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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagataataaaaaccagaatcggtacaaactgcttcagactgttttttttcctgttccgattttaacttatataaatgttgctttctaatagGTATGTGGCACCGGAATACGCAATGACAGGGCATCTTTTGGTGAAGAGTGATGTGTATAGTTACGGAGTTGTGCTTCTCGAGCTACTTACAGGGCGGAAA

Basic information

species Arabidopsis thaliana
transcript AT5G56890.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G56890.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: LOC_Os01g51290.1 (Oryza sativa), 3'ss of exon 12
gtaagataataaaaaccagaatcggtacaaactgcttcagactgttttttttcctgttccgattttaacttatataaat-gttgctttctaatagGTATGTGGCACCGGAATACGCAATGACAGGGCATCTTTTGGTGAAGAGTGATGTGTATAGTTACGGAGTTGTGCTTCTCGAGCTACTTACAGGGCGGAAA
            ||      ||| | |   | |   | |  ||   | |  |    |  |    | | |||| | | ||  |    |  |  ||||||||| || || |||||||||||||| ||||||||| | || ||||||||||| || || || || || || || || ||||| ||||| ||  |||||
----------gtaagttttgatctgaaattattatctta--ctacctgtagttggttaacatcctcaccttaaaaagattatgaactctttttagGTATGTTGCTCCTGAATACGCAATGACTGGGCATCTTCTAGTAAAGAGTGATGTCTACAGCTATGGTGTCGTCCTCCTTGAGCTTCTTACCGGAAGGAAA

upper sequence: AT5G56890.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GRMZM2G330298_T01 (Zea mays), 3'ss of exon 6
gtaagataataaaaaccagaatcggtacaaactgcttcagactgttttttttcctgttccgattttaacttatataaat---gttgctttctaatagGTATGTGGCACCGGAATACGCAATGACAGGGCATCTTTTGGTGAAGAGTGATGTGTATAGTTACGGAGTTGTGCTTCTCGAGCTACTTACAGGGCGGAAA
     ||  ||||  |   |||   ||     | ||||    |  ||  ||   |      |  | |  ||| | || |   ||   |||||  ||||||| | || || ||||| |||||||| || |||||| | || ||||||||||| || || ||||| ||||| ||||| ||||| ||||||||| |||||
---gtatgctaaat-ctgaaattactatct-ttacttcttcatagttgattcaataccatcaactcatattacaaaattctggtcaatttctcttagGTATCTTGCTCCTGAATATGCAATGACTGGCCATCTTCTAGTAAAGAGTGATGTTTACAGCTACGGTGTTGTTCTTCTTGAGCTTCTTACAGGGAGGAAA

upper sequence: AT5G56890.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GRMZM2G404207_T01 (Zea mays), 3'ss of exon 5
gtaagataa--taaaaaccagaatcggtacaaactgcttcagactgttttttttcctgttccgattttaacttatataaatgttgctttctaatagGTATGTGGCACCGGAATACGCAATGACAGGGCATCTTTTGGTGAAGAGTGATGTGTATAGTTACGGAGTTGTGCTTCTCGAGCTACTTACAGGGCGGAAA
||| | | |     || | |  |||  ||||   |  |  |   |      |  ||   |    ||  || || |||    ||   ||| |  |||||| || ||||| ||||| |||||||| || |||||| |||| ||||||||||| || || ||||| || || || || ||||| |||||||||  ||||
gtacgctgaatctgaacctactatctttacatttttatagatgattcaacatcaccaacttatgttccaaattttatg---gtcaatttttcttagGTACGTTGCACCTGAATATGCAATGACTGGCCATCTTCTGGTAAAGAGTGATGTTTACAGCTACGGCGTAGTTCTCCTTGAGCTCCTTACAGGGATGAAA

upper sequence: AT5G56890.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA13G16380.1 (Glycine max), 3'ss of exon 9
-gtaagataataaaaaccagaatcggtacaaactgcttcagactgttt--tttttcctgttccg-attt--taacttatataaatgttgctttctaat--agGTATGTGGCACCGGAATACGCAATGACAGGGCATCTTTTGGTGAAGAGTGATGTGTATAGTTACGGAGTTGTGCTTCTCGAGCTACTTACAGGGCGGAAA
  |   ||| ||  |    |  |||  ||  | |  |||   ||| ||  ||||  || |   | ||||  | || ||||||  | |||     | ||  || |||||||| ||||| || |||||||| ||||||||| | || ||||||||||| || || || || ||||| ||||| |||||  | || ||  | |||
attgcaatattaccacttgg--tcgaaacctattttttccagctggttgattttcactatcatgcatttgctgacatatatatcttttgaaaattgatgtagTTATGTGGCGCCGGAGTATGCAATGACTGGGCATCTTCTTGTTAAGAGTGATGTTTACAGCTATGGTGTTGTTCTTCTTGAGCTTTTGACTGGAAGAAAA

upper sequence: AT5G56890.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA09G07140.1 (Glycine max), 3'ss of exon 9
--gtaagataataaaaaccagaatcggtacaaa-ctgcttcagactgttttttttcctgttccgattt-ta-acttatataaatgttgctttctaat-agGTATGTGGCACCGGAATACGCAATGACAGGGCATCTTTTGGTGAAGAGTGATGTGTATAGTTACGGAGTTGTGCTTCTCGAGCTACTTACAGGGCGGAAA
  | |  ||  |      || ||    |  ||  ||   |     |  | || ||      | ||| | || | |  |  | || |      ||| | || |||||||| ||||| || |||||||| || |||||| | |||||||||||||| || || || || ||||| || || |||||  | || ||  | |||
ctgaactattttttgtttcaaaactattgtaattctttgttgttttactattatttactccctgatatatatattctttcatatttgaaaaactattcagTTATGTGGCTCCGGAGTATGCAATGACGGGACATCTTCTTGTGAAGAGTGATGTTTACAGCTATGGTGTTGTCCTCCTTGAGCTTTTGACCGGAAGAAAA

upper sequence: AT5G56890.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: Vv11s0016g02150.t01 (Vitis vinifera), 3'ss of exon 11
gtaagataataaaaaccagaatcggtacaaa----ctgcttcagactgttttttttcctgttccg-attttaacttatataaatgttgctttct---aatagGTATGTGGCACCGGAATACGCAATGACAGGGCATCTTTTGGTGAAGAGTGATGTGTATAGTTACGGAGTTGTGCTTCTCGAGCTACTTACAGGGCGGAAA
  |   |  |     |   |||   |  ||     ||| ||  | || ||||||||    ||     | |    |    ||| | ||  ||| |   |  ||||||||||| || || || |||||||| || |||||| | |||||||||||||| ||||| || ||||| || ||||| ||||| || |||||  | |||
--atattcctgctttctttaatatttttaagtcccctgtttgtgtcttttttttttttaattttatgtctctgttctcctaattattattttttcccatcagGTATGTGGCTCCAGAGTATGCAATGACTGGCCATCTTCTTGTGAAGAGTGATGTTTATAGCTATGGAGTAGTCCTTCTTGAGCTCCTAACAGGAAGAAAA

upper sequence: AT5G56890.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: PP1S343_14V6.1 (Physcomitrella patens), 3'ss of exon 7
-------gtaagataataaaaaccagaatcggtacaaactgcttcagactgttttttttcctgttccgattttaacttatataaatgttgctttctaatagGTATGTGGCACCGGAATACGCAATGACAGGGCATCTTTTGGTGAAGAGTGATGTGTATAGTTACGGAGTTGTGCTTCTCGAGCTACTTACAGGGCGGAAA
       |||   |  |     | |   |    | |   |      ||| | |    ||  |  |  ||||    |   ||   ||     | |     ||||||||||| || |||||||||||||||||||||||  | |||||||||||||| || ||||||||||| |||||||| ||||| ||  | || ||||||
ttctcttgtattctcgtttcttctattttttagatatctttggctggaccgctagcgttgttactt-gattcctgcacttactgattgatttctactgcagGTATGTGGCCCCTGAATACGCAATGACAGGGCATCTACTTGTGAAGAGTGATGTTTACAGTTACGGAGTAGTGCTTCTAGAGCTCCTCTCTGGACGGAAA

upper sequence: AT5G56890.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: PP1S43_35V6.1 (Physcomitrella patens), 3'ss of exon 2
--------gtaagataataaaaaccagaatcggtacaaactgcttcagactgttttttttcctgttccgatt-ttaacttatataaat-gttgctttctaat--agGTATGTGGCACCGGAATACGCAATGACAGGGCATCTTTTGGTGAAGAGTGATGTGTATAGTTACGGAGTTGTGCTTCTCGAGCTACTTACAGGGCGGAAA
         | | ||   || |   || ||   |    ||     ||||||| |    ||  |||   |||| || |||||    | | |||| |||| | |  ||||||||||| ||||| ||||| |||||||||||| |  | |||||||||||||| |||||||| ||||| |||||||| ||||| ||| | || || |||
ctttcaccttcacatctgaatatttaggatgtattttgac-----cagactggtaaggttg-tgtcttgattattgacttacggtagtagttgatttcaactgcagGTATGTGGCCCCGGAGTACGCTATGACAGGGCATTTACTTGTGAAGAGTGATGTTTATAGTTATGGAGTGGTGCTTCTGGAGCTCCTTTCTGGACGAAAA

upper sequence: AT5G56890.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: PP1S255_47V6.1 (Physcomitrella patens), 3'ss of exon 6
gtaagataataaaaaccagaatcggtacaaactgcttcagactgtttttttt-----cctgttccgattttaacttatataaa-tgttgctttctaat---agGTATGTGGCACCGGAATACGCAATGACAGGGCATCTTTTGGTGAAGAGTGATGTGTATAGTTACGGAGTTGTGCTTCTCGAGCTACTTACAGGGCGGAAA
    | |  |    ||| || |   | |||| ||        |||   | ||     | ||    | |||   |    | ||| | |||  |   ||    || |||||||| || ||||||||||||||||| ||| |  | ||||||||||| || |||||||| ||||| || || |||||||| ||  | ||||| |||
---tgtttctttgcaccggattacctccaaaatggccatatttgtcactattaggatcgtgccttggtttctgcactgacaaaatattggatctaaactgcagATATGTGGCTCCTGAATACGCAATGACAGGACATTTGCTTGTGAAGAGTGACGTTTATAGTTATGGAGTGGTACTGCTCGAGCTCCTCTCGGGGCGTAAA

upper sequence: AT5G56890.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: EFJ20296 (Selaginella moellendorffii), 3'ss of exon 2
gtaagataataaaaaccagaatcggtacaaactgcttcagact-gttttttttcctgttccgattttaacttatataaatgttgctttctaatagGTATGTGGCACCGGAATACGCAATGACAGGGCATCTTTTGGTGAAGAGTGATGTGTATAGTTACGGAGTTGTGCTTCTCGAGCTACTTACAGGGCGGAAA-
                      || |      | |  |||  | ||||| |||  |  || ||    |||| || |     || ||  |    || || || || || || ||||||||||| || ||||||||||||||||| ||||| || || ||||| |||||||| |||||||||||  | |||| |||| 
-------------------gtacgctttggttttcaacagcgtagttttcttttatcctctgaga--aactgatctctggtttactggc--gcagTTACGTCGCTCCAGAGTACGCAATGACCGGACATCTTTTGGTGAAGAGCGATGTCTACAGCTACGGGGTTGTGCTACTCGAGCTACTGTC-GGGCAGAAAG

upper sequence: AT5G56890.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: EFJ23292 (Selaginella moellendorffii), 3'ss of exon 2
gtaagataataaaaaccagaatcggtacaaactgcttcagactgttttttttcctgttccgattttaacttatataaatgttgctttctaatagGTATGTGGCACCGGAATACGCAATGACAGGGCATCTTTTGGTGAAGAGTGATGTGTATAGTTACGGAGTTGTGCTTCTCGAGCTACTTACAGGGCGGAAA-
                     |  |  |    |        |    |||| || ||| |       |||| || |   || |  | |     || || || || || || ||||||||||| || ||||||||||||||||| ||||| || || ||||| |||||||| |||||||||||  | |||| |||| 
--------------------gtaagctctggttttcaacagcgtagttttctcttgtcctctgagaaactgatctc--tggttttctggcgcagTTACGTCGCTCCAGAGTACGCAATGACCGGACATCTTTTGGTGAAGAGCGATGTCTACAGCTACGGGGTTGTGCTACTCGAGCTACTGTC-GGGCAGAAAG

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|125069586|gb|EL135311.1|EL135311
EST:     GATGATGAAGATAACAGACATATATCGACACGCGTTATGGGAACGTTTGG                         GTATGTGGCACCGGAATACGCAATG
genomic: GATGATGAAGATAACAGACATATATCGACACGCGTTATGGGAACGTTTGGgtaagataat ... tttctaatagGTATGTGGCACCGGAATACGCAATG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gactgttttttttcctgttccgattttaacttatataaatgttgctttctaatagGTATGTGGCACCGGAATACGCAATGACAGGGCATCTTTTGGTGAAGAGTGATGTGTATAGTTACGGAGTTGTGCTTCTCGAGCTACTTACAGGGCGGAAA
                       ttttaac  putative branch site (score: 2)
                                         ttgctttct  putative PPT
                      attttaacttatataa  TA-rich tract