttctcatggacttgtgatttttttggggcagTTCGGTTACATTGTATTGACGACCTCAGCTGGTATTATGGATCACGATGAGGCCAGGCGTAAGAACGTAGGAGGCAAAGTCCTGGGTTTCTTCTATTGAG

upper sequence: AT5G59850.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S61_209V6.1 (Physcomitrella patens), 3'ss of exon 2
-gtctgtcttttaagtcttgttcat-attttggttctggttttttaaagagcaatctt--atattcagtgatcttacattgagttc-ttaaattgtgcagTTTGGGTACATTGTTCTTACGACCTCGGCTGGTATTATGGACCACGAAGAAGCCAGGAGAAAGAATGTTGGTGGCAAGGTTCTTGGCTTCTTTTACTGAA
  | |  |||     ||| || ||  |||| |  |    |      |  || ||      || |||    || | |  |   |||  |    ||||||||||||| ||||||||  | |||||||| |||||||||||||| ||||| || || ||| | ||||| || || || |||||  | || ||||| || | | 
catgtaacttacccttctagtgcaggatttcgagtagtataaacgtacaagtaaatcagaatgttcgaccatgtcatttactgtttgtcctgttgtgcagTTTGGCTACATTGTATTGACGACCTCAGCTGGTATTATGGATCACGATGAGGCTAGGCGTAAGAACGTAGGAGGAAAGGTCTTAGGATTCTTCTATTAAG

upper sequence: AT5G59850.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S1_304V6.1 (Physcomitrella patens), 3'ss of exon 2
---gtctgtcttttaagtcttgttcata-----ttttggttctggttttttaaagagcaatcttatattcagtgatcttacattgagttcttaaa---ttgtgcagTTTGGGTACATTGTTCTTACGACCTCGGCTGGTATTATGGACCACGAAGAAGCCAGGAGAAAGAATGTTGGTGGCAAGGTTCTTGGCTTCTTTTACTGAA
   |        ||||  ||  |  | |     |  || | | | |  ||| | |    | | |  | ||  ||||      ||||||| || |    || |||||||||| ||||||||| | || ||||| ||||| || ||||||||||| || || || || ||||||||||| || ||||| ||||| |||||||||||| 
aacgatcaagcgttaatcctcctcaagaggatttcatgttaccgctgcttttaggtatgaacctgaaatc--tgat----tgttgagtttttcatcttttttgcagTTTGGATACATTGTTTTGACCACCTCAGCTGGCATCATGGACCACGACGAGGCTAGAAGGAAGAATGTTGGAGGAAAGGTCCTTGGTTTCTTTTACTGAG

upper sequence: AT5G59850.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S45_88V6.1 (Physcomitrella patens), 3'ss of exon 2
----gtctg-tcttttaagtcttgttcatattttggttctggttttttaaagagcaatcttatattcagtgatcttacattgagttc-ttaaattgtgcagTTTGGGTACATTGTTCTTACGACCTCGGCTGGTATTATGGACCACGAAGAAGCCAGGAGAAAGAATGTTGGTGGCAAGGTTCTTGGCTTCTTTTACTGAA
     |||  ||||     ||   |||| | | | | |    |||   | | |  || |   ||  | ||         |||  ||  ||   | ||||||||||| ||||||||  | || || || ||||| |||||||| ||||| || |||||| ||||||| || || |||||||| |||||||||||||||||| 
gtttctctactcttccgcatcgctttcaaaatatagcttctatttca-agaaaataaacccgtaagccgtatcgacttgttgttttggttttgtggtgcagTTTGGTTACATTGTGATGACAACGTCAGCTGGCATTATGGATCACGATGAGGCCAGGCGAAAGAACGTAGGAGGCAAGGTCCTTGGCTTCTTTTACTGAG

upper sequence: AT5G59850.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: EFJ14550 (Selaginella moellendorffii), 3'ss of exon 2
gtctgtcttttaagtcttgttcatattttggttctggttttttaaagagcaatcttatattcagtgatcttacattgagttcttaaattgtgcagTTTGGGTACATTGTTCTTACGACCTCGGCTGGTATTATGGACCACGAAGAAGCCAGGAGAAAGAATGTTGGTGGCAAGGTTCTTGGCTTCTTTTACTGAA
        ||| | | |     |    | | |   || ||  |  | || | |         |  ||| ||   ||   |   |     |  |||||||| |||||||| || || || ||| | ||||| ||||| ||||| ||||| ||||| |||||||||||||||||||| || |||||||| || ||| 
-------gtttgattttgagagacgaatcgat---ggcttggtgcaaagaagt---------aacgattttctcttcgatctctg----gctcagTTTGGTTACATTGTGCTGACAACATCGTCCGGTATCATGGATCACGACGAAGCGAGGAGGAAGAATGTTGGTGGCAAGGTCCTCGGCTTCTTCTATTGAT

upper sequence: AT5G59850.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: EFJ26253 (Selaginella moellendorffii), 3'ss of exon 2
gtctgtcttttaagtcttgttcatattttggttctggttttttaaagagcaatcttatattcagtgatcttacattgagttcttaaatt----gtgcagTTTGGGTACATTGTTCTTACGACCTCGGCTGGTATTATGGACCACGAAGAAGCCAGGAGAAAGAATGTTGGTGGCAAGGTTCTTGGCTTCTTTTACTGAA
                          |||| || ||       ||         |  |   ||  || || ||  |    ||||  ||     |  |||||||| |||||||| || || || ||| ||||||| ||||| ||||| ||||| ||||| |||||||||||||||||||| || |||||||| || ||| 
-------------------------gtttgattttgagagacgaatcgatggcttggtg--caaagaactaacgattttctcttcgatctctggctcagTTTGGCTACATTGTGCTGACAACATCGTCTGGTATCATGGATCACGACGAAGCGAGGAGGAAGAATGTTGGTGGCAAGGTCCTCGGCTTCTTCTATTGAT

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|86080051|gb|DR375808.1|DR375808
EST:     GAGTTAAGGAGATTGAAGGCTGGACCGCTCGTCTTCTTCCTTCCAGACAG                         TTTGGGTACATTGTTCTTACGACCTCGGCTGGTATTATGGACCACGAAGAA
genomic: GAGTTAAGGAGATTGAAGGCTGGACCGCTCGTCTTCTTCCTTCCAGACAGgtctgtcttt ... aattgtgcagTTTGGGTACATTGTTCTTACGACCTCGGCTGGTATTATGGACCACGAAGAA
EST: gi|124774597|gb|EH864726.1|EH864726
EST:     GAGTTAAGGAGATTGAAGGCTGGACCGCTCGTCTTCTTCCTTCCAGACAG                         TTTGGGTACATTGTTCTTACGACCTCGG
genomic: GAGTTAAGGAGATTGAAGGCTGGACCGCTCGTCTTCTTCCTTCCAGACAGgtctgtcttt ... aattgtgcagTTTGGGTACATTGTTCTTACGACCTCGG
EST: gi|125027932|gb|EL100201.1|EL100201
EST:     TCGTCTTCTTCCTTCCAGACAG                         TTTGGGTACATTGTTCTTACGACCTCGGCTGGTATTATGGACCACGAAGAA
genomic: TCGTCTTCTTCCTTCCAGACAGgtctgtcttt ... aattgtgcagTTTGGGTACATTGTTCTTACGACCTCGGCTGGTATTATGGACCACGAAGAA
EST: gi|164206160|gb|ES175027.1|ES175027
EST:     GAGTTAAGGAGATTGAAGGCTGGACCGCTCGTCTTCTTCCTTCCAGACAG                         TTTGGGTACATTGTTCT
genomic: GAGTTAAGGAGATTGAAGGCTGGACCGCTCGTCTTCTTCCTTCCAGACAGgtctgtcttt ... aattgtgcagTTTGGGTACATTGTTCT
EST: gi|164031367|gb|ES193570.1|ES193570
EST:     GAGTTAAGGAGATTGAAGGCTGGACCGCTCGTCTTCTTCCTTCCAGACAG                         TTTGGGTACATTGT-CTTACG
genomic: GAGTTAAGGAGATTGAAGGCTGGACCGCTCGTCTTCTTCCTTCCAGACAGgtctgtcttt ... aattgtgcagTTTGGGTACATTGTTCTTACG
EST: gi|86052270|gb|DR348027.1|DR348027
EST:     GAGTTAAGGAGATTGANGGCTGGACCGCTCGTCTTCTTCCTTCCAGACAG                         TTTGGGTACATTGTTCTTACGACCTCGGCTGGTATTATGGACCACGAAGAA
genomic: GAGTTAAGGAGATTGAAGGCTGGACCGCTCGTCTTCTTCCTTCCAGACAGgtctgtcttt ... aattgtgcagTTTGGGTACATTGTTCTTACGACCTCGGCTGGTATTATGGACCACGAAGAA
EST: gi|164215327|gb|ES072448.1|ES072448
EST:     TCTTCTTCCTTCCAGACAG                         TTTGGGTACATTGTTCTTACGACCTCGGCTGGTATTATGGACCACGAAGAA
genomic: TCTTCTTCCTTCCAGACAGgtctgtcttt ... aattgtgcagTTTGGGTACATTGTTCTTACGACCTCGGCTGGTATTATGGACCACGAAGAA
EST: gi|164230170|gb|ES198507.1|ES198507
EST:     GAGTTAAGGAGATTGAAGGCTGGACCGCTCGTCTTCTTCCTTCCAGACAG                         TTTGGGTACATTG
genomic: GAGTTAAGGAGATTGAAGGCTGGACCGCTCGTCTTCTTCCTTCCAGACAGgtctgtcttt ... aattgtgcagTTTGGGTACATTG
EST: gi|163995610|gb|ES193370.1|ES193370
EST:     GAGTTAAGGAGATTGAAGGCTGGACCGCTCGTCTTCTTCCTTCCAGACAG                         TTTGGGTACATTGTTCT
genomic: GAGTTAAGGAGATTGAAGGCTGGACCGCTCGTCTTCTTCCTTCCAGACAGgtctgtcttt ... aattgtgcagTTTGGGTACATTGTTCT
EST: gi|86081708|gb|DR377465.1|DR377465
EST:     GAGTTAAGGAGATTGAAGGCTGGACCGCTCGTCTTCTTCCTTCCAGACAG                         TTTGGGTACATTGTTCTTACGACCTCGGCTGGTATTATGGACCACGAAGAA
genomic: GAGTTAAGGAGATTGAAGGCTGGACCGCTCGTCTTCTTCCTTCCAGACAGgtctgtcttt ... aattgtgcagTTTGGGTACATTGTTCTTACGACCTCGGCTGGTATTATGGACCACGAAGAA
EST: gi|164066042|gb|ES038026.1|ES038026
EST:     GAGTTAAGGAGATTGAAGGCTGGACCGCTCGTCTTCTTCCTTCCAGACAG                         TTTGGGTACATTGTTC
genomic: GAGTTAAGGAGATTGAAGGCTGGACCGCTCGTCTTCTTCCTTCCAGACAGgtctgtcttt ... aattgtgcagTTTGGGTACATTGTTC
EST: gi|125234215|gb|EL248300.1|EL248300
EST:     TTCTTCCTTCCAGACAG                         TTTGGGTACATTGTTCTTACGACCTCGGCTGGTATTATGGACCACGAAGAA
genomic: TTCTTCCTTCCAGACAGgtctgtcttt ... aattgtgcagTTTGGGTACATTGTTCTTACGACCTCGGCTGGTATTATGGACCACGAAGAA
EST: gi|164072277|gb|ES177950.1|ES177950
EST:     GGCTGGACCGCTCGTCTTCTTCCTTCCAGACAG                         TTTGGGTACATTGTTCTTACGACCTCGGCTGGTATTATGGACCACGAAGAA
genomic: GGCTGGACCGCTCGTCTTCTTCCTTCCAGACAGgtctgtcttt ... aattgtgcagTTTGGGTACATTGTTCTTACGACCTCGGCTGGTATTATGGACCACGAAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttaaagagcaatcttatattcagtgatcttacattgagttcttaaattgtgcagTTTGGGTACATTGTTCTTACGACCTCGGCTGGTATTATGGACCACGAAGAAGCCAGGAGAAAGAATGTTGGTGGCAAGGTTCTTGGCTTCTTTTACTGAA
                          atcttac  putative branch site (score: 3)
          aatcttatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctgtcttttaagtcttgttcatattttggttctggttttttaaagagcaatcttatattcagtgatcttacattgagttcttaaattgtgcagTTTGGGTACATTGTTCTTACGACCTCGGCTGGTATTATGGACCACGAAGAAGCCAGGAGAAAGAATGTTGGTGGCAAGGTTCTTGGCTTCTTTTACTGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG