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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catcatactgtcatcagttatcatcaccgttaaagtcatcatcctcatatcatcataatcatagtatcacttttatgtaaacatcatttttatgttacagAGGATAACGGAGAAACAGAACCATGTGGTGATCACAGACAGGATGTGGGCAAGGCTACTCTCTTCGACAAACCAGCCGAGTTTCTTGGGCCCCAAAGATG

Basic information

species Arabidopsis thaliana
transcript AT4G26270.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G26270.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: LOC_Os05g10650.1 (Oryza sativa), 3'ss of exon 2
catcatactgtcatcagttatcatcaccgttaaagtcatca-tcctcatatcatcataatcatagtatcacttttatgtaaacatcatttttatgttacagAGGATAACGGAGAAACAGAACCATGTGGTGATCACAGACAGGATGTGGGCAAGGCTACTCTCTTCGACAAACCAGCCGAGTTTCTTGGGCCCCAAAGATG
             | || | || || ||  |     ||| | | ||  | ||  ||| |        | | |   ||      |  ||||||  | | |||||||| |||||||| |||||| | ||||| ||||| |||||||||||||| ||| | ||||  ||||| ||||||||| | ||| |  || |  | || |
------------gtaagct-tcgtctcctcttcctccattaattcttctttcgccatgaattcgagctgattgagattggggaa--attttt--gctgcagAGGATCACGGAGAAGCAGAACAAGGTGGTCATCACGGACAGGATGTGGGCGAGGGTGCTCTGCTCGACGAACCAGCCGTGCTTCCTCAGCACGGAGGACG

upper sequence: AT4G26270.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: LOC_Os01g09570.1 (Oryza sativa), 3'ss of exon 10
----------------------catcatactgtcatcagttatcatcaccgttaaagtcatcat-cctcatatcatcataatcatagtatcacttttatgtaaacatcatttttatgttacagAGGATAACGGAGAAACAGAACCATGTGGTGATCACAGACAGGATGTGGGCAAGGCTACTCTCTTCGACAAACCAGCCGAGTTTCTTGGGCCCCAAAGATG
                      ||     |  || | |||  |||   | ||| |  || |||  ||  | |||| |   ||| |  ||        |   ||||  |     | |  ||||||| || |||||||| |||||| | ||||||||||| |||||||||||||| ||| | || |  ||||| ||||||||  | ||| || ||| | | || |
gtaagtccagaacactctttttcaatgatcaatctttagtgttcagttcagttcagttcttcacaccagacatcaaccatatcctgataatctggacactgaaactccggcgattt-ctacagAGAATCACGGAGAAGCAGAACAAGGTGGTGATCACGGACAGGATGTGGGCGAGGGTGCTGTGCTCGACGAACCAGCCATGCTTCCTGAGCCACGAGGACG

upper sequence: AT4G26270.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GRMZM2G443985_T01 (Zea mays), 3'ss of exon 13
------------------------------------catcatactg---tcatcag-ttatcatcaccgttaaagtcatcatcctcatatcatcataatc-atagtatcacttttatgtaaacatcatttttatgttacagAGGATAACGGAGAAACAGAACCATGTGGTGATCACAGACAGGATGTGGGCAAGGCTACTCTCTTCGACAAACCAGCCGAGTTTCTTGGGCCCCAAAGATG
                                    | |  ||| |   ||||||  | | ||||   |    | | ||  | ||   |  |      ||  || ||    ||||   |   | ||| |       | ||||||||||| ||||| ||||||   ||   ||| || |||||||||||||||||||| ||||| ||||| |||||||| || ||| |  ||  |||||  |
gtaagtcacacccctgccggagcagggcacggaattctttttaccgcattcatcatctcagcatctgagacctacttattctgcttgaactaatgccctccgtactaattgttttgcattcgcgtcactc----acttcagAGGATAACAGAGAAGCAGAACAGAGTTTCGATAACCGACAGGATGTGGGCAAGGCTTCTCTCGTCGACGAACCAGCCAAGCTTCCTTTGCAACAAAGTCG

upper sequence: AT4G26270.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GRMZM5G816636_T02 (Zea mays), 3'ss of exon 13
---catcatactgtcatcagttatcat-caccgttaaagtcatcatcctcatatcatcataatcatagtatcacttttatgtaaacatcatttttatgttacagAGGATAACGGAGAAACAGAACCATGTGGTGATCACAGACAGGATGTGGGCAAGGCTACTCTCTTCGACAAACCAGCCGAGTTTCTTGGGCCCCAAAGATG
     |||  || | |     |   |  ||   ||      |  |   |||      ||  ||| || ||  || |  |  |     | |         | ||||||||||| ||||| ||||||   ||   ||| || |||||||||||||||||||| || || ||||| ||||||||||| ||| |  ||  |||||   
gtaagtcaccctatgaaggagtgggacacagaattctttctactaaattcaacatcgcagcatc-taataagacctacacattgttttgaaccacccactccagAGGATAACAGAGAAGCAGAACAGGGTCTCGATAACCGACAGGATGTGGGCAAGGCTTCTGTCGTCGACCAACCAGCCGAGCTTCCTCTGCAACAAAGTCA

upper sequence: AT4G26270.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GRMZM2G004932_T01 (Zea mays), 3'ss of exon 13
-catcatactgtcatcagttatcatcaccgttaaagtcatcatcctcatatcatcataatcatagt-atcacttttatgtaaacatcatttttatgttacagAGGATAACGGAGAAACAGAACCATGTGGTGATCACAGACAGGATGTGGGCAAGGCTACTCTCTTCGACAAACCAGCCGAGTTTCTTGGGCCCCAAAGATG
  | |||      |    | |  |   |  ||||| | |  |   |    |  | ||   || | | || |     |   ||   |  || | |||   |||||| | ||    | |  |||| | ||     |||| |||||||||||||||||||| || || || || |||||||| |||||| || | |  || ||| 
gaaccatgtcacgaaacataactagatcaattaaattaaaaaaagtgcattactgatctgcacactgatgatgagcaccaaattcttgttctgatg--gcagAGGGTGACATCCACAAGGAACAAGGTTAAAGTCACTGACAGGATGTGGGCAAGGCTTCTGTCGTCCACCAACCAGCCAAGTTTCCTGAGTCAGAAGGATA

upper sequence: AT4G26270.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GRMZM2G132069_T01 (Zea mays), 3'ss of exon 10
catcatactgtcatcagttatcatcaccgttaaagtcatcatcctcatatcatcataatcatagtatcacttttatgtaaacatcatttttatgttacagAGGATAACGGAGAAACAGAACCATGTGGTGATCACAGACAGGATGTGGGCAAGGCTACTCTCTTCGACAAACCAGCCGAGTTTCTTGGGCCCCAAAGATG
     ||  |||    ||  |  |    ||  |  | | | ||||     ||||    || | |      |  |   |||||     | || | || |||||||| || ||||| |||||| | ||||||||||| ||| |||||||||| ||| | || |  ||||| ||||||||  | ||| || ||| | | || |
----gtaa-gtcgagggtc-ttgtgcttgtgcagttgagcttcctgga--catc-cggtcttgga-----tcctggataaacccttctcttgttttgcagAGGATCACCGAGAAGCAGAACAAGGTGGTGATCACGGACCGGATGTGGGCGAGGGTGCTGTGCTCGACGAACCAGCCCTGCTTCCTGAGCCACGAGGACG

upper sequence: AT4G26270.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GRMZM2G080375_T04 (Zea mays), 3'ss of exon 10
catcatactgtcatcagttatcatcaccgttaaagtcatcatcctcatatcatcataatcatagtatcacttttatgtaaacatcatttttatgttacagAGGATAACGGAGAAACAGAACCATGTGGTGATCACAGACAGGATGTGGGCAAGGCTACTCTCTTCGACAAACCAGCCGAGTTTCTTGGGCCCCAAAGATG
     ||  |||    |     |   | ||| |   ||          | |||     |  |  |   || || |||   |    || | |   || |||||||| || ||||| |||||| | ||||||||||| ||| |||||||||| ||| | || |  ||||| ||||||||  | ||| || ||| | | || |
----gtaa-gtcgaaggccg--aatgcagttgagcacacagcttcttgaacatggc--ttgttctgaaaccttgatgggcaatcgatctcttgtttgcagAGGATCACCGAGAAGCAGAACAAGGTGGTGATCACGGACCGGATGTGGGCGAGGGTGCTGTGCTCGACGAACCAGCCCTGCTTCCTGAGCCACGAGGACG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catatcatcataatcatagtatcacttttatgtaaacatcatttttatgttacagAGGATAACGGAGAAACAGAACCATGTGGTGATCACAGACAGGATGTGGGCAAGGCTACTCTCTTCGACAAACCAGCCGAGTTTCTTGGGCCCCAAAGATG
                                      tcattttt  CT-rich tract
                         ttttatgtaaacatca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catcatactgtcatcagttatcatcaccgttaaagtcatcatcctcatatcatcataatcatagtatcacttttatgtaaacatcatttttatgttacagAGGATAACGGAGAAACAGAACCATGTGGTGATCACAGACAGGATGTGGGCAAGGCTACTCTCTTCGACAAACCAGCCGAGTTTCTTGGGCCCCAAAGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - -catcacc
- - - - - - - - - - - - - - - - - - - - atcctca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - aatcata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtaaaca