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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACAAAGCAGAAGTGAGAAGAAGAGTCGCAAAGCCATGCTCAAGCTTGGCATGAAACCCATCACTGGTGTTAGCCGAGTCACCGTCAAAAAGAGCAAGAATgtttgtgttttctctttaatattcagtcaatcttaatttcttttattcacacatcaggctttaatattgatctgttttggggacatttgctttggaacacag

Basic information

species Arabidopsis thaliana
transcript AT3G12390.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G12390.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: LOC_Os01g71230.2 (Oryza sativa), 5'ss of exon 3
ACAAAGCAGAAGTGAGAAGAAGAGTCGCAAAGCCATGCTCAAGCTTGGCATGAAACCCATCACTGGTGTTAGCCGAGTCACCGTCAAAAAGAGCAAGAATgtttgtgttttctctttaatattcagtcaatcttaatttcttttattcacacatcaggctttaatattgatctgttttggggacatttgctttggaacacag-
 || || || || ||||| |||||  | ||||||||||  || |||||||||||  ||||||||||||| ||||| |||||  |||||||||||||||| ||  | | |   |  | | | ||  | || |     |||||| ||  | ||||  |   ||  |||    |   |||||   |  ||| |  || |  ||   
GCAGAGTAGGAGCGAGAAAAAGAGCAGGAAAGCCATGCAGAAACTTGGCATGAAGACCATCACTGGTGTGAGCCGTGTCACTATCAAAAAGAGCAAGAACgt--gagctgcttaatcactgttatgccatt----gtttcttgtaggctcacagaattgttatataccattgcattttgcttaacttttccctgcactaccag

upper sequence: AT3G12390.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: LOC_Os05g31000.1 (Oryza sativa), 5'ss of exon 3
ACAAAGCAGAAGTGAGAAGAAGAGTCGCAAAGCCATGCTCAAGCTTGGCATGAAACCCATCACTGGTGTTAGCCGAGTCACCGTCAAAAAGAGCAAGAATgtttgtgttttctctttaatattcagtcaatcttaat--ttcttttattcacacatcaggctttaatattgatctgttttggggacatttgctttggaacacag
 || ||  | |||||||| || ||  | || |||||| | ||||||||||||||  | ||||||||||| ||||| || || ||||| ||||||||||||||  |  |        |  |||  || |||||| |||  |||| ||| |   |   | |    |  |    || | |||||           ||  |       
GCAGAGTCGTAGTGAGAAAAAAAGCAGGAAGGCCATGGTGAAGCTTGGCATGAAGTCTATCACTGGTGTGAGCCGTGTTACTGTCAAGAAGAGCAAGAATgtgagcttacgactgctcttatctagccaatctaaatagttctattagttggattcctgttgatgtttgctatttcttttgc-----cccatttcag-------

upper sequence: AT3G12390.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G465333_T01 (Zea mays), 5'ss of exon 3
ACAAAGCAGAAGTGAGAAGAAGAGTCGCAAAGCCATGCTCAAGCTTGGCATGAAACCCATCACTGGTGTTAGCCGAGTCACCGTCAAAAAGAGCAAGAATgtttgtgttttctctttaatattcagtcaatcttaatt--tcttttattcacacatcaggctttaatattgatctgttttggggacatttgctttggaacacag---------
 |||||||| |||||||||||||| |||||||||||||| |||||||||||||| |||||||||||||| ||||| ||||| || || || |||||||||||       ||| |      |    | | ||||| |||  | | |   | |||    |    |||   ||  | |  | |||  |   |       | ||| |          
GCAAAGCAGGAGTGAGAAGAAGAGCCGCAAAGCCATGCTGAAGCTTGGCATGAAGCCCATCACTGGTGTCAGCCGTGTCACTGTGAAGAAAAGCAAGAATgtaa-----ttcaccacgcaaactggcctatctttattgttgtctggctaacatggtatatattatctttattgttgtctggctaacatgataaatgcacatatttttcccag

upper sequence: AT3G12390.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G000923_T01 (Zea mays), 5'ss of exon 3
ACAAAGCAGAAGTGAGAAGAAGAGTCGCAAAGCCATGCTCAAGCTTGGCATGAAACCCATCACTGGTGTTAGCCGAGTCACCGTCAAAAAGAGCAAGAATgtttgtgttttctctttaatattcagtcaatcttaatttcttttattcacacatcaggctttaatattgatctgttttggggacatttgctttggaacacag
 |||||||| |||||||||||||| ||||| |||||||| |||||||||||||| |||||||||||||| ||||| ||||| || || || |||||||||||   |      |   | | || ||  ||| ||   ||   ||||||    | |  ||||   ||  |   || |||   |                     
GCAAAGCAGGAGTGAGAAGAAGAGCCGCAAGGCCATGCTGAAGCTTGGCATGAAGCCCATCACTGGTGTCAGCCGCGTCACTGTAAAGAAAAGCAAGAATgtaattcaccatttactcagat-cacacaaactggcttatctttattgttgcct--ggctaacatgatatgctatttccag---------------------

upper sequence: AT3G12390.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA19G30540.1 (Glycine max), 5'ss of exon 3
ACAAAGCAGAAGTGAGAAGAAGAGTCGCAAAGCCATGCTCAAGCTTGGCATGAAACCCATCACTGGTGTTAGCCGAGTCACCGTCAAAAAGAGCAAGAATgtttgtgttt------tctctttaatattcagtcaatcttaatttcttttattc-acacatcaggctttaatattgatctgttttggggacatttgctttggaacacag
 || | ||||||||| |||||||||||||| || ||||| || ||||| ||||||||  |||| ||||| |||||||| || ||||| ||||||||||||||| |  |||      ||| ||| |  ||    || ||||  |||| ||| |   |   ||   |||||  ||   ||      |  |||| ||   | |  |      
GCAGACCAGAAGTGAAAAGAAGAGTCGCAAGGCAATGCTTAAACTTGGAATGAAACCTGTCACAGGTGTCAGCCGAGTGACAGTCAAGAAGAGCAAGAATgttagcatttgactcatctttttcacttttcaccactctt--tttcatttgtcagatctattttgctttggtaaaaattgaaactttggactttgtttgtttag-----

upper sequence: AT3G12390.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA19G30550.1 (Glycine max), 5'ss of exon 3
ACAAAGCAGAAGTGAGAAGAAGAGTCGCAAAGCCATGCTCAAGCTTGGCATGAAACCCATCACTGGTGTTAGCCGAGTCACCGTCAAAAAGAGCAAGAATgtttgtgttt------tctctttaatattcagtcaatcttaatttcttttattc-acacatcaggctttaatattgatctgttttggggacatttgctttggaacacag
 || | ||||||||| |||||||||||||| || ||||| || ||||| ||||||||  |||| ||||| || ||||| || ||||| ||||||||||||||| |  |||      ||| |||    ||    ||  |||  |||| ||| |   |   ||   |||||  ||   ||      |  |||| ||   | |  |      
GCAGACCAGAAGTGAAAAGAAGAGTCGCAAGGCAATGCTTAAACTTGGAATGAAACCTGTCACAGGTGTCAGTCGAGTGACAGTCAAGAAGAGCAAGAATgttagcatttgactcatctttttcgcttttcaccaccctt--tttcatttgtcagatctattttgctttggtaaaaattgaaactttggactttgtttgtttag-----

upper sequence: AT3G12390.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA03G27570.1 (Glycine max), 5'ss of exon 3
ACAAAGCAGAAGTGAGAAGAAGAGTCGCAAAGCCATGCTCAAGCTTGGCATGAAACCCATCACTGGTGTTAGCCGAGTCACCGTCAAAAAGAGCAAGAATgtttgtg---ttt------tctctttaatattcagtcaatcttaatttcttttattc-acacatcaggctttaatattgatctgttttggggacatttgctttggaacacag
 || | ||||||||| |||||||||||||| || ||||| || ||||| ||||||||  | || ||||| |||||||| || ||||| ||||||||||||||| ||    |||      ||| ||||   ||    || ||||  || | ||| |   |   ||   |||||  ||   ||      |  |||| |||| ||    |     
GCAGACCAGAAGTGAAAAGAAGAGTCGCAAGGCAATGCTTAAACTTGGAATGAAACCTGTAACAGGTGTCAGCCGAGTGACGGTCAAGAAGAGCAAGAATgttagtagcatttgacacgtctttttagcttttcaccactcttttttgcatttgtcagatttattttgctttggtaaaaattgaaactttggacttttgtttgtttag----

upper sequence: AT3G12390.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA03G27580.2 (Glycine max), 5'ss of exon 3
ACAAAGCAGAAGTGAGAAGAAGAGTCGCAAAGCCATGCTCAAGCTTGGCATGAAACCCATCACTGGTGTTAGCCGAGTCACCGTCAAAAAGAGCAAGAATgtttgtgttttctctttaat--attcagtcaatcttaatttcttttattcacacatcaggctttaatattga-tctgttttggggacatttgctttggaacacag
 || | |||||| || |||||||||||||| || |||||||| ||||| ||||||||  |||| ||||| || || || || || || |||||||| |||||| |  |||    | || |   ||     ||  ||   || ||| ||  |      |    | |||||||| | | |||        |||| || |        
GCAGACCAGAAGCGAAAAGAAGAGTCGCAAGGCAATGCTCAAACTTGGAATGAAACCTGTCACAGGTGTCAGTCGTGTGACTGTTAAGAAGAGCAAAAATgttagcatttgacatctatttattttgaagaacttttcattgtttcatctatttcgtacttgtcaatattgaatttatttctcctttgtttgtttag--------

upper sequence: AT3G12390.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv13s0067g00710.t01 (Vitis vinifera), 5'ss of exon 3
ACAAAGCAGAAGTGAGAAGAAGAGTCGCAAAGCCATGCTCAAGCTTGGCATGAAACCCATCACTGGTGTTAGCCGAGTCACCGTCAAAAAGAGCAAGAATgtttgtgttttctctttaatattcagtcaatcttaatttctt-ttattcacacatcaggc-tttaatattgatctgttttggggacatttgctttggaacacag-----------------------------
 || ||| | ||||| |||||||| ||||| || ||| | |||||||| |||||||||||  | ||||||||||| || || || || || ||||| |||||| || |       ||    ||  ||  || ||    ||||  |   ||  |  ||     |||||  |  | |  |          |  ||||| |   | |                             
GCAGAGCCGTAGTGAAAAGAAGAGCCGCAAGGCAATGTTGAAGCTTGGAATGAAACCCATTCCAGGTGTTAGCCGTGTTACGGTGAAGAAAAGCAAAAATgttagtttccctctcttttctttgtgtgtatattcccctcttgctccccatgccccatctgcttaatccttttgtcctccttttgtcctccctttgaacttctgttgtaatctcggttattacttgctatcag

upper sequence: AT3G12390.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: EDO97954 (Chlamydomonas reinhardtii), 5'ss of exon 2
ACAAAGCAGAAGTGAGAAGAAGAGTCGCAAAGCCATGCTCAAGCTTGGCATGAAACCCATCACTGGTGTTAGCCGAGTCACCGTCAAAAAGAGCAAGAATgtttgtgttttctctttaatattcagtcaatcttaat-ttcttttattcacacatcaggctttaatattgatctgttttggggacatttgctttggaacacag
 || ||| | || ||||||||||| ||||| |||||||  ||||| |||||||| ||| ||||||| || |  || || ||| |||| ||||||||||| ||  |  ||    | || |  | ||||||  |      || |   |    |            |    |   ||| | |||||  |   |    ||    |||
GCAGAGCCGCAGCGAGAAGAAGAGCCGCAAGGCCATGCAGAAGCTGGGCATGAAGCCCGTCACTGGCGTGACTCGCGTGACCATCAAGAAGAGCAAGAACgtaaggattg---cattgaagtccagtcaggccaggggttatgggaggggcgagctgcaggggacgggtacactgctgtggggggaaggggaagggggggcag

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|124749604|gb|EH839734.1|EH839734
EST:     ACCCATCACTGGTGTTAGCCGAGTCACCGTCAAAAAGAGCAAGAAT                         ATCTTGTTTGTCATATCAAAGCCTGATGTG
genomic: ACCCATCACTGGTGTTAGCCGAGTCACCGTCAAAAAGAGCAAGAATgtttgtgttt ... tggaacacagATCTTGTTTGTCATATCAAAGCCTGATGTG
EST: gi|124734160|gb|EH825562.1|EH825562
EST:     TCACCGTCAAAAAGAGCAAGAAT                         ATCTTGTTTGTCATATCAAAGCCTGATGTGTTCAAGAGTCCAGCATCAGAC
genomic: TCACCGTCAAAAAGAGCAAGAATgtttgtgttt ... tggaacacagATCTTGTTTGTCATATCAAAGCCTGATGTGTTCAAGAGTCCAGCATCAGAC
EST: gi|116471411|gb|EG514003.1|EG514003
EST:     TGAAACCCATCACTGGTGTTAGCCGAGTCACCGTCAAAAAGAGCAAGAAT                         ATCTTGTTTGTCATATCAAAGCCTGATGTGTTCAAGAGTCCAGCATCAGAC
genomic: TGAAACCCATCACTGGTGTTAGCCGAGTCACCGTCAAAAAGAGCAAGAATgtttgtgttt ... tggaacacagATCTTGTTTGTCATATCAAAGCCTGATGTGTTCAAGAGTCCAGCATCAGAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACAAAGCAGAAGTGAGAAGAAGAGTCGCAAAGCCATGCTCAAGCTTGGCATGAAACCCATCACTGGTGTTAGCCGAGTCACCGTCAAAAAGAGCAAGAATgtttgtgttttctctttaatattcagtcaatcttaatttcttttattcacacatcaggctttaatattgatctgttttggggacatttgctttggaacacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA