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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactgacaaaaacaaatttgtgctattgttgtatatatggtattgtttctgctcatttaacatgacttttctacttactttggcaaatagATACTTCTCATATGAGCATTTCTATGTCATATACTGCAAGTTCTGGGAGCTGGATACGGATCACGATTTCCTGATTGACAAAGAAAATCTTATGAGATAT

Basic information

species Arabidopsis thaliana
transcript AT5G28850.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G28850.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os10g33680.1 (Oryza sativa), 3'ss of exon 7
--gtactgacaaaaacaaatttgtgctattgttgtat-----atatggtattgtttctgctcatttaacatgacttttctacttactttggcaaat--agATACTTCTCATATGAGCATTTCTATGTCATATACTGCAAGTTCTGGGAGCTGGATACGGATCACGATTTCCTGATTGACAAAGAAAATCTTATGAGATAT
  | | |      |   || || |  ||||  |||       | |    ||| |||    |  |||  ||    | ||    ||    || | |||  |||||||||||||| ||||| || ||||| ||||||||||| || |||||| |||| || ||||| |||||  ||||||| ||||| || ||||| ||||||
acgaattacttggattcaagttatattatttatgtgcgaatcaaacaagattttttacattttttttccaaatgtgttaattttctgatgcctaatgcagATACTTCTCATACGAGCACTTTTATGTGATATACTGCAAATTTTGGGAGTTGGACACAGATCATGATTTTTTGATTGATAAAGAGAACCTTATCAGATAT

upper sequence: AT5G28850.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G148323_T01 (Zea mays), 3'ss of exon 7
------gtactgacaaaaacaaatttgtgctat-tgttgtatatatggtattgtttctgctca--tttaacatgacttttctacttactttggcaaatagATACTTCTCATATGAGCATTTCTATGTCATATACTGCAAGTTCTGGGAGCTGGATACGGATCACGATTTCCTGATTGACAAAGAAAATCTTATGAGATAT
      ||  ||     |  | |||||| |  | | || | ||||| || ||   | ||   |   || ||     |  |   |||   |        ||||| ||||||||||| || || ||||| || |||||||| ||||||||||||||| | || ||||||||  ||||||| || |||||||| || | ||||
ccatttgttttgtgtggattacatttgttcactgttttctttatatagtcttaactgtgtataacgtttactgagttaataatcttggatcatggtgcagATATTTCTCATATGAACACTTTTATGTGATCTACTGCAAATTCTGGGAGCTGGATGCAGACCACGATTTTTTGATTGATAAGGAAAATCTCATCAAATAT

upper sequence: AT5G28850.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA10G30930.1 (Glycine max), 3'ss of exon 7
-----------------------gtactgacaaaaacaaatttgtgctattgttgtatatatggtattgtttctgctcatttaacatgacttttctacttactt-tggcaaatagATACTTCTCATATGAGCATTTCTATGTCATATACTGCAAGTTCTGGGAGCTGGATACGGATCACGATTTCCTGATTGACAAAGAAAATCTTATGAGATAT
                         | | ||| ||   | | |||  |   |    | ||||  |  |         |||| |   |   |  | ||| || |  | |    ||| |||||||| ||||||||||| ||||| ||||||||||| || |||||||||||||| |||||||||||| | || |||||||| |||||||| ||||||
gtagatatactatcattatcattaaattcacacaa-tgactctgtttttcagccaaa-atatattgataccagaatgcattgagtgtttttactttacctaataattgtctgtagGTACTTCTCTTATGAGCATTTTTATGTTATATACTGCAAATTTTGGGAGCTGGATACAGATCACGATTTCTTAATAGACAAAGAGAATCTTATCAGATAT

upper sequence: AT5G28850.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA19G43790.1 (Glycine max), 3'ss of exon 7
-----------------------------gtactgacaaaaacaaatttg-tgctattgttgta------tatatggtattgt-ttctgctcatttaacatgactt--ttctacttactttggcaaatagATACTTCTCATATGAGCATTTCTATGTCATATACTGCAAGTTCTGGGAGCTGGATACGGATCACGATTTCCTGATTGACAAAGAAAATCTTATGAGATAT
                               |||    ||||  |  ||| ||  ||| ||  |      || ||    |||| || || |   ||||  |   ||   | | |||| | |       || |||||||| ||||||||||| ||||| |||||||||||||| |||||||||||||| ||||| |||||| |||| |||||||| ||||| || ||||||
gtagatataattgaaaatgtcatttcaattaacttcagaaaatgaccttggtgtcattattcaaatgaactaaatatatttgtattatgatgccttaatcttttttacctttccttaatgttatctgcagGTACTTCTCTTATGAGCATTTTTATGTTATATACTGCAAGTTTTGGGAGCTGGATACAGATCATGATTTCTTGATAGACAAAGAGAATCTCATCAGATAT

upper sequence: AT5G28850.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA20G36530.1 (Glycine max), 3'ss of exon 7
------gtactga--caaaaacaaatttgtgctattgttgtatatatggtattgtttctgctcatt-taacatgacttttctacttactttggcaaata----------gATACTTCTCATATGAGCATTTCTATGTCATATACTGCAAGTTCTGGGAGCTGGATACGGATCACGATTTCCTGATTGACAAAGAAAATCTTATGAGATAT
       ||||     |  |  |||||    | ||   | | | | |         | |  ||||   || |||  || | |  ||||||   | ||||          | |||||||| ||||||||||| ||||| ||||||||||| || |||||||||||||| |||||||||||| | || |||||||| |||||||| ||||||
gtagatatactatattatcattaaattcacacaatgactctgtttttcagccaaaatatattcataacaaaatgcattgtgtttttacttcacctaataattgtctgtagGTACTTCTCTTATGAGCATTTTTATGTTATATACTGCAAATTTTGGGAGCTGGATACAGATCACGATTTCTTTATAGACAAAGAGAATCTTATCAGATAT

upper sequence: AT5G28850.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA03G41180.1 (Glycine max), 3'ss of exon 7
-----------------------------gtactgacaaaaacaaatttg-tgctattgttgta------tatatggtattgt-ttctgctcatttaacatgactt--ttctacttactttggcaaatagATACTTCTCATATGAGCATTTCTATGTCATATACTGCAAGTTCTGGGAGCTGGATACGGATCACGATTTCCTGATTGACAAAGAAAATCTTATGAGATAT
                               |||    ||||  |  ||| |   ||| ||  |      || ||    |||| || || |   ||||  |   ||   | | || | | |       || |||||||| || |||||||| ||||| |||||||||||||| |||||||||||||| ||||| |||||| |||| |||||||| ||||| || ||||||
gtagatataattgaaaatttcatttcaattaacttcagaaaatgaccttggtttcattattcaaacgaactaaatatatttgtattatgatgccttaatcttttttacctttcctaaatattatctgcagGTACTTCTCTTACGAGCATTTTTATGTTATATACTGCAAGTTTTGGGAGCTGGATACAGATCATGATTTCTTGATAGACAAAGAGAATCTCATCAGATAT

upper sequence: AT5G28850.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: EDP08306 (Chlamydomonas reinhardtii), 3'ss of exon 3
-----------gtactgacaaaaacaaatttgtgctattgttgtatatatggt--attgtttctgctcatttaacatgacttttctacttactttggcaaat----agATACTTCTCATATGAGCATTTCTATGTCATATACTGCAAGTTCTGGGAGCTGGATACGGATCACGATTTCCTGATTGACAAAGAAAATCTTATGAGATAT
           | |  | |     |         |   ||  |   |               | ||||   |  |         |     | |    || ||    |  | |||||| || ||||| ||||| ||||| |||||||||||||||||||||||   ||| ||||| |||| | | |||||   | | ||          
caccaagccgagcagcggctgcggcttcccctcacgcctgcagcccacccacccagcctcacccgctcgcctccctccctccggcctaccaatgcatcagATCCTCAAGTTCTTCTCCTACGAGCACTTCTACGTCATCTACTGCAAGTTCTGGGAGCTGGACCAGGACCACGACTTCCAGCTGGACAAGACAGACCTGG--------

upper sequence: AT5G28850.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: PP1S7_163V6.1 (Physcomitrella patens), 3'ss of exon 7
---------gtactgacaaaaacaaattt--gtgctattgt-tgtatatatggtattgtttctgctcatttaacatgacttttctacttactttggcaaatagATACTTCTCATATGAGCATTTCTATGTCATATACTGCAAGTTCTGGGAGCTGGATACGGATCACGATTTCCTGATTGACAAAGAAAATCTTATGAGATAT
         |  || || ||||  ||||    | | |     ||    || | |  || |  ||  |  |||   | | | || ||    ||| |      || |||||||||||||| ||||| ||||||||||| ||||||||||||||||||||| | |||||||||||  | || ||||||||  ||||  |  |||||
tatcagtttgccctcacgaaaagtaattatgataccacgacgtgagcttaagtttctgatcatgtgcccttaggctaaatattgtaagcgcttcg---tgcagTTACTTCTCATATGAACATTTTTATGTCATATATTGCAAGTTCTGGGAGCTGGATTCAGATCACGATTTTTTAATAGACAAAGATGATCTCCTTCGATAT

upper sequence: AT5G28850.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: PP1S147_62V6.2 (Physcomitrella patens), 3'ss of exon 7
---------gtact-gacaaaaacaaatttgtgctattgttgtatatatggtattgtttctgctcatttaacatgacttttctacttactt-tggcaaatagATACTTCTCATATGAGCATTTCTATGTCATATACTGCAAGTTCTGGGAGCTGGATACGGATCACGATTTCCTGATTGACAAAGAAAATCTTATGAGATAT
         |  ||  | | ||   | | ||    |||| |||  || | |  || |   ||   || |     | ||  || || || |     |    || |||||||||||||| ||||| ||||||||||| ||||| ||||||||||||||| | |||||||| ||  |||| ||||||||  | ||| |  |||||
tattggcatgccctcaatagaagacagtatggtacattgatgtgaatttaggtttctacttgtgtatctgta--ggctcatccacgtaatcgcttcgtgcagGTACTTCTCATATGAACATTTTTATGTCATATATTGCAAATTCTGGGAGCTGGATTCAGATCACGACTTTTTGATAGACAAAGATGACCTTCTTCGATAT

upper sequence: AT5G28850.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: PP1S34_411V6.1 (Physcomitrella patens), 3'ss of exon 7
-------------------------------------gtactgacaaaaacaaatttgtgctattgttgtat------atatggtattgtttctgctcatttaacatgacttttctacttactttg------gcaaatagATACTTCTCATATGAGCATTTCTATGTCATATACTGCAAGTTCTGGGAGCTGGATACGGATCACGATTTCCTGATTGACAAAGAAAATCTTATGAGATAT
                                        |||||   |     ||   | |||| ||   |      | |  ||   | || |   |||  ||      |||     ||| ||||      |     || || || || ||||||||||| || |||||||| |||||||||||||| || ||| | ||||| || ||  | || ||||| ||  ||||  |  |||||
gtcaactccgatcaacctttctttcacgttgtttgatcccctgacttgatttttttgtcgatatttttcattttctcaacagagtgcagctttttaccatc-aattgagttttcaagattattttgaacgctgtgtgcagGTATTTTTCGTATGAGCATTTTTACGTCATATATTGCAAGTTCTGGGAACTAGATTCAGATCATGACTTTTTCATAGACAAGGATGATCTCCTTCGATAT

upper sequence: AT5G28850.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: PP1S68_31V6.1 (Physcomitrella patens), 3'ss of exon 7
-gtactgacaaaaac----aaatttgtgctattgttgtatatatggtattgtttctgctcatttaacatgacttttctacttactt----tggcaaatagATACTTCTCATATGAGCATTTCTATGTCATATACTGCAAGTTCTGGGAGCTGGATACGGATCACGATTTCCTGATTGACAAAGAAAATCTTATGAGATAT
   |  ||  | | |    |  ||| ||  ||  |    | ||   |  |      |   ||   |  |||| |||  |   |  |    ||  |   || || || |||||||| ||||||||||| || ||||||||||| |||||| ||||  |||||||||| ||  |||||||||| ||  | ||  || |||| 
gcgagggatgagagcttggatctttttgtcatattccagtttagtatgctaacaaagactataataattgacctttggatacatgtggtgtgcgacgcagCTATTTTTCATATGAACATTTCTATGTTATTTACTGCAAGTTTTGGGAGTTGGACTCGGATCACGACTTTGTGATTGACAAGGATGACCTATTGCGATAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatggtattgtttctgctcatttaacatgacttttctacttactttggcaaatagATACTTCTCATATGAGCATTTCTATGTCATATACTGCAAGTTCTGGGAGCTGGATACGGATCACGATTTCCTGATTGACAAAGAAAATCTTATGAGATAT
                                    tacttac  putative branch site (score: 1)
                              cttttctacttacttt  CT-rich tract
                   atttaacat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactgacaaaaacaaatttgtgctattgttgtatatatggtattgtttctgctcatttaacatgacttttctacttactttggcaaatagATACTTCTCATATGAGCATTTCTATGTCATATACTGCAAGTTCTGGGAGCTGGATACGGATCACGATTTCCTGATTGACAAAGAAAATCTTATGAGATAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA