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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggtcttaaaagctccccttttcttctcactgtaccatctggtgtttacttcttttagtttgatgcacatttcttttatgtgcagTGTACAAGAAGCATTATCCACCTGCTCTGAATGATGATGTGTGGAGATTGGACAAGATCGGCAAGGATGGGGCATTCCATAAAAAGCTTACTGCTGAAGG

Basic information

species Arabidopsis thaliana
transcript AT5G57580.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G57580.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os02g35470.3 (Oryza sativa), 3'ss of exon 5
gtatggtcttaa-aagctccccttttcttctcactgtaccatctggtgtttacttcttttagtttgatgcacatttcttttatgt-gcagTGTACAAGAAGCATTATCCACCTGCTCTGAATGATGATGTGTGGAGATTGGACAAGATCGGCAAGGATGGGGCATTCCATAAAAAGCTTACTGCTGAAGG
||||| |   ||  || |    ||||  ||  ||||  | |  || | || | |  |  | |||      |  | | || ||| | ||||||||||| ||||| ||||||||||| || || |||||||| |||||||| || ||||| ||||||||||| |||||||| || ||| | | |||    ||
gtatgtttgcaatgagttattgttttactcatactg--ctagatgat-ttgaatgttactcgttaaccatatttctattgtatcttgcagTGTACAAAAAGCACTATCCACCTGCCCTAAAGGATGATGTTTGGAGATTAGAAAAGATTGGCAAGGATGGTGCATTCCACAAGAAGTTAAATGCAAGTGG

upper sequence: AT5G57580.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os04g36660.1 (Oryza sativa), 3'ss of exon 5
gtatggtcttaaaagctccccttttcttctc--actgtaccatctggtgtttacttcttttagtttgatgcacatttcttttatgtgcagTGTACAAGAAGCATTATCCACCTGCTCTGAATGATGATGTGTGGAGATTGGACAAGATCGGCAAGGATGGGGCATTCCATAAAAAGCTTACTGCTGAAGG
||||| |   | |  ||   ||  |||| |   |||||  ||| |     |||     |  |  || |   | | | | | |   || |||||||||||| || || || ||||| || || |||||||| ||||||||||| ||||| || |||||||| ||||| || || ||||| |   |  | ||
gtatgattccatatactttactgatcttgtgtaactgttacatgt----cttaacatatagatcttaaattataatccctct---tgtagTGTACAAGAAACACTACCCTCCTGCCCTAAAGGATGATGTTTGGAGATTGGAGAAGATTGGAAAGGATGGTGCATTTCACAAGAAGCTAAACTCAAATGG

upper sequence: AT5G57580.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G113453_T01 (Zea mays), 3'ss of exon 5
gtatggtcttaaaagctccccttttcttctcactgtaccatctggtgtttactt---cttttag--tttg-------atgcacatttcttttatgtgca---gTGTACAAGAAGCATTATCCACCTGCTCTGAATGATGATGTGTGGAGATTGGACAAGATCGGCAAGGATGGGGCATTCCATAAAAAGCTTACTGCTGAAGG
|||||   |   |  | |   |  | | |||| |  |  |      | |||| |    ||||||  ||||       | |||   |  |||| | |  |   |||||||||||||| || |||||||| ||||| |||||||| |||||||| || ||||| ||||||||||| |||||||| || ||| | | |||    ||
gtatg---tgtgacacactgttgatttactcattagatgaaacaaagattacctgtatttttagaatttgcatcgccaagcatgctgattttgtatttattagTGTACAAGAAGCACTACCCACCTGCGCTGAAGGATGATGTTTGGAGATTAGAAAAGATTGGCAAGGATGGCGCATTCCACAAGAAGTTAAATGCCAGTGG

upper sequence: AT5G57580.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G018837_T04 (Zea mays), 3'ss of exon 5
gtatggtcttaaaagctccccttttcttctcactgtaccatctggtgtttacttcttttagtttgatgcacatttcttttatgtgcagTGTACAAGAAGCATTATCCACCTGCTCTGAATGATGATGTGTGGAGATTGGACAAGATCGGCAAGGATGGGGCATTCCATAAAAAGCTTACTGCTGAAGG
|||  |||  ||||      || |       | |   |||  ||   | ||  |    || ||  ||      ||| ||||| |  ||||||||||||||| ||||||||| | ||||| ||||| || ||||| ||||| || || || ||||||||| |||||||||| | ||| |        ||
gta-agtcccaaaaatgtatctgtgtactgtattc--ccacttgacatatatctaaactatttcaat------ttcatttatct--agTGTACAAGAAGCACTATCCACCTACACTGAAAGATGAGGTCTGGAGGTTGGAAAAAATAGGGAAGGATGGGTCATTCCATAAGAGGCTGAACAAATCTGG

upper sequence: AT5G57580.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G010471_T01 (Zea mays), 3'ss of exon 1
gtatggtcttaaaagctccccttttcttctcactgtaccatctggtgtttacttcttttagtttgatgcacatttcttttatgtgcagTGTACAAGAAGCATTATCCACCTGCTCTGAATGATGATGTGTGGAGATTGGACAAGATCGGCAAGGATGGGGCATTCCATAAAAAGCTTACTGCTGAAGG
|||  |||  ||||       | |       | | |  ||  ||   | ||  |    || ||  ||      ||| ||||| |  ||||||||||||||| ||||||||| | ||||| ||||| || ||||| ||||| || || || ||||||||| |||||||||| | ||| |        ||
gta-agtcccaaaaatgtatttgtgtgctgtattct--cacttgacatatatctaaactatttcaat------ttcatttatct--agTGTACAAGAAGCACTATCCACCTACACTGAAAGATGAGGTCTGGAGGTTGGAAAAAATAGGGAAGGATGGGTCATTCCATAAGAGGCTGAACAAATCTGG

upper sequence: AT5G57580.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: AC202073.4_FGT001 (Zea mays), 3'ss of exon 4
gtatggtcttaaaagctccccttttcttctcactgtaccatctggtgtttacttcttttagtttgatgcac-atttcttttatgtgcagTGTACAAGAAGCATTATCCACCTGCTCTGAATGATGATGTGTGGAGATTGGACAAGATCGGCAAGGATGGGGCATTCCATAAAAAGCTTACTGCTGAAGG
||||| |  |  |        |  | |  |   |  |  ||||    | ||    ||  |  |  || |   |  |   |  | || |||||| |||||||||||||| ||||| || || ||||| || |||||||| || ||||| || ||||||||  ||||||| || |   | |   |    ||
gtatgtttatttag-----tgtgatgtcattgttaaataatctaacatataggctttaaacatgaatacgttaactaactcttttgtagTGTATAAGAAGCATTATCCTCCTGCACTAAAGGATGAGGTATGGAGATTAGAAAAGATTGGAAAGGATGGTTCATTCCACAAGAGATTAAACTCAAGTGG

upper sequence: AT5G57580.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G054109_T01 (Zea mays), 3'ss of exon 5
---------gtatggtcttaaaa-gctccccttttcttctcactgtaccatctggtgttt---acttcttttagtttgatgcacatttcttttatgtgc---agTGTACAAGAAGCATTATCCACCTGCTCTGAATGATGATGTGTGGAGATTGGACAAGATCGGCAAGGATGGGGCATTCCATAAAAAGCTTACTGCTGAAGG
          ||   | || |    |||      |  |   |   |  | | |  | |||   ||||   | ||||  | |||   |  || | | |     ||||||||| || || || |||||  | ||||| |||||||| |||||||| || ||||| ||||||||||| |||||||| || ||| | | ||||   ||
gtatgtgtgatacattgttgatttactcattagatgatacaaagattacgtgtattttttagaacttgcatcagttgcaagcatgctgattctgtatttattagTGTACAAAAAACACTACCCACCCACGCTGAAGGATGATGTTTGGAGATTAGAAAAGATTGGCAAGGATGGCGCATTCCACAAGAAGTTAAATGCTAGTGG

upper sequence: AT5G57580.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G451882_T01 (Zea mays), 3'ss of exon 5
gtatggtcttaaaagctccccttttcttctcactgtaccatctggtgtttacttcttttagtttgatgcacatttcttttatgtgcagTGTACAAGAAGCATTATCCACCTGCTCTGAATGATGATGTGTGGAGATTGGACAAGATCGGCAAGGATGGGGCATTCCATAAAAAGCTTACTGCTGAAGG
||| |  |  ||||  |    || | ||   | ||   ||| |     | |  | ||  || || ||  || |             ||||||||||||||| ||||||||| | || || ||||| || ||||| ||||| || || || ||||||||  |||||||||| | ||| |        ||
gtaagtcccaaaaaattgtttttgtatttctattgacacatat----ctaaactattccagattcatttacct-------------agTGTACAAGAAGCACTATCCACCTACGCTAAAAGATGAGGTCTGGAGGTTGGAAAAAATAGGAAAGGATGGCTCATTCCATAAGAGGCTGAACAAATCTGG

upper sequence: AT5G57580.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA13G01160.1 (Glycine max), 3'ss of exon 5
------gtatggtcttaaaagctccccttttcttct--------cactgtac---catctggtgtttact----tcttttagtttgatgcacatttcttttatgtgcagTGTACAAGAAGCATTATCCACCTGCTCTGAATGATGATGTGTGGAGATTGGACAAGATCGGCAAGGATGGGGCATTCCATAAAAAGCTTACTGCTGAAGG
       |||| |  || |   |    ||||  |||         ||| | |   |||||    |||| |    |||||||  ||  |  |  ||    || |   |||| || ||||||||||||||||| ||  ||| |||||| |||||||||||||| ||||| |||||||||||| |||||||||| ||||| | |  || |||
gtagggctatgcttctacatcttttagtttttctctagcatcaatactctccctgcatctacactttaataccatcttttaaattt-tatattttgacctttttctcagTATATAAGAAGCATTATCCACCAGCATTGACTGATGAAGTGTGGAGATTGGAGAAGATAGGCAAGGATGGGTCATTCCATAAGAAGCTGAATAATGCAGG

upper sequence: AT5G57580.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA17G07290.1 (Glycine max), 3'ss of exon 6
------gtatggtcttaaaagctccccttttcttct-----cactgtaccatctg----------gtgtttacttcttttagtttgatgcacatttcttttatgtgcagTGTACAAGAAGCATTATCCACCTGCTCTGAATGATGATGTGTGGAGATTGGACAAGATCGGCAAGGATGGGGCATTCCATAAAAAGCTTACTGCTGAAGG
       |||| |  || |   |    ||||  |||     || ||  |   |||          ||  |  | |||||||  ||  |  |  ||    || |   |||| || ||||||||||||||||||||  ||| |||||| |||||||||||||| ||||| |||||||||||| |||| ||||| ||||| | |  || |||
gtagggttatgcttctacatcttttagtttttctctagcatcagtgctctccctgctcctacactgtaatagcatcttttaaattt-tatattttgacctttttctcagTATATAAGAAGCATTATCCACCTGCATTGACTGATGAAGTGTGGAGATTGGAGAAGATAGGCAAGGATGGGTCATTTCATAAGAAGCTGAATAGTGCAGG

upper sequence: AT5G57580.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv11s0052g01380.t01 (Vitis vinifera), 3'ss of exon 4
gtatggtcttaaaagctccccttttcttctcactgtaccatctggtgtttacttcttttagtt-tgatg-cacatt--------------tcttttatgtgcagTGTACAAGAAGCATTATCCACCTGCTCTGAATGATGATGTGTGGAGATTGGACAAGATCGGCAAGGATGGGGCATTCCATAAAAAGCTTACTGCTGAAGG
||| | ||         |   | || |  | | || |  || |  |  ||  || | |||  | ||||| ||  ||              | ||   || | |||||| ||||| || |||||||||||  | | ||||||||||||||||||||| ||||| |||||||||||  ||||||| || | ||| | |  |     
gtaggttcaggctcatccttgtcttttatttattgaattattttattgttctttttcttatctgtgatgacatgttattgaatctgctgtttttccctgggtagTGTATAAGAAACACTATCCACCTGCATTAACTGATGATGTGTGGAGATTGGAGAAGATTGGCAAGGATGGTTCATTCCACAAGAGGCTAAATAATTCCCA

upper sequence: AT5G57580.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S336_7V6.1 (Physcomitrella patens), 3'ss of exon 4
--------------------------------------------------gtatggtcttaa---aagctccccttttcttctcactgt-accatctggtgtttacttcttt---tagtttgatgcac---atttcttttat-----------gtgcagTGTACAAGAAGCATTATCCACCTGCTCTGAATGATGATGTGTGGAGATTGGACAAGATCGGCAAGGATGGGGCATTCCATAAAAAGCTTACTGCTGAAGG
                                                   |  | || |||   |   |    ||   ||    | || |  |   |  ||||   | |||   ||| | || | |    || | || ||            ||||||||||||||||||| |||||||||||  ||||||| || || ||| | ||||||||||| || ||||| || || || || ||    || | |    |   
gtacgttgactgttttgaaccttgggtcatcttacgctataagagtttgtctgcgttcctaatttacagttagtttcgttttaggcagttaataaaagcagtttgaatatttatctagatggaagtattgaatcttttctacttgggaatttcgtgcagTGTACAAGAAGCACTATCCACCTGCCTTGAATGACGAGGTATGGCGCTTGGACAAGATTGGGAAGGACGGAGCCTTTCACAAGCGCCTCAATCAAAACCA

upper sequence: AT5G57580.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S98_167V6.1 (Physcomitrella patens), 3'ss of exon 4
--------gtatggtcttaaaagctccccttttcttctcactgtaccatctggtgtttacttcttttagtttgatgcacatttctttta----tgtgcagTGTACAAGAAGCATTATCCACCTGCTCTGAATGATGATGTGTGGAGATTGGACAAGATCGGCAAGGATGGGGCATTCCATAAAAAGCTTACTGCTGAAGG
        | |    | |     ||   ||      |    |  ||          | |  ||| |   | | ||     ||  |  |     ||| |||| ||||||||||| ||||| |||||| | ||||| || || ||| ||||||||||||| || || || || || ||||| |||   || | |   | | |
tgccctgtgcacatccattcgttctgtgctgaatgccgtgattaacagaagaaaaatcatatctctatatctaataattgttgttggtcaccttgtacagTCTACAAGAAGCACTATCCGCCTGCTTTAAATGACGAGGTTTGGCGATTGGACAAGATTGGAAAAGACGGTGCTTTCCACAAACGTCTAAATCAAGCAAG

upper sequence: AT5G57580.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S51_322V6.1 (Physcomitrella patens), 3'ss of exon 4
----------gtatggtcttaaaagctccccttttcttctcactgtacc-atctggtgtttacttcttttagtttgatgcacatttct-tttatgtgcagTGTACAAGAAGCATTATCCACCTGCTCTGAATGATGATGTGTGGAGATTGGACAAGATCGGCAAGGATGGGGCATTCCATAAAAAGCTTACTGCTGAAGG
            |  || ||  ||        |       ||  ||||     |||     ||  |||  |||||  |      |     ||  ||||||||||||| ||||| || ||||||||  ||||||| || |||||| | ||||||||||| || || ||||| || ||||| ||    |||| |   |    
ttgttcggtgccaaagtttttgaaaaaaagaatcaggcagcatggtacttgattggatgcaaccacttacagttttctttgtgctgaaactttcgtgcagTGTACAAAAAGCACTACCCACCTGCCTTGAATGACGAGGTGTGGCGCTTGGACAAGATTGGGAAAGATGGTGCTTTCCACAAGCGTCTTAATCAAGCCAA

upper sequence: AT5G57580.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S34_132V6.1 (Physcomitrella patens), 3'ss of exon 4
-----------------gtatggtcttaaaagctccccttttcttctcactgtaccatctggtgtttacttcttttagtttgatgcacatttcttttatgtgcagTGTACAAGAAGCATTATCCACCTGCTCTGAATGATGATGTGTGGAGATTGGACAAGATCGGCAAGGATGGGGCATTCCATAAAAAGCTTACTGCTGAAGG
                  | || ||  || |            |  | |  |  ||| |   | | || || |  |  || | ||   ||| || |   || |||| ||||||||||| |||||||| ||  ||||||| || || ||| ||||||||||||| || || || || || ||||| ||    || | |   |    
tctgccagatttccaagttgtgatcagaagaagaaagaagggatggtgaaagc-ccaacatatctgtatttttgattatt-gttgttgattactct---gttcagTTTACAAGAAGCACTATCCACCAGCCTTGAATGACGAGGTTTGGCGATTGGACAAGATTGGGAAAGACGGTGCTTTCCACAAGCGTCTAAATCAAGCTCA

upper sequence: AT5G57580.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: EFJ11344 (Selaginella moellendorffii), 3'ss of exon 4
gtatggtcttaaaagctccccttttcttctcactgtaccatctggtgtttacttcttttagtttgatgcacatttcttttatgtgcagTGTACAAGAAGCATTATCCACCTGCTCTGAATGATGATGTGTGGAGATTGGACAAGATCGGCAAGGATGGGGCATTCCATAAAAAGCTTACTGCTGAAGG
   |    |    |     |  |||||| |   |||      |||| || || |  |       ||||     | |  |  ||||||||||||||||||||||||||||||||  | |  || || |||||| |  |||| |||||||| ||||| ||||| ||||| ||   ||| | |    | ||
--gtaagttggcgactgaactgtttcttttttttgt-----ttggttttgacatgctgcttaccgatgttacgtgcgctcttgtgcagTGTACAAGAAGCATTATCCACCTGCATTAACGGACGAGGTGTGGCGTCTGGATAAGATCGGAAAGGACGGGGCTTTCCACAAGCGGCTGAATCAAAACGG

upper sequence: AT5G57580.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: EFJ11323 (Selaginella moellendorffii), 3'ss of exon 4
gtatggtcttaaaagctccccttttct-tctcactgtaccatctggtgtttacttcttttagtttgatgcacatttcttttatgtgcagTGTACAAGAAGCATTATCCACCTGCTCTGAATGATGATGTGTGGAGATTGGACAAGATCGGCAAGGATGGGGCATTCCATAAAAAGCTTACTGCTGAAGG
         |||     || |||  || | ||  | |    | |||| || || |  |       ||||     | |  |  ||||||||||||||||||||||||||||||||  | |  || || |||||| |  |||| |||||||| ||||| ||||| ||||| ||   ||| | |    | ||
--------gtaagttggccacttaactgtttcttttttttgtttggttttgacatgctgcttaccgatgttacgtgcgctcttgtgcagTGTACAAGAAGCATTATCCACCTGCATTAACGGACGAGGTGTGGCGTCTGGATAAGATCGGAAAGGACGGGGCTTTCCACAAGCGGCTGAATCAAAACGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtaccatctggtgtttacttcttttagtttgatgcacatttcttttatgtgcagTGTACAAGAAGCATTATCCACCTGCTCTGAATGATGATGTGTGGAGATTGGACAAGATCGGCAAGGATGGGGCATTCCATAAAAAGCTTACTGCTGAAGG
                           gtttgat  putative branch site (score: 5)
                                     catttctttt  putative PPT
                                      atttcttttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatggtcttaaaagctccccttttcttctcactgtaccatctggtgtttacttcttttagtttgatgcacatttcttttatgtgcagTGTACAAGAAGCATTATCCACCTGCTCTGAATGATGATGTGTGGAGATTGGACAAGATCGGCAAGGATGGGGCATTCCATAAAAAGCTTACTGCTGAAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG