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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaaaaagccaaagaaaatataaaaatccttgcaacatatatatccggcctatatattttgttatcataatattaatgaattggaacaaaataaatgacagTGTGGAAGGAGCTGGAGAAAGAGAACAAGGAATTCTTCAAGGCGTATGAGGAGAGGCAAAGCAAACAAGAGCAAATGTCGGAGGAAGAGACAAACCAGAT

Basic information

species Arabidopsis thaliana
transcript AT3G55240.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G55240.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os05g38680.1 (Oryza sativa), 3'ss of exon 2
aaaaaagccaaagaaaatataaaaatccttgcaacatatatatccggcctatatattttgttatcataatattaa--tgaattggaacaaaataaatgacagTGTGGAAGGAGCTGGAGAAAGAGAACAAGGAATTCTTCAAGGCGTATGAGGAGAGGCAAAGCAAACAAGAGCAAATGTCGGAGGAAGAGACAAACCAGAT---
  | |    ||      |||    ||   |   |       | ||||   || || |   ||  ||| || | ||  |  |||   |          | |||| ||||||||||||||||| ||||||||||| |||||| || | ||  |  || | ||  ||  |    | ||  |   || |||   ||   | | |||   
-tatattttaatctttgtatggctatgtatcttatgacagaagccggag-atgtaatccatttgcattatctaaaaatatattttgatctttgtggcggcagTATGGAAGGAGCTGGAGAAGGAGAACAAGGAGTTCTTCGAGACCTACAACAAG-GACAGGGCGGAGCGCAACA--TCGAGGCGGAGACGATGCAGCGGATCCA

upper sequence: AT3G55240.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G108723_T01 (Zea mays), 3'ss of exon 2
-------------------------------------------------------------------------------------aaaaaagccaaagaaaatataaaaatcc-ttgcaacatatatatccggcctatatattttgttat--cataatattaatgaattggaacaaaataaatgacagTGTGGAAGGAGCTGGAGAAAGAGAACAAGGAATTCTTCAAGGCGTATGAGGAGAGGCAAAGCAAACAAGAGCAAATGTCGGAGGAAGAGACAAACCAGAT---
                                                                                         | ||  || |   |  || ||||  |   |   |||||    |   | | |||| | | ||  |||    |     ||     || | ||  ||| |||||||||||||||| ||||||||||||||||| |||||| || ||||  |  ||   |   || |  |   | |  ||  || |||   ||     | |||   
gtaccggccgtactaccgtgcatatatactggacacgcgcacgcgttatgctttccttcccccgttcaaccatttctcgtttaccttccatgcataatatgcttcaataatcgatcatagattatattgttgttgt-tctattctatcatttcatgtggtctgaaaaagcacaccacatgcatg-cagTGTGGAAGGAGCTAGAGAAAGAGAACAAGGAGTTCTTCGAGACGTACAACAAGGACC---GCGAGGAGCGGAAGGTGGAGGCGGAGACGATGGCGCGGATCGA

upper sequence: AT3G55240.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G370044_T01 (Zea mays), 3'ss of exon 2
---------------------------------------------------------------------aaaaaagccaaagaaaatataaaaatccttgcaacatatatatccggcctatatattttgttatcataatattaatgaattggaacaaaataaatgacagTGTGGAAGGAGCTGGAGAAAGAGAACAAGGAATTCTTCAAGGCGTATGAGGAGAGGCAAAGCAAACAAGAGCAAATGTCGGAGGAAGAGACAAACCAGAT---
                                                                         | ||||||  |||  ||  | |  | |   |     ||||   |  ||  |  |  |   | |   |||| |  | |  |         ||  |||||||||||||||||||||| ||||||| ||| |||||| || ||||  || ||   |   |   |||||||     |  | || |  |  ||  | |      
gtaggccgtaggcggcactcttgcaagcaagcgattaatcgagattatttcaagagtagttaagttgtcgtccacgccaaattaaagctactactagtcgactcgatcgtatcgatctcattgacctctt---cttggcattattatactatacatgctgctatagcagTGTGGAAGGAGCTGGAGAAGGAGAACAGGGAGTTCTTCGAGACGTACAAGAAGTATCTGGG---ACAAGAGTCGGCGCTGCAGAAGAATCCATCCGATGGACA

upper sequence: AT3G55240.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA10G43720.1 (Glycine max), 3'ss of exon 2
----aaaaaagccaaagaaaatataaaaatccttgcaacatatatatccggcctatatattttgttatcataatattaatgaattggaacaaaataaatg--acagTGTGGAAGGAGCTGGAGAAAGAGAACAAGGAATTCTTCAAGGCGTATGAGGAGAGGCAAAGCAAACAAGAGCAAATGTCGGAGGAAGAGACAAACCAGAT
      |  | ||||  |||| | ||  || |     || |  ||||   |    |||||  | |||| | |  ||  ||  | |        |||  ||   |||||||||||||||| ||||| || ||||||||||||||| || | ||   | ||  | ||   ||| | ||   ||||||  |||||||||||||||||||
tccactaccaaccaaccaaaagacaagcatgc-----acgtgcatatgttgaaagtatatgattttatga-agcatggatataatacgtatggatacgtgcttcagTGTGGAAGGAGCTAGAGAAGGAAAACAAGGAATTCTTCGAGCCTTACATGAAGTCGAAAGCTAAAGACGACAGAATGTCTCAGGAAGAGACAAACCAGAT

upper sequence: AT3G55240.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA20G38420.1 (Glycine max), 3'ss of exon 2
-aaaaaagccaaagaaaatataaaaatccttgcaacatatatatccggcctatatattttgttatcataatattaatgaattggaacaaaataaatg--acagTGTGGAAGGAGCTGGAGAAAGAGAACAAGGAATTCTTCAAGGCGTATGAGGAGAGGCAAAGCAAACAAGAGCAAATGTCGGAGGAAGAGACAAACCAGAT
  ||    ||||  |||| | ||  || |  |   ||||| |     || ||   ||  | |||| | || || |||  | |        |||  ||   |||||||||||||||| ||||| || ||||||||||||||  |||| ||   | ||  | |    ||| | ||   ||||||  ||||||||||||| |||||
ccaacctaccaaccaaaacagaagcatgcacgtg-catatgttgaaagcatacg-atgattttatga-aacatgaatataatacgtatggatacgtgcttcagTGTGGAAGGAGCTAGAGAAGGAAAACAAGGAATTCTTTGAGGCTTACATGAAGTCGAAGGCTAAAGACGACAGAATGTCTCAGGAAGAGACAAATCAGAT

upper sequence: AT3G55240.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv00s0317g00030.t01 (Vitis vinifera), 3'ss of exon 2
aaaaaagccaaagaaaatataaaaatccttgcaacatatatatccggcctatatattttgttatcataatattaatgaattggaacaaaataaatg---acagTGTGGAAGGAGCTGGAGAAAGAGAACAAGGAATTCTTCAAGGCGTATGAGG---AGAGGCAAAGCAAACAAGAGCAAATGTCGGAGGAAGAGACAAACCAGAT
   |    ||   |  |         |  ||     | |  |||  |   ||    | | |  |  |   ||||  |  |    | ||| |   ||    |||||||||| ||  |||||||||||||||||||||||||  | |  ||  |     | |  ||||  ||  | || |   |||| |||| ||||||  || |   
---accatcatgcatgagcatgtgccctatgtcttcttttcatcaagtaaatggcatatatagtggttgcattatggcctctagaaaaagtttgtgcatgcagTGTGGAATGAATTGGAGAAAGAGAACAAGGAATTCTTTGAAGGCTACAACACTCAAACTCAAACTAAGGACGACCGTCTGTCAGAGGCAGAGACCGACGA---

upper sequence: AT3G55240.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv00s0317g00020.t01 (Vitis vinifera), 3'ss of exon 2
-aaaaaagccaaagaaaatataaaaatc-cttgcaacatatatatccg--gcctatatattttgttatcataatattaatgaattggaacaaaataaatg-acagTGTGGAAGGAGCTGGAGAAAGAGAACAAGGAATTCTTCAAGGCGTATGAGG---AGAGGCAAAGCAAACAAGAGCAAATGTCGGAGGAAGAGACAAACCAGAT
   |    |   |||  ||  |  |||| ||  | |  | | |  |    |   | |||  |   ||   |  || || |    |  || ||  ||  ||  |||||||||| ||  |||||||||||||||||||||||||  |||| ||  |     | |  |||| || | | ||   |||||| ||||  ||||||||| |   
gttagctcctttagatcatgcacgaatctctctctatgtgtttgcctttcgttcacataactccgtacggtcgtaatatttttgtataaaaatttatgtgtgcagTGTGGAATGAATTGGAGAAAGAGAACAAGGAATTCTTTGAGGCCTACCATACTCAAACCCAAACCAGAGATGACAGAATGTCAGAGGCTGAGACAAACGA---

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|125078060|gb|EL140594.1|EL140594
EST:     TCACCTCTACTG                         TGTGGAAGGAGCTGGAGAAAGAGAACAAGGAATTCTTCAAGGCGTATGAGG
genomic: TCACCTCTACTGgttttaattc ... taaatgacagTGTGGAAGGAGCTGGAGAAAGAGAACAAGGAATTCTTCAAGGCGTATGAGG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggcctatatattttgttatcataatattaatgaattggaacaaaataaatgacagTGTGGAAGGAGCTGGAGAAAGAGAACAAGGAATTCTTCAAGGCGTATGAGGAGAGGCAAAGCAAACAAGAGCAAATGTCGGAGGAAGAGACAAACCAGAT
                        tattaat  putative branch site (score: 2)
     atatattttgttatca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaaaaagccaaagaaaatataaaaatccttgcaacatatatatccggcctatatattttgttatcataatattaatgaattggaacaaaataaatgacagTGTGGAAGGAGCTGGAGAAAGAGAACAAGGAATTCTTCAAGGCGTATGAGGAGAGGCAAAGCAAACAAGAGCAAATGTCGGAGGAAGAGACAAACCAGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - -agccaaa
- - - - - - - - - ataaaaa
- - - - - - - - - - - - - - - -caacata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - atcataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aacaaaa