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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATCTTTGAAGAAGCTGGCTGTGACACACCAGCCAGCCCTAGCTGTGGTGCTTGCCTTGGTGGCCCAGCAGACACCTACGCTCGCTTGAATGAACCTCAAgtacgtacccattacttaccctacttatccaattatctgcacttcacctattcttgaaagtgagactaacaaagacgtgttttaaaatgtttgttacag

Basic information

species Arabidopsis thaliana
transcript AT4G13430.1
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G13430.1 (Arabidopsis thaliana), 5'ss of exon 14
lower sequence: LOC_Os02g03260.3 (Oryza sativa), 5'ss of exon 12
GATCTTTGAAGAAGCTGGCTGTGACACACCAGCCAGCCCTAGCTGTGGTGCTTGCCTTGGTGGCCCAGCAGACACCTACGCTCGCTTGAATGAACCTCAAgtacgtacccattacttaccctacttatccaa------ttatctgcacttcacctattcttgaaagtgagactaacaaagacgtgttttaaaatgtttgttacag
||| ||||| || ||||| ||||| |||||||| |||||||| |||||||||||  | ||||| ||    || || || |||||| |||||||||||   ||| || ||    |  ||    | | |  ||       || | |    |  || |  ||   | |||   | | | | |    |   || |||  |  | |    
GATATTTGAGGAGGCTGGTTGTGATACACCAGCTAGCCCTAGTTGTGGTGCTTGTTTGGGTGGTCCTCGTGATACATATGCTCGCATGAATGAACCTATGgtaagtgcct-ccaaatatttcagtaaaacaggaaatgttgtttcgtatgaactttatcaacatagtagaatttatagatgtcttccttgaaagataaggt----

upper sequence: AT4G13430.1 (Arabidopsis thaliana), 5'ss of exon 14
lower sequence: GLYMA14G40570.1 (Glycine max), 5'ss of exon 14
GATCTTTGAAGAAGCTGGCTGTGACACACCAGCCAGCCCTAGCTGTGGTGCTTGCCTTGGTGGCCCAGCAGACACCTACGCTCGCTTGAATGAACCTCAAgtacgtacccattacttaccctacttatccaattatctgc-acttcacctattcttgaaagtgagactaacaaagacgt-gttttaaaatgtttgttacag
||| |||||||||| ||| |||||||||||||| || ||||| |||||||||||  | |||||||||  ||| || ||||| ||| ||||||||||| | | | || ||       | ||| |   |||   | || | | | |  |  |    ||  |  ||  |||   |      |  | || ||    |||  |   
GATATTTGAAGAAGTTGGGTGTGACACACCAGCTAGTCCTAGTTGTGGTGCTTGTTTGGGTGGCCCAAAAGATACTTACGCACGCATGAATGAACCTAAGgcaagttccttgcttctgccccaac-atcttgtaatatactagtgtagttcaaattctacttgttacttttatccttattatattgaaggaattgcaaata

upper sequence: AT4G13430.1 (Arabidopsis thaliana), 5'ss of exon 14
lower sequence: GLYMA17G37540.1 (Glycine max), 5'ss of exon 14
GATCTTTGAAGAAGCTGGCTGTGACACACCAGCCAGCCCTAGCTGTGGTGCTTGCCTTGGTGGCCCAGCAGACACCTACGCTCGCTTGAATGAACCTCAAgtacgtaccc-attacttaccctacttatccaattat-ctgcacttcacctattcttgaaagtgagactaa--caaagacgtgttttaaaatgtttgttacag
||| |||||||||||||| |||||||||||||| || ||||| || ||||||||  | ||||||||   ||| || ||||| ||| ||||||||||| | | | || ||    | |   |||| | | |   | ||| ||    |    | | |  |    || |   | |  |  |    | | || ||    |||  |   
GATATTTGAAGAAGCTGGGTGTGACACACCAGCTAGTCCTAGTTGCGGTGCTTGTTTGGGTGGCCCGAAAGATACTTACGCACGCATGAATGAACCTAAGgcaagttccttgcttcggcccctgcatcttgtaatatactagtgtagttcaaattctacctgttacttttatccttattattatattgaaggaattgcaa---

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|124740055|gb|EH831217.1|EH831217
EST:     CTTGCCTTGGTGGCCCAGCAGACACCTACGCTCGCTTGAATGAACCTCAA                         GTGTGTGTCTCAACGACAAA
genomic: CTTGCCTTGGTGGCCCAGCAGACACCTACGCTCGCTTGAATGAACCTCAAgtacgtaccc ... tttgttacagGTGTGTGTCTCAACGACAAA
EST: gi|125091710|gb|EL149533.1|EL149533
EST:     CTCGCTTGAATGAACCTCAA                         GTGTGTTGTCTCAACGACAAACAGGAACTTCCCCGGTCGGATGGGACACAA
genomic: CTCGCTTGAATGAACCTCAAgtacgtaccc ... tttgttacagGTGTG-TGTCTCAACGACAAACAGGAACTTCCCCGGTCGGATGGGACACAA
EST: gi|124948780|gb|EL024491.1|EL024491
EST:     AGCAGACACCTACGCTCGCTTGAATGAACCTCAA                         GTGTGTGTCTCAACGACAAACAGGAACTTCCCCGGTCGGATGGGACACAAA
genomic: AGCAGACACCTACGCTCGCTTGAATGAACCTCAAgtacgtaccc ... tttgttacagGTGTGTGTCTCAACGACAAACAGGAACTTCCCCGGTCGGATGGGACACAAA
EST: gi|116423657|gb|EG466249.1|EG466249
EST:     CTTGCCTTGGTGGCCCAGCAGACACCTACGCTCGCTTGAATGAACCTCAA                         GTGTGTGTCTCAACGACAAACAGGAACTTCCCCGGTCGGATGGGACACAAA
genomic: CTTGCCTTGGTGGCCCAGCAGACACCTACGCTCGCTTGAATGAACCTCAAgtacgtaccc ... tttgttacagGTGTGTGTCTCAACGACAAACAGGAACTTCCCCGGTCGGATGGGACACAAA
EST: gi|125073954|gb|EL138091.1|EL138091
EST:     CTTGCCTTGGTGGCCCAGCAGACACCTACGCTCGCTTGAATGAACCTCAA                         GTGTGTGTCTCAACGACAAACAGGAACTTC
genomic: CTTGCCTTGGTGGCCCAGCAGACACCTACGCTCGCTTGAATGAACCTCAAgtacgtaccc ... tttgttacagGTGTGTGTCTCAACGACAAACAGGAACTTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATCTTTGAAGAAGCTGGCTGTGACACACCAGCCAGCCCTAGCTGTGGTGCTTGCCTTGGTGGCCCAGCAGACACCTACGCTCGCTTGAATGAACCTCAAgtacgtacccattacttaccctacttatccaattatctgcacttcacctattcttgaaagtgagactaacaaagacgtgttttaaaatgtttgttacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG