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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgttacttatgtggtgatacgttgtcctgcataatagtatggatcaataaattccatatttctaagatcttgcctttcgcagCTTTTGTTGAGAAAATGCAATCAAGTGGGGATTTGAACCTTATTGGACAATTTGGAGTTGGATTCTACTCTGCCTATCTTGTTGCTGACTACATTGAAGT

Basic information

species Arabidopsis thaliana
transcript AT4G24190.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G24190.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA14G40320.1 (Glycine max), 3'ss of exon 5
----gtacgttacttatgtggtgat--acgttgtcctgcataatagtatggatcaataaattccatatttctaagatcttgcctttcgcagCTTTTGTTGAGAAAATGCAATCAAGTGGGGATTTGAACCTTATTGGACAATTTGGAGTTGGATTCTACTCTGCCTATCTTGTTGCTGACTACATTGAAGT
    ||| |||    |  |  |     | ||  |  |   |  |  | ||| |    | ||   |    |   || | |    |    |||| ||||||||||| |||||| ||||||| ||| | || || ||||| || |||||||| || ||||||||||  |||||||| || |||||  | |||||
gtacgtatgttgtggacattattgctgaagtaatttttgcttgtgatgtggttgggaatatgttaa---ttggagctgtgtgttaattcagCATTTGTTGAGAAGATGCAAACAAGTGGAGATCTCAATCTGATTGGGCAGTTTGGAGTCGGCTTCTACTCTGTTTATCTTGTGGCCGACTATGTCGAAGT

upper sequence: AT4G24190.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA17G37820.1 (Glycine max), 3'ss of exon 5
gtacgttacttatgtggtgatacgttgtc----ctgcataatagtatggatcaataaattccatatttctaagatcttgcctttcgcagCTTTTGTTGAGAAAATGCAATCAAGTGGGGATTTGAACCTTATTGGACAATTTGGAGTTGGATTCTACTCTGCCTATCTTGTTGCTGACTACATTGAAGT
    | ||  ||||| |||  || |||        |  |     | |       |       || ||  |  || ||    |    |||| ||||||||||| |||||| ||||||| ||| | || || ||||| || |||||||| || ||||||||||  ||||| || ||||||||  | |||| 
----ggtatgtatgttgtggcacattgctgaagtagtttttgcttgtaatgtggttgggaagatgttaattggagctgtgttaattcaGCATTTGTTGAGAAGATGCAAACAAGTGGAGATCTCAATCTGATTGGGCAGTTTGGAGTCGGCTTCTACTCTGTTTATCTCGTGGCTGACTATGTCGAAG-

upper sequence: AT4G24190.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv18s0001g14500.t01 (Vitis vinifera), 3'ss of exon 5
gtacgttacttatgtggtg----atacgttgtcctgcat--aat-----agtatgga--tcaataaattcc---atattt-ctaagatcttgcctttcgcagCTTTTGTTGAGAAAATGCAATCAAGTGGGGATTTGAACCTTATTGGACAATTTGGAGTTGGATTCTACTCTGCCTATCTTGTTGCTGACTACATTGAAGT
|||  ||  || ||   ||    |||  |||| ||| |   |||     ||| |||   | ||| ||||     |||||   | | || ||   ||    ||||||||| |||||||||||| | ||||||||| | || || |||||||||||||||||||| ||||||||||  ||||||||||| |||||  |||||||
gtatctttattttgcaatgtctaatatcttgttctgaaatgaattctgaagtttggggtttaatgaattattgaatattaatttatattttcttttatatagCTTTTGTGGAGAAAATGCAAACCAGTGGGGATCTTAATCTCATTGGACAATTTGGAGTTGGGTTCTACTCTGTATATCTTGTTGCAGACTATGTTGAAGT

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|124979548|gb|EL052581.1|EL052581
EST:     GGAAGACTTAATCAAGAACCTTGGTACCATAGCAAAATCTGGAACGTCAG                         CTTTTGTTGAGAAAATGCAATCAAGTGGGGATTTGAACCTTATTGGACAAT
genomic: GGAAGACTTAATCAAGAACCTTGGTACCATAGCAAAATCTGGAACGTCAGgtacgttact ... cctttcgcagCTTTTGTTGAGAAAATGCAATCAAGTGGGGATTTGAACCTTATTGGACAAT
EST: gi|164221214|gb|ES092428.1|ES092428
EST:     CAAGAACCTTGGTACCATAGCAAAATCTGGAACGTCAG                         CTTTTGTTGAGAAAATGCAATCAAGTGGGGATTTGAACC
genomic: CAAGAACCTTGGTACCATAGCAAAATCTGGAACGTCAGgtacgttact ... cctttcgcagCTTTTGTTGAGAAAATGCAATCAAGTGGGGATTTGAACC
EST: gi|125092775|gb|EL150598.1|EL150598
EST:     CCTTGGTACCATAGCAAAATCTGGAACGTCAG                         CTTTTGTTGAGAAAATGCAATCAAGTGGGGATTTGAACCTTATTGGACAAT
genomic: CCTTGGTACCATAGCAAAATCTGGAACGTCAGgtacgttact ... cctttcgcagCTTTTGTTGAGAAAATGCAATCAAGTGGGGATTTGAACCTTATTGGACAAT
EST: gi|163967418|gb|ES040101.1|ES040101
EST:     GGAAGACTTAATCAAGAACCTTGGTACCATAGCAAAATCTGGAACGTCAG                         CTTTTGTTGAGAAAAT
genomic: GGAAGACTTAATCAAGAACCTTGGTACCATAGCAAAATCTGGAACGTCAGgtacgttact ... cctttcgcagCTTTTGTTGAGAAAAT
EST: gi|164056045|gb|ES033236.1|ES033236
EST:     TCAAGAACCTTGGTACCATAGCAAAATCTGGAACGTCAG                         CTTTTGTTGAGAAAATGCAATCAAGTGGGGATTTGAACCTTATTGGACAAT
genomic: TCAAGAACCTTGGTACCATAGCAAAATCTGGAACGTCAGgtacgttact ... cctttcgcagCTTTTGTTGAGAAAATGCAATCAAGTGGGGATTTGAACCTTATTGGACAAT
EST: gi|164091948|gb|ES079306.1|ES079306
EST:     GGAAGACTTAATCAAGAACCTTGGTACCATAGCAAAATCTGGAACGTCAG                         CTTTTGTTGAGAAAATGCAATCAAGTGGGGATTTGAACC
genomic: GGAAGACTTAATCAAGAACCTTGGTACCATAGCAAAATCTGGAACGTCAGgtacgttact ... cctttcgcagCTTTTGTTGAGAAAATGCAATCAAGTGGGGATTTGAACC
EST: gi|164104521|gb|ES170781.1|ES170781
EST:     AAGAACCTTGGTACCATAGCAAAATCTGGAACGTCAG                         CTTTTGTTGAGAAAATGCAATCAAGTGGG-ATTTGAACCTTATTGGACAAT
genomic: AAGAACCTTGGTACCATAGCAAAATCTGGAACGTCAGgtacgttact ... cctttcgcagCTTTTGTTGAGAAAATGCAATCAAGTGGGGATTTGAACCTTATTGGACAAT
EST: gi|116483054|gb|EG525646.1|EG525646
EST:     GGAAGACTTAATCAAGAACCTTGGTACCATAGCAAAATCTGGAACGTCAG                         CTTTTGTTGAGAAAATGCAATCAAGTGGGGATTTGAACCTTATTGGACAAT
genomic: GGAAGACTTAATCAAGAACCTTGGTACCATAGCAAAATCTGGAACGTCAGgtacgttact ... cctttcgcagCTTTTGTTGAGAAAATGCAATCAAGTGGGGATTTGAACCTTATTGGACAAT
EST: gi|86067432|gb|DR363189.1|DR363189
EST:     GGAAGACTTAATCAAGAACCTTGGTACCATAGCAAAATCTGGAACGTCAG                         CTTTTGTTGAGAAAATGCAATCAAGTGGGGATTTGAACCTTATTGGACAAT
genomic: GGAAGACTTAATCAAGAACCTTGGTACCATAGCAAAATCTGGAACGTCAGgtacgttact ... cctttcgcagCTTTTGTTGAGAAAATGCAATCAAGTGGGGATTTGAACCTTATTGGACAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcataatagtatggatcaataaattccatatttctaagatcttgcctttcgcagCTTTTGTTGAGAAAATGCAATCAAGTGGGGATTTGAACCTTATTGGACAATTTGGAGTTGGATTCTACTCTGCCTATCTTGTTGCTGACTACATTGAAGT
                                        tcttgcctttc  CT-rich tract
                  aataaattccatattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgttacttatgtggtgatacgttgtcctgcataatagtatggatcaataaattccatatttctaagatcttgcctttcgcagCTTTTGTTGAGAAAATGCAATCAAGTGGGGATTTGAACCTTATTGGACAATTTGGAGTTGGATTCTACTCTGCCTATCTTGTTGCTGACTACATTGAAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG