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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgatggtttgaattgattctgttttgcttgcattcggatgaagtttaatgcttttttgtttgtttcactcatctgtagGCTAATCCTGACTACAAAGGTGTTTGCCATGTTGCACTTGCACAAGAAGGTCATTGCAGGCCAGGAGAG

Basic information

species Arabidopsis thaliana
transcript AT4G13430.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G13430.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os02g03260.1 (Oryza sativa), 3'ss of exon 3
----------------------------------------gtatgat-ggtttgaattgattctgttttgct-tgcattcggatgaagtttaatgcttttttgtttgtttcactcatctgtagGCTAATCCTGACTACAAAGGTGTTTGCCATGTTGCACTTGCACAAGAAGGTCATTGCAGGCCAGGAGAG
                                        |  || | | |||| ||  |  |||||||  | | ||||  || ||| |||  |   |         |||   |  | || |||| ||||| |||||||| ||||||||||| ||||| ||||| ||||| ||||||||||| ||||| |||
gtatgccgatccattttcattatcttttctccaattgatagcttgtttgttttgtatcaaacctgttttcatgttcattttgaagaaattttttaaataaactgcaatttgtgttgtttgcagGCAAATCCAGACTACAAGGGTGTTTGCCACGTTGCTCTTGCTCAAGAGGGTCATTGCAGACCAGGCGAG

upper sequence: AT4G13430.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA14G40570.1 (Glycine max), 3'ss of exon 4
-----------------gtatgatggtttgaattgattctgttttgctt-------gcatt----cggatgaagtttaatgcttttttgtttgtttcactcatctgtagGCTAATCCTGACTACAAAGGTGTTTGCCATGTTGCACTTGCACAAGAAGGTCATTGCAGGCCAGGAGAG
                  | |     | |  |||  |||  ||   ||        |||||     | |  | ||  ||     ||   | ||      | |  |  |||  ||||| ||||| || ||||||||||||||||| ||||| || ||||||||||| ||||||||||||
gtatgcattcttttgatttttttcaatcttgatttgttcgtttcaactcttaaagagcattgtaatgcacaatgtccaagaacattgactgtgagattataaaatacagGTAAATCCAGACTATAAGGGTGTTTGCCATGTTGCTCTTGCTCAGGAAGGTCATTGTAGGCCAGGAGAG

upper sequence: AT4G13430.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA17G37540.1 (Glycine max), 3'ss of exon 4
-------------------gtatgatggtttgaattgattctgttttgctt-------gcattcggatgaa----gtttaatgcttttttgtttgtttcactcatctgtagGCTAATCCTGACTACAAAGGTGTTTGCCATGTTGCACTTGCACAAGAAGGTCATTGCAGGCCAGGAGAG
                    | |     | |  |||  |||| ||    |        |||||   ||| |    ||  ||     ||   | ||      | |  |  |||  ||||| ||||| || ||||||||||||||||| ||||| || ||||||||||| ||||| ||||| 
ggtatgcattcttttgtttttttttcaatcttgatttgttcttttcaattcttaaagagcattttaatgcacaatgtccaagaacattgactgtgagattataaaatacaGGTAAATCCAGACTATAAGGGTGTTTGCCATGTTGCCCTTGCTCAGGAAGGTCATTGTAGGCCTGGAGA-

upper sequence: AT4G13430.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA20G34160.1 (Glycine max), 3'ss of exon 4
-----------------gtatgatggt-ttgaattgattctgttttgcttgcattcgg--atgaagtttaatgcttttttgtttgtttcactcatctgtagGCTAATCCTGACTACAAAGGTGTTTGCCATGTTGCACTTGCACAAGAAGGTCATTGCAGGCCAGGAGAG
                  | | |||   ||||| | | | |  |       |||   |  || |||||| ||           |  || |  ||| || |||||||||| || || ||||||||||| || ||||| || ||||| |||||||||||||| || ||||||
taaacattagcagtttattttcatgtcattgaagtaactttaatcattaaccatcaagaaataaagttttatagaccgcataataatttatacat-tgcagGCTAATCCAGATTATAAAGGTGTTTGTCACGTTGCTCTAGCACAGGAAGGTCATTGCAGACCTGGAGAG

upper sequence: AT4G13430.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv08s0056g01640.t01 (Vitis vinifera), 3'ss of exon 4
------------------gtatgatggtttgaattgattctgttttgcttgcattcggatgaagtttaatgcttttttgtttgt----------------ttcactcat---ctgtagGCTAATCCTGACTACAAAGGTGTTTGCCATGTTGCACTTGCACAAGAAGGTCATTGCAGGCCAGGAGAG
                  || | ||| |||   ||    | | |   ||  | | |  |     | | ||   |  |||||| |                ||  || ||   ||| ||| ||| || || || |||||||| ||||||||||| ||||| |||||||||||||||||||| ||||||
gtatgatgcctttcaggtgtttcatgttttagtttccaaccgctaaactatcttgctaaaaggttatcatctgtccttgtttatcacatggaatgtaaagtttgcttattgactgcagGTTAACCCAGATTATAAAGGTGTATGCCATGTTGCTCTTGCCCAAGAAGGTCATTGCAGGCCTGGAGAG

upper sequence: AT4G13430.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv05s0049g01980.t01 (Vitis vinifera), 3'ss of exon 4
--------------------gtatgatggtttgaattgatt---ctgttttgct-----tgcat--tcggatgaagtttaatgcttttt-tgtttgtttcactcatc----tgtagGCTAATCCTGACTACAAAGGTGTTTGCCATGTTGCACTTGCACAAGAAGGTCATTGCAGGCCAGGAGAG
                     | |  | ||||  |   | |   || | |||||     || ||  ||   |   ||||| |||  |   |||    || ||  ||     || |||| ||||| || ||||||||||| ||||||||||| ||||| |||||||||||||||||||| ||||||
gtatgcctctctggtctttcatgttttagtttccaaccactgaactatattgctgaaggtgtatcatctattcttgtttattgcactgaatgtaaactttacgtatgagcatgcagGCCAATCCGGATTACAAAGGTGTATGCCATGTTGCCCTTGCCCAAGAAGGTCATTGCAGGCCTGGAGAG

upper sequence: AT4G13430.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: EFJ16666 (Selaginella moellendorffii), 3'ss of exon 3
gtatgatggtttgaattgattctgttttgcttgcattcggatgaagtttaatgcttttttgtttgtttcactcatctgtagGCTAATCCTGACTACAAAGGTGTTTGCCATGTTGCACTTGCACAAGAAGGTCATTGCAGGCCAGGAGAG
                         |  | ||||  |  | |    | | || || |     |        |    || |||| ||||| |||||||| ||||||||||| ||||| ||||| ||||||||||| ||| | || || |||
------------------------gtacgtttgcggt--gtttgtatgtgattctgtcgctctaacccggatttgatgcagGCAAATCCCGACTACAAGGGTGTTTGCCACGTTGCTCTTGCTCAAGAAGGTCACTGCCGTCCGGGCGAG

upper sequence: AT4G13430.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: EFJ16664 (Selaginella moellendorffii), 3'ss of exon 1
gtatgatggtttgaattgattctgttttgcttgcattcggatgaagtttaatgcttttttgtttgtttcactcatctgtagGCTAATCCTGACTACAAAGGTGTTTGCCATGTTGCACTTGCACAAGAAGGTCATTGCAGGCCAGGAGAG
                      |   ||    |  || | | |   ||   |   | |      | ||        || |||| ||||| |||||||| ||||||||||| ||||| ||||| || |||||||| ||||| || || |||
---------------------gtacgtttgcggtgtttgtacgtgattcggtcgctctaacccggatttg-----atgcagGCAAATCCCGACTACAAGGGTGTTTGCCACGTTGCTCTTGCTCAGGAAGGTCACTGCAGTCCGGGCGAG

upper sequence: AT4G13430.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: EFJ32611 (Selaginella moellendorffii), 3'ss of exon 3
gtatgatggtttgaattgattctgttttgcttgcattcggatgaagtttaatgcttttttgtttgtttcactcatctgtagGCTAATCCTGACTACAAAGGTGTTTGCCATGTTGCACTTGCACAAGAAGGTCATTGCAGGCCAGGAGAG
                         |  | ||||  |  | |      | || || |     |        |    || |||| ||||| |||||||| ||||||||||| ||||| ||||| ||||||||||| ||| | || || |||
------------------------gtacgtttgcggt--gtttgtacgtgattctgtcgctctaacccggatttgatgcagGCGAATCCCGACTACAAGGGTGTTTGCCACGTTGCTCTTGCTCAAGAAGGTCACTGCCGTCCGGGCGAG

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|124795951|gb|EH885630.1|EH885630
EST:     TATCACTGACCTTGGAAATTTTAAG                         GCTAATCCTGACTACAAAGGTGTTTGCCATGTTGCACTTGCACAAGAAGGT
genomic: TATCACTGACCTTGGAAATTTTAAGgtatgatggt ... tcatctgtagGCTAATCCTGACTACAAAGGTGTTTGCCATGTTGCACTTGCACAAGAAGGT
EST: gi|163978264|gb|ES064959.1|ES064959
EST:     AACAGAATATTAAGTATTTCTATGATATCACTGACCTTGGAAATTTTAAG                         GCTAATCCTGACTACAAAGGTGTTTGCCATGTTGCAC
genomic: AACAGAATATTAAGTATTTCTATGATATCACTGACCTTGGAAATTTTAAGgtatgatggt ... tcatctgtagGCTAATCCTGACTACAAAGGTGTTTGCCATGTTGCAC
EST: gi|124752085|gb|EH842215.1|EH842215
EST:     TCACTGACCTTGGAAATTTTAAG                         GCTAATCCTGACTACAAAGGTGTTTGCCATGTTGCACTTGCACAAGAAGGT
genomic: TCACTGACCTTGGAAATTTTAAGgtatgatggt ... tcatctgtagGCTAATCCTGACTACAAAGGTGTTTGCCATGTTGCACTTGCACAAGAAGGT
EST: gi|125135279|gb|EL175688.1|EL175688
EST:     AACAGAATATTAAGTATTTCTATGATATCACTGACCTTGGAAATTTTAAG                         GCTAATCCTGACTACAAAGGTGTTTG
genomic: AACAGAATATTAAGTATTTCTATGATATCACTGACCTTGGAAATTTTAAGgtatgatggt ... tcatctgtagGCTAATCCTGACTACAAAGGTGTTTG
EST: gi|124769545|gb|EH859675.1|EH859675
EST:     ATATTAAGTATTTCTATGATATCACTGACCTTGGAAATTTTAAG                         GCTAATCCTGACTACAAAGGTGTTTGCCATGTTGCACTTGCACAAGAAGGT
genomic: ATATTAAGTATTTCTATGATATCACTGACCTTGGAAATTTTAAGgtatgatggt ... tcatctgtagGCTAATCCTGACTACAAAGGTGTTTGCCATGTTGCACTTGCACAAGAAGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgcttgcattcggatgaagtttaatgcttttttgtttgtttcactcatctgtagGCTAATCCTGACTACAAAGGTGTTTGCCATGTTGCACTTGCACAAGAAGGTCATTGCAGGCCAGGAGAG
                   gtttaat  putative branch site (score: 4)
                                       tttcactc  putative PPT
                    tttaatgctttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgatggtttgaattgattctgttttgcttgcattcggatgaagtttaatgcttttttgtttgtttcactcatctgtagGCTAATCCTGACTACAAAGGTGTTTGCCATGTTGCACTTGCACAAGAAGGTCATTGCAGGCCAGGAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA