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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtctgataataataaaaagttgatattcaagtatgcatgtactttcgatatactgagcaagtttatatatttctgtttagGTTGATGGAAGTGTTGCATCCAAGCAAGGTGTTCGGTTTGTGTTCACGGATGGATCCAGAATCATATTTCGTTTATCC

Basic information

species Arabidopsis thaliana
transcript AT5G51820.1
intron # 19
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G51820.1 (Arabidopsis thaliana), 3'ss of exon 19
lower sequence: GLYMA20G29230.1 (Glycine max), 3'ss of exon 19
----------------------gtaagtctgataataataaaaagttga-tattca-agtatgcatgtactttcgatatactgagcaagtttatatatttctgtttagGTTGATGGAAGTGTTGCATCCAAGCAAGGTGTTCGGTTTGTGTTCACGGATGGATCCAGAATCATATTTCGTTTATCC
                       |   |    |  ||||   |  |  |  | ||| | |   ||| ||| ||  |  | ||  |      |  |  ||   ||  |||| ||||||||||| | ||| || ||||||||||||||||| || || ||||| || || || |||| ||||||||| 
gtgagtttttacatcatgcccatttttttcttttctaattcgagatcaagcaatcataattcacatttaccttgcaattgcttggttctgatccaatttagagtgcagGTAGATGGAAGTGTGGTATCAAAACAAGGTGTTCGGTTTGTTTTTACAGATGGTTCAAGGATTATATATCGTTTATCA

upper sequence: AT5G51820.1 (Arabidopsis thaliana), 3'ss of exon 19
lower sequence: Vv16s0022g02320.t01 (Vitis vinifera), 3'ss of exon 19
gtaagtctgataataataaaaagttgatattcaagtatgcatgtactttcgatatact-gagcaagtttatatatttctgtttagGTTGATGGAAGTGTTGCATCCAAGCAAGGTGTTCGGTTTGTGTTCACGGATGGATCCAGAATCATATTTCGTTTATCC
|||||||| |   |||| |    || |    |    |  | ||   | | ||||   | ||    | || ||| |   || | |||| ||||||||||| ||||| |||||||||||||| ||||| || ||||||||||| || ||||||| ||||||||| 
gtaagtctcaatctaattac--tttaaggaaccttaaaacttggtatctggataggtttgacttggattttatttaattgctcagGTGGATGGAAGTGTGGCATCAAAGCAAGGTGTTCGATTTGTTTTTACGGATGGATCAAGGATCATATATCGTTTATCA
















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|125283912|gb|EL297997.1|EL297997
EST:     GAAACTAATGTCCTCCAGTTTGCAGATGACTTCTCATACACAGACCCT                         GTTGATGGAAGTGTTGCATCCAAGCAAGGTG
genomic: GAAACT-ATGTCCTCCAGTTTGCAGATGACTTCTCATACACAGACCCTgtaagtctga ... ttctgtttagGTTGATGGAAGTGTTGCATCCAAGCAAGGTG
EST: gi|86088359|gb|DR384118.1|DR384118
EST:     GAAACTATGTCCTCCAGTTTGCAGATGACTTCTCATACACAGACCCT                         GTTGATGGAAGTGTTGCATCCAAGCAAGGTGTTCGGTTTGTGTTCACGGAT
genomic: GAAACTATGTCCTCCAGTTTGCAGATGACTTCTCATACACAGACCCTgtaagtctga ... ttctgtttagGTTGATGGAAGTGTTGCATCCAAGCAAGGTGTTCGGTTTGTGTTCACGGAT
EST: gi|124752886|gb|EH843016.1|EH843016
EST:     GAAACTATGTCCTCCAGTTTGCAGATGACTTCTCATACACAGACCCT                         GTCGATGGAAGTGTTGCATCCAAGCAAGG
genomic: GAAACTATGTCCTCCAGTTTGCAGATGACTTCTCATACACAGACCCTgtaagtctga ... ttctgtttagGTTGATGGAAGTGTTGCATCCAAGCAAGG
EST: gi|124737748|gb|EH829150.1|EH829150
EST:     AGTTTGCAGATGACTTCTCATACACAGACCCT                         GTTGATGGAAGTGTTGCATCCAAGCAAGGTGTTCGGTTTGTGTTCACGGAT
genomic: AGTTTGCAGATGACTTCTCATACACAGACCCTgtaagtctga ... ttctgtttagGTTGATGGAAGTGTTGCATCCAAGCAAGGTGTTCGGTTTGTGTTCACGGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcaagtatgcatgtactttcgatatactgagcaagtttatatatttctgtttagGTTGATGGAAGTGTTGCATCCAAGCAAGGTGTTCGGTTTGTGTTCACGGATGGATCCAGAATCATATTTCGTTTATCC
                                            tttctgttt  CT-rich tract
                                 aagtttatatatttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtctgataataataaaaagttgatattcaagtatgcatgtactttcgatatactgagcaagtttatatatttctgtttagGTTGATGGAAGTGTTGCATCCAAGCAAGGTGTTCGGTTTGTGTTCACGGATGGATCCAGAATCATATTTCGTTTATCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA