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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtctaattgaattttactttttggttgctttaactttcacttgtttcgatcaaattttttttactggcgaaaaagtaataaaatgtaatctaattgctattagATGCTTATGGGAGGAGGTGGCTCATTCTCTGCGGGAGGTCCTGGAAAAGGAATGCACTCGTGGCTTT

Basic information

species Arabidopsis thaliana
transcript AT1G51980.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G51980.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os01g53700.1 (Oryza sativa), 3'ss of exon 6
------------------------------------------gtgtctaattgaattttactttttggttgctttaactttcacttgtttcgatcaaattttttttactggcgaaaaagtaataaaatgtaatctaattgctat-tagATGCTTATGGGAGGAGGTGGCTCATTCTCTGCGGGAGGTCCTGGAAAAGGAATGCACTCGTGGCTTT
                                                || |    | ||| ||||   |  ||||   |  | | |  |   | | || ||    | |     | | | ||||     |  |||  ||  | |  ||||||| |||||||||||||| || |||||||| || |||||||| || || ||||| ||  |  | |
gtattgttggcaaacatcaaatttaaccattattcagagacaaaactcaactatggtataccttttatgtagtttactgtctagtagactgccttatatgttcaccatttctttatacgcaatatgg-atggtcttgttattttgcagATGCTCATGGGAGGAGGTGGTTCTTTCTCTGCTGGTGGTCCTGGGAAGGGCATGCATTCTCGATTGT

upper sequence: AT1G51980.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G005036_T01 (Zea mays), 3'ss of exon 6
---gtgtctaattg-aattttactttttggttgctttaactttcacttgtttcgatcaaattttttttactggcgaaaaagtaataaaatgtaatctaattgctattagATGCTTATGGGAGGAGGTGGCTCATTCTCTGCGGGAGGTCCTGGAAAAGGAATGCACTCGTGGCTTT
    | |||  | |   | |||        |  | |   || |  | | |    ||| |||  |  ||     | ||    |  | |    | |  |  |||    |||||||| ||||||||||| || || |||||||| || || |||||||| |||||||| ||  |  | |
gccatttcttctagcggtgttaaaaaacaatcacatgtgctgttgcatatgctaatctaatagtgctt-----caaaggtatgttga----tcaatttgttgtctgtagATGCTCATGGGAGGAGGAGGGTCCTTCTCTGCTGGTGGGCCTGGAAAGGGAATGCATTCTCGATTGT

upper sequence: AT1G51980.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA13G43000.1 (Glycine max), 3'ss of exon 7
---------------gtgtctaattgaattttactttttggttgctt-taacttt---cacttgtttcgatcaaattttttttactggcgaaaaagtaataaaatg---taatctaattgcta------------ttagATGCTTATGGGAGGAGGTGGCTCATTCTCTGCGGGAGGTCCTGGAAAAGGAATGCACTCGTGGCTTT
               | |||    ||| ||  |  | | |  ||  | |   |||    | ||  |||        ||  |  ||  |  ||  || ||  |||     ||||  || |  ||            | |||||||||||||||||||||| || |||||||| ||||| ||||||||||| ||||| ||  |||| |
gtactcactttgtgtgagtcattctgatttcaagatatagcatgtctatggatttgcatattttcttctgctggcattcatgcacaagaaaaggaggaaagaaacaatttaatagaagtaataattctgagtcgttcagATGCTTATGGGAGGAGGTGGGTCGTTCTCTGCTGGAGGGCCTGGAAAAGGGATGCATTCAAGGCTGT

upper sequence: AT1G51980.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA08G21380.1 (Glycine max), 3'ss of exon 6
-----------------gtgtctaattgaatt-ttactttttggttgctttaacttt-cacttgtt--tcgatcaaattttttttactggcgaaaaagtaataaaatgtaatctaattgctattagATGCTTATGGGAGGAGGTGGCTCATTCTCTGCGGGAGGTCCTGGAAAAGGAATGCACTCGTGGCTTT
                 | || | || ||| |   |   |||||||  ||   | || |  |||||  || |  || | | |   |   |    || | ||  ||   |  |  |||       |||||||||||||||||||||| |||||||| || || || ||||||||||| ||||||||  |||| |
gtacacattttgtgtctgagtgtgatagaaataccatgctttggttttttcgtccttacttttgttgctcaaaaaagtatgtacaaaatgattgaatggaactaataattcttgaatcatg--cagATGCTTATGGGAGGAGGTGGGTCATTCTCAGCAGGGGGGCCTGGAAAAGGGATGCACTCAAGGCTAT

upper sequence: AT1G51980.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA15G02390.1 (Glycine max), 3'ss of exon 6
--------------------------gtgtctaattgaattttactttttggttgctttaactttcacttgtttcgatcaaattttttttactggcg--aaaaagtaataaaatgtaatc--taattgctatt----agATGCTTATGGGAGGAGGTGGCTCATTCTCTGCGGGAGGTCCTGGAAAAGGAATGCACTCGTGGCTTT
                           | || |     ||  |   | | | ||    ||  ||||  |||||   ||            |  || |  || ||  |||  |||  ||    || ||   | |    |||||||||||||||||||||| |||||||| || ||||| ||||| ||||| ||||||||  |||| |
gtactcactttgtgtgagccattctgatttcaagagatatcatgtctatggatttgcatatttttcttttgttggcattcgtgcacaagaaaaggaggaaagaaacaattgaatagaagtagtatttctgagtgtgcagATGCTTATGGGAGGAGGTGGGTCATTCTCAGCCGGAGGGCCTGGGAAAGGGATGCACTCAAGGCTGT

upper sequence: AT1G51980.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA07G01720.1 (Glycine max), 3'ss of exon 6
------------------gtgtctaattgaattttactttttggttgctttaactttcacttgtttcgatcaaattttttttactggcgaaaaagtaataaaatg-taatctaattgctat-tagATGCTTATGGGAGGAGGTGGCTCATTCTCTGCGGGAGGTCCTGGAAAAGGAATGCACTCGTGGCTTT
                  | |||| || |||||    | ||| |||  |||     | |||| | | |  |||         | ||     |  | |   || |  ||||        | |  |||||||||||||||||||||| |||||||| || || || ||||||||||| ||||||||  |||| |
gtactccattttgtgtttgagtctgatagaattactgtattttgtt-ttttggtccttacttttgttgcacaataaaggacaaatgaaatgattgaatggaagtaataattcttgaattgtgcagATGCTTATGGGAGGAGGTGGATCATTCTCAGCAGGGGGGCCTGGAAAAGGGATGCACTCAAGGCTAT

upper sequence: AT1G51980.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv09s0002g03200.t01 (Vitis vinifera), 3'ss of exon 6
-----------------------------------------------------------------------gtgtctaattgaattttactttttggttgctttaactttcacttgtttcgatcaa--attttttttactggcgaaaaagtaataaaatgtaatctaattgctattagATGCTTATGGGAGGAGGTGGCTCATTCTCTGCGGGAGGTCCTGGAAAAGGAATGCACTCGTGGCTTT
                                                                        | | ||  |  || |   | | |   |   || |  ||| ||  ||||  |||   |   | ||| |         | |||  |||||| ||      ||    ||||||||||||||||||||||||||||||||||||| || ||||||||||||||||||||  | || |
gtgctgcatttgatcttttcttcttaaagagattctgctatctctctctctctctctctctctctctctatatatatatatatatatatatatatatatatattcatattccctcttttcattcatccaccatgttttccttttttgcattaa-gaaatgtgatagtcccgc----agATGCTTATGGGAGGAGGTGGCTCATTCTCTGCGGGGGGCCCTGGAAAAGGAATGCACTCACGACTAT

upper sequence: AT1G51980.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv10s0003g03230.t01 (Vitis vinifera), 3'ss of exon 5
---------------------------------------------------------------------------------gtgtctaattgaattttactttttggttgctttaactttcacttgtttcgatcaa--attttttttactggcgaaaaagtaataaaatgtaatctaattgctattagATGCTTATGGGAGGAGGTGGCTCATTCTCTGCGGGAGGTCCTGGAAAAGGAATGCACTCGTGGCTTT
                                                                                  | | ||  |  || |   | | |   |   |  |  ||| ||  ||||  |||   |   | ||| |         | |||  |||||| ||     |||    |||| ||||||||||||||||||||||||||| |||| || ||||||||||||||||||||  | || |
gtgctgcatttgatcttttcttcttaaagagattctgctatttggaaatctctctctctctctctctctctctctctctctctatatatatatatatatatatatatatatatatatattccctcttttcattcatccaccatgttttccttttttgcattaa-gaaatgtgatagtcctgc----agATACTTATGGGAGGAGGTGGCTCATTCTCTACGGGGGGCCCTGGAAAAGGAATGCACTCACGACTAT

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|47831013|gb|CK120697.1|CK120697
EST:     TGCCTGGCTGGAATAACGAGAAAGAAGCAGTCACCGCCACTGTTCTCCAG                         ATGCTTATGGGAGGAGGTGGCTCATTCTCTGCGGGAGGTCCTGGAAAAGGA
genomic: TGCCTGGCTGGAATAACGAGAAAGAAGCAGTCACCGCCACTGTTCTCCAGgtgtctaatt ... ttgctattagATGCTTATGGGAGGAGGTGGCTCATTCTCTGCGGGAGGTCCTGGAAAAGGA
EST: gi|124879327|gb|EH958764.1|EH958764
EST:     AGCAGTCACCGCCACTGTTCTCCAG                         ATGCTTATGGGAGGAGGTGGCTCATTCTCTGCGGGAGGTCCTGGAAAAGGA
genomic: AGCAGTCACCGCCACTGTTCTCCAGgtgtctaatt ... ttgctattagATGCTTATGGGAGGAGGTGGCTCATTCTCTGCGGGAGGTCCTGGAAAAGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcaaattttttttactggcgaaaaagtaataaaatgtaatctaattgctattagATGCTTATGGGAGGAGGTGGCTCATTCTCTGCGGGAGGTCCTGGAAAAGGAATGCACTCGTGGCTTT
                                       atctaat  putative branch site (score: 3)
                     aaaaagtaataaaatg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtctaattgaattttactttttggttgctttaactttcacttgtttcgatcaaattttttttactggcgaaaaagtaataaaatgtaatctaattgctattagATGCTTATGGGAGGAGGTGGCTCATTCTCTGCGGGAGGTCCTGGAAAAGGAATGCACTCGTGGCTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA