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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatcatttcataaacatagttgctccatttttgctttatggatttgattaaagtactaagaggcttttttttggtgaaagagcagAATGGACATGTAGGGTTCATGTTGTCATGCTATGATGCGGAGCTCAGCTATGATACTCACACGGATACGTTCCAAGCCAG

Basic information

species Arabidopsis thaliana
transcript AT2G32560.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G32560.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os01g17390.1 (Oryza sativa), 3'ss of exon 1
------------gtaatcatttcataaacatagttgctcca---tttttgctttatggatttgattaaagt--actaagaggcttttttttggtgaaagagcagAATGGACATGTAGGGTTCATGTTGTCATGCTATGATGCGGAGCTCAGCTATGATACTCACACGGATACGTTCCAAGCCAG
             |     |||| | |  ||  |  || ||   |||| | | | |       |    |    |    |||||||||| || ||      |||| |||| ||||| || |||||| |||||||||| ||||| |||||||||||||||   ||||  ||||| ||||  || ||
ctagatgagctcatttgtgtttctttaggatcttatcttcaaacttttagttatgtttgagcaaccggaaccaatcttgaggctttttgtttgttt----gcagCATGGGCATGTTGGATTCATGATGTCATGCTACGATGCAGAGCTCAGCTATGATTTCCACAGTGATACCTTCCGTGCAAG

upper sequence: AT2G32560.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G130348_T01 (Zea mays), 3'ss of exon 1
--gtaatcatttcataaacatagttgctccatttttgctttatggatttgatta-----aagtactaagaggctt------ttttttggtgaaagagcagAATGGACATGTAGGGTTCATGTTGTCATGCTATGATGCGGAGCTCAGCTATGATACTCACACGGATACGTTCCAAGCCAG
  || |      | |    | |  ||     || |||  | |||   ||  |||     ||  | | | ||  |       |||  |         |||| | || ||||| ||||||||| |||||||||||||||| | |||||| || |||   || || || || ||||  || ||
tggtcagagcagcttgcttacatctgtgttcttgttgtctcatgatctttgttagtttcaaacattgaaagaatcctgagatttcctatctgttttgcagCACGGGCATGTTGGGTTCATGATGTCATGCTATGATGCAGCGCTCAGTTACGATTTCCATACCGACACATTCCGTGCAAG

upper sequence: AT2G32560.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA02G44660.1 (Glycine max), 3'ss of exon 1
----------------------------------------------------------gtaatcatttcataaacatagttgctccatttttgctttatggatttgattaaagtactaagaggcttttttttggtgaaaga---------gcagAATGGACATGTAGGGTTCATGTTGTCATGCTATGATGCGGAGCTCAGCTATGATACTCACACGGATACGTTCCAAGCCAG
                                                           |  |   ||||  |    |     |   ||||| | |  |  | | || || |  | ||    | |||| |     |  | |         ||||||||| ||||| || || |||||||||||||||||||| ||||| ||||||||| ||||||| || || ||||| |||||
gtatcaatcatcatgaacccctttgtgcttttttcctattgaaaacttatattctatcatgctaccttcaatagtgaaacaaattagttttttcatggta-actagaatagacgattattgtgtttttctcacaagttacatttttcactgcagAATGGCCATGTTGGATTTATGTTGTCATGCTATGATGCTGAGCTTAGCTATGATCCTCACACTGACACCTTCCAGGCCAG

upper sequence: AT2G32560.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA14G04080.1 (Glycine max), 3'ss of exon 1
---------------------------------------------------------gtaatcatttcataaacatagttgctccatttttgctttatggatttgattaaagtactaagaggcttttttttggtgaa--------agagcagAATGGACATGTAGGGTTCATGTTGTCATGCTATGATGCGGAGCTCAGCTATGATACTCACACGGATACGTTCCAAGCCAG
                                                          |  |   ||||  |    |     |   |||||    |    | | || || |  | |     | ||| |        |        |  ||||||||| ||||| || || ||||| |||||||||||||| ||||| ||||||||| ||||||  || || ||||| |||||
gtatcaatgattatgaatccctttgtgctttttggtattgaaaacttatattctttcatgctaccttcaatagtgaaacaaattagttttt--catggcaactagaatagaagattgttgtgttttctcacaagttacatttttcactgcagAATGGCCATGTTGGATTTATGTTATCATGCTATGATGCTGAGCTTAGCTATGATCCTCACAATGACACCTTCCAGGCCAG

upper sequence: AT2G32560.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv06s0009g02700.t01 (Vitis vinifera), 3'ss of exon 1
----------------------------------------------------------------------------gtaatcatttcataaacatagttgctcca-------tttttgctttatggatttgattaaagtactaagaggcttttttttggtgaaagagcagAATGGACATGTAGGGTTCATGTTGTCATGCTATGATGCGGAGCTCAGCTATGATACTCACACGGATACGTTCCAAGCCAG
                                                                             |    |   | |||||  |||  || |         ||||||| | ||| |||  ||    |  |||  |   | |||||| ||    |||||| ||| ||||| || || ||||| |||||||||||||| ||||| ||||||||| | ||||| ||||| ||||| |||||
gtatggactgtaactgcttgtttccagctataaattgtctgtctttcaacttcaatctcccacttccttaaggctcatgtctacaacctaaacgaagtcacttctgtttattcttttgctctctgggttt--ttcttttcataatggaagtgtttttgctgttt-agcagAGTGGCCATGTTGGCTTTATGTTATCATGCTATGATGCAGAGCTTAGCTATGATTCCCACACTGATACCTTCCAGGCCAG

upper sequence: AT2G32560.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S194_4V6.3 (Physcomitrella patens), 3'ss of exon 2
--------gtaatcattt--cataaacatagttgctccat------ttttgctttatggatttgattaaagtactaagaggcttttttttggtgaaagagcagAATGGACATGTAGGGTTCATGTTGTCATGCTATGATGCGGAGCTCAGCTATGATACTCACACGGATACGTTCCAAGCCAG
        ||   || |   | ||  | | ||| |||  |      ||      | ||    || ||     | ||||| |  || || |  ||      ||||||||||||||||| |||||| ||||||| ||||||||||| || | ||| |||  ||  ||||| || ||| |||| ||
aaaatgccgtttccagtgagcctatgcttggttactctttacagcattgcatcctgtgacggtggttttctcattaagacgacttcttctactgtt---tcagAATGGACATGTAGGCTTCATGCTGTCATGTTATGATGCGGAACTGAACTACGATCGTCGAACGGACACATTCAAAGCAAG

upper sequence: AT2G32560.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S194_4V6.4 (Physcomitrella patens), 3'ss of exon 2
--------gtaatcattt--cataaacatagttgctccat------ttttgctttatggatttgattaaagtactaagaggcttttttttggtgaaagagcagAATGGACATGTAGGGTTCATGTTGTCATGCTATGATGCGGAGCTCAGCTATGATACTCACACGGATACGTTCCAAGCCAG--------------------
        ||   || |   | ||  | | ||| |||  |      ||      | ||    || ||     | ||||| |  || || |  ||      ||||||||||||||||| |||||| ||||||| ||||||||||| || | ||| |||  ||  ||||| || ||| |||| ||                    
aaaatgccgtttccagtgagcctatgcttggttactctttacagcattgcatcctgtgacggtggttttctcattaagacgacttcttctactgtt---tcagAATGGACATGTAGGCTTCATGCTGTCATGTTATGATGCGGAACTGAACTACGATCGTCGAACGGACACATTCAAAGCAAGGTACTGTCTGCATTTTGGAC

upper sequence: AT2G32560.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: EFJ30849 (Selaginella moellendorffii), 3'ss of exon 1
gtaatcatttcataaacatagttgctccatttttgctttatggatttgattaaagtactaagaggcttttttttggtgaaagagcagAATGGACATGTAGGGTTCATGTTGTCATGCTATGATGCGGAGCTCAGCTATGATACTCACACGGATACGTTCCAAGCCAG
                      | || | | ||   |  | | |||   ||    | || |  |||||  ||      |     |||||||||||||| || ||  | ||||| ||||| ||||||||||||||||| | |      |  ||  |||| |  || ||
---------------gttcgtgttcttcgtgttctttcaaagaattctcttt---tgctcac-ggcttacttccctcca-----cagAATGGACATGTCGGATTTCTCTTGTCTTGCTACGATGCGGAGCTCAGCTACGTTCGCTCGAGCGACTCGTTTCGTGCGAG

upper sequence: AT2G32560.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: EFJ22793 (Selaginella moellendorffii), 3'ss of exon 1
gtaatcatttcataaacatagttgctccatttttgctttatggatttgattaaagtactaagaggcttttttttggtgaaagagcagAATGGACATGTAGGGTTCATGTTGTCATGCTATGATGCGGAGCTCAGCTATGATACTCACACGGATACGTTCCAAGCCAG
                      | || | | ||   |  |   |||   ||    | || |  |||||  ||      |     |||||||||||||| || ||  | ||||| ||||| ||||||||||||||||| | |      |  ||  |||| |  || ||
---------------gttcgtgttcttcgtgttctttcaaaaaattctcttt---tgctcac-ggcttgcttccctcca-----cagAATGGACATGTCGGATTTCTCTTGTCTTGCTACGATGCGGAGCTCAGCTACGTTCGCTCGAGCGACTCGTTTCGGGCGAG

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|125223179|gb|EL237264.1|EL237264
EST:     CCCTTGAAACAGGTCGTTTTTGGTTCCCAGCTCAAGTTTACAACCGTGAG                         AATGGACATGTAGGGTTCATGT
genomic: CCCTTGAAACAGGTCGTTTTTGGTTCCCAGCTCAAGTTTACAACCGTGAGgtaatcattt ... gaaagagcagAATGGACATGTAGGGTTCATGT
EST: gi|125266629|gb|EL280714.1|EL280714
EST:     CCTTGAAACAGGTCGTTTTTTGGTTCCCAGCTCAAGTTTACAACCGTGAG                         AATGGACATGTAGGGTTCATGTTGTCATGCTA
genomic: CCTTGAAACAGGTCG-TTTTTGGTTCCCAGCTCAAGTTTACAACCGTGAGgtaatcattt ... gaaagagcagAATGGACATGTAGGGTTCATGTTGTCATGCTA
EST: gi|124911028|gb|EH985108.1|EH985108
EST:     TTTTTGGTTCCCAGCTCAAGTTTACAACCGTGAG                         AATGGACATGTAGGGTTCATGTTGTCATGCTATGATGCGGAGCTCAGCTAT
genomic: TTTTTGGTTCCCAGCTCAAGTTTACAACCGTGAGgtaatcattt ... gaaagagcagAATGGACATGTAGGGTTCATGTTGTCATGCTATGATGCGGAGCTCAGCTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgctttatggatttgattaaagtactaagaggcttttttttggtgaaagagcagAATGGACATGTAGGGTTCATGTTGTCATGCTATGATGCGGAGCTCAGCTATGATACTCACACGGATACGTTCCAAGCCAG
           atttgat  putative branch site (score: 5)
           atttgattaaagta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatcatttcataaacatagttgctccatttttgctttatggatttgattaaagtactaagaggcttttttttggtgaaagagcagAATGGACATGTAGGGTTCATGTTGTCATGCTATGATGCGGAGCTCAGCTATGATACTCACACGGATACGTTCCAAGCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT