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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGTCAAGCATGAGCAGAAGCTTGACTGTGGTGGTGGCTACATGAAGTTGCTAAGTGATGATGTTGACCAGACGAAATTCGGAGGAGACACTCCTTACAGgtgtgtttttcggttactttcatatcaaacttcaaacattcaaacaccaggcttatctttctttttttatctgcag

Basic information

species Arabidopsis thaliana
transcript AT1G56340.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G56340.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: LOC_Os07g14270.3 (Oryza sativa), 5'ss of exon 3
CTGTCAAGCATGAGCAGAAGCTTGACTGTGGTGGTGGCTACATGAAGTTGCTAAGTGATGATGTTGACCAGACGAAATTCGGAGGAGACACTCCTTACAGgtg-tgtttttcggttactttcatatcaaacttcaaacattcaaacaccag----gcttatctttctt----tttttatctgcag
|||| ||||||||||| |||||||||||||||||||| ||  | ||||||||  ||| |||||||||||||| |||||| || || ||||| || |||||||  || |||||   || | |       |   |||    |   || |  ||      ||||||  |||     ||||   |||||
CTGTAAAGCATGAGCAAAAGCTTGACTGTGGTGGTGGATATGTCAAGTTGCTTGGTGGTGATGTTGACCAGAAGAAATTTGGTGGGGACACACCGTACAGgtaatgattttcttctattgtagctctgattctcacttttctcaagattagtactagttatctaacttggtacttttgaatgcag

upper sequence: AT1G56340.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G074687_T01 (Zea mays), 5'ss of exon 3
CTGTCAAGCATGAGCAGAAGCTTGACTGTGGTGGTGGCTACATGAAGTTGCTAAGTGATGATGTTGACCAGACGAAATTCGGAGGAGACACTCCTTACAGgtg---------tgtttttcggttactttcatatcaa--acttcaaacattcaaacaccaggcttatctttctttttttatctgcag
|||| ||||| |||||||||||||||||||||||||| ||| | ||||||||  ||| |||||| |||||||  |||||||| || |||||  |||||||||          | | ||   ||   |||  |  | |  |  ||  |  ||  |  |  ||  ||| |||  || || | | |||||
CTGTGAAGCACGAGCAGAAGCTTGACTGTGGTGGTGGTTACGTCAAGTTGCTGGGTGGTGATGTAGACCAGAAAAAATTCGGTGGGGACACAACTTACAGgtagcctatggatatattcttgtactttttctccctatcatatctgatcttgtagtagtag--ttaacttcattcttctgtatgcag

upper sequence: AT1G56340.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G358059_T01 (Zea mays), 5'ss of exon 3
CTGTCAAGCATGAGCAGAAGCTTGACTGTGGTGGTGGCTACATGAAGTTGCTAAGTGAT---GATGTTGACCAGACGAAATTCGGAGGAGACACTCCTTACAGgtgtgtttt--tcggt-tactttcatatcaaacttcaaacat-tcaaacaccaggcttat--ctttctttttttat-ctgcag
   | ||||| ||||||||||||||||| |||||||||||| | ||||||||  ||| |   ||||| ||||||| |||||| || ||||||||  |||||||||    |||   |  | |  || |    |      | | ||| ||  |       ||| |  | |  || || | | ||||||
---TGAAGCACGAGCAGAAGCTTGACTGCGGTGGTGGCTACGTCAAGTTGCTGGGTGGTGGTGATGTAGACCAGAAGAAATTTGGTGGAGACACATCTTACAGgtagactttgaacaatattgttgcgctccttctccctatcatatctcatcttgtacttgtaacctcattcttctgtactgcag

upper sequence: AT1G56340.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA20G23080.2 (Glycine max), 5'ss of exon 3
CTGTCAAGCATGAGCAGAAGCTTGACTGTGGTGGTGGCTACATGAAGTTGCTAAGTGATGATGTTGACCAGACGAAATTCGGAGGAGACACTCCTTACAGgtgtgtt----------tttcggtta------ctttcatatcaaa----cttcaaacattcaaacaccaggcttatctttctttttttatctgcag---
||||||||||||| |||||||||||||| ||||||||||||||||||||||| |||| ||||||||| |||| |||||| || || || ||||||||||||||  ||          ||| | ||       ||||| |            ||| |     ||||||| | | | |     ||| ||  ||||  |   
CTGTCAAGCATGAACAGAAGCTTGACTGCGGTGGTGGCTACATGAAGTTGCTCAGTGGTGATGTTGATCAGAAGAAATTTGGTGGGGATACTCCTTACAGgtgatttatatatccccttttgatttgttgctctttcctgatgggtgcctctcatatcgcaaaacacctgaccttttaacatttgttgttctgttgcag

upper sequence: AT1G56340.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA10G28890.1 (Glycine max), 5'ss of exon 3
CTGTCAAGCATGAGCAGAAGCTTGACTGTGGTGGTGGCTACATGAAGTTGCTAAGTGATGATGTTGACCAGACGAAATTCGGAGGAGACACTCCTTACAGgtg-----------------tgtttttcggttactttcatatcaa-acttcaaacattc--aaacaccaggcttatctttctttttttatctgcag---
|||| ||||| || |||||||||||||||||||||||||||||||||||||| ||||  |||||||| |||| |||||| || || || ||||||||||||||                 || ||| | | |  || |  ||     | |   |  ||   ||||| | |   | |     ||| ||  ||||  |   
CTGTTAAGCACGAACAGAAGCTTGACTGTGGTGGTGGCTACATGAAGTTGCTCAGTGGGGATGTTGATCAGAAGAAATTTGGCGGGGATACTCCTTACAGgtgatttatatatccccttttgatttgctgctctttcctgatgggtgcctttgatgttgtaaaacagctgatcttttgacatttgttgttctgttgcag

upper sequence: AT1G56340.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv07s0005g01390.t01 (Vitis vinifera), 5'ss of exon 3
CTGTCAAGCATGAGCAGAAGCTTGACTGTGGTGGTGGCTACATGAAGTTGCTAAGTGATGATGTTGACCAGACGAAATTCGGAGGAGACACTCCTTACAGgtg---tgtttttcggtta-------cttt-----catatcaaacttcaaacat--tcaaacaccaggctta-----tctttctttttttatctgcag
|||| ||||| || || ||||| || |||||||||||||||||||||||||| |||| ||| ||||| || | |||||| || || || || ||||| |||||   |||   || | |        ||||     | | ||||  |||   | |  |      | |  || |     | | | || | |   ||||||
CTGTTAAGCACGAACAAAAGCTAGATTGTGGTGGTGGCTACATGAAGTTGCTCAGTGGTGAAGTTGATCAAAAGAAATTTGGTGGTGATACCCCTTATAGgtgacatgtgcctctgctgaacaatcctttttgctcctttcaattttctttcctagttgggttctaacctgacaaattttgtattctgtggactgcag

upper sequence: AT1G56340.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv14s0060g01290.t01 (Vitis vinifera), 5'ss of exon 3
CTGTCAAGCATGAGCAGAAGCTTGACTGTGGTGGTGGCTACATGAAGTTGCTAAGTGATGATGTTGACCAGACGAAATTCGGAGGAGACACTCCTTACAGgt--gtgtt--tttcggttact-ttcatatcaaacttcaaacattcaaacaccaggcttatctttctttttttatctgcag------------------------
|||| || ||||| ||||||||||||||||||||||| |||||||||||||| |||| ||| ||||| || | |||||| || || || || || |||||||  |||||  ||| | ||||| ||  | |    |||     ||    || |||  ||| |  | | ||||  |  ||  |                        
CTGTTAAACATGAACAGAAGCTTGACTGTGGTGGTGGATACATGAAGTTGCTCAGTGGTGAGGTTGATCAAAAGAAATTTGGTGGTGATACCCCATACAGgtcagtgttatttttgcttactgtttgtttgtccctttgtctat---gactccaaacttcttatcccttttaaagttgttgatttgttataaaacatgattgcag

upper sequence: AT1G56340.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: EDP09399 (Chlamydomonas reinhardtii), 5'ss of exon 3
----CTGTCAAGCATGAGCAGAAGCTTGACTGTGGTGGTGGCTACATGAAGTTGCTAAGTGATGATGTTGACCAGACGAA-ATTCGGAGGAGACACTCCTTACAGgtgtgtttttcggttactttcatatcaaacttcaaacattcaaacaccaggcttatctttctttttttatctgcag
    | ||||||||||||||| | || ||||| |||||||||||||| |||       ||| ||      |||||      ||| ||   | || | | ||   |||| || |  ||     |        |  |||||     | |     || ||  |                     
TTCTCCGTCAAGCATGAGCAGGACCTGGACTGCGGTGGTGGCTACATCAAG-------GTGGTGCCCGCTACCAGgtacgcattgggctcacacgcgcattg-gggtgcgtgtggcgacggttgctg----acccttcacctggtgatgttgcacgcgcag--------------------

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|86070958|gb|DR366715.1|DR366715
EST:     CTAAGTGATGATGTTGACCAGACGAAATTCGGAGGAGACACTCCTTACAG                         CATTATGTTTGGGCCAGATATTTGTGGCTACAGCACTAAGAAAGTACATGC
genomic: CTAAGTGATGATGTTGACCAGACGAAATTCGGAGGAGACACTCCTTACAGgtgtgttttt ... ttatctgcagCATTATGTTTGGGCCAGATATTTGTGGCTACAGCACTAAGAAAGTACATGC
EST: gi|86070961|gb|DR366718.1|DR366718
EST:     CTAAGTGATGATGTTGACCAGACGAAATTCGGAGGAGACACTCCTTACAG                         CATTATGTTTGGGCCAGATATTTGTGGCTACAGCACTAAGAAAGTACATGC
genomic: CTAAGTGATGATGTTGACCAGACGAAATTCGGAGGAGACACTCCTTACAGgtgtgttttt ... ttatctgcagCATTATGTTTGGGCCAGATATTTGTGGCTACAGCACTAAGAAAGTACATGC
EST: gi|86070960|gb|DR366717.1|DR366717
EST:     CTAAGTGATGATGTTGACCAGACGAAATTCGGAGGAGACACTCCTTACAG                         CATTATGTTTGGGCCAGATATTTGTGGCTACAGCACTAAGAAAGTACATGC
genomic: CTAAGTGATGATGTTGACCAGACGAAATTCGGAGGAGACACTCCTTACAGgtgtgttttt ... ttatctgcagCATTATGTTTGGGCCAGATATTTGTGGCTACAGCACTAAGAAAGTACATGC
EST: gi|116465716|gb|EG508308.1|EG508308
EST:     CTAAGTGATGATGTTGACCAGACGAAATTCGGAGGAGACACTCCTTACAG                         CATTATGTTTGGGCCAGATATTTGTGGCTACAGCACTAAGAAAGTACATGC
genomic: CTAAGTGATGATGTTGACCAGACGAAATTCGGAGGAGACACTCCTTACAGgtgtgttttt ... ttatctgcagCATTATGTTTGGGCCAGATATTTGTGGCTACAGCACTAAGAAAGTACATGC
EST: gi|86070963|gb|DR366720.1|DR366720
EST:     CTAAGTGATGATGTTGACCAGACGAAATTCGGAGGAGACACTCCTTACAG                         CATTATGTTTGGGCCAGATATTTGTGGCTACAGCACTAAGAAAGTACATGC
genomic: CTAAGTGATGATGTTGACCAGACGAAATTCGGAGGAGACACTCCTTACAGgtgtgttttt ... ttatctgcagCATTATGTTTGGGCCAGATATTTGTGGCTACAGCACTAAGAAAGTACATGC
EST: gi|116465699|gb|EG508291.1|EG508291
EST:     CTAAGTGATGATGTTGACCAGACGAAATTCGGAGGAGACACTCCTTACAG                         CATTATGTTTGGGCCAGATATTTGTGGCTACAGCACTAAGAAAGTACATGC
genomic: CTAAGTGATGATGTTGACCAGACGAAATTCGGAGGAGACACTCCTTACAGgtgtgttttt ... ttatctgcagCATTATGTTTGGGCCAGATATTTGTGGCTACAGCACTAAGAAAGTACATGC
EST: gi|164146865|gb|ES090967.1|ES090967
EST:     TGTTGACCAGACGAAATTCGGAGGAGACACTCCTTACAG                         CATTATGTTTGGGCCAGATATTTGTGGCTACAGCACTAAGAAAGTACATGC
genomic: TGTTGACCAGACGAAATTCGGAGGAGACACTCCTTACAGgtgtgttttt ... ttatctgcagCATTATGTTTGGGCCAGATATTTGTGGCTACAGCACTAAGAAAGTACATGC
EST: gi|116465698|gb|EG508290.1|EG508290
EST:     CTAAGTGATGATGTTGACCAGACGAAATTCGGAGGAGACACTCCTTACAG                         CATTATGTTTGGGCCAGATATTTGTGGCTACAGCACTAAGAAAGTACATGC
genomic: CTAAGTGATGATGTTGACCAGACGAAATTCGGAGGAGACACTCCTTACAGgtgtgttttt ... ttatctgcagCATTATGTTTGGGCCAGATATTTGTGGCTACAGCACTAAGAAAGTACATGC
EST: gi|116465718|gb|EG508310.1|EG508310
EST:     CTAAGTGATGATGTTGACCAGACGAAATTCGGAGGAGACACTCCTTACAG                         CATTATGTTTGGGCCAGATATTTGTGGCTACAGCACTAAGAAAGTACATGC
genomic: CTAAGTGATGATGTTGACCAGACGAAATTCGGAGGAGACACTCCTTACAGgtgtgttttt ... ttatctgcagCATTATGTTTGGGCCAGATATTTGTGGCTACAGCACTAAGAAAGTACATGC
EST: gi|116465735|gb|EG508327.1|EG508327
EST:     CTAAGTGATGATGTTGACCAGACGAAATTCGGAGGAGACACTCCTTACAG                         CATTATGTTTGGGCCAGATATTTGTGGCTACAGCACTAAGAAAGTACATGC
genomic: CTAAGTGATGATGTTGACCAGACGAAATTCGGAGGAGACACTCCTTACAGgtgtgttttt ... ttatctgcagCATTATGTTTGGGCCAGATATTTGTGGCTACAGCACTAAGAAAGTACATGC
EST: gi|86070962|gb|DR366719.1|DR366719
EST:     CTAAGTGATGATGTTGACCAGACGAAATTCGGAGGAGACACTCCTTACAG                         CATTATGTTTGGGCCAGATATTTGTGGCTACAGCACTAAGAAAGTACATGC
genomic: CTAAGTGATGATGTTGACCAGACGAAATTCGGAGGAGACACTCCTTACAGgtgtgttttt ... ttatctgcagCATTATGTTTGGGCCAGATATTTGTGGCTACAGCACTAAGAAAGTACATGC
EST: gi|116482410|gb|EG525002.1|EG525002
EST:     CTAAGTGATGATGTTGACCAGACGAAATTCGGAGGAGACACT-CTTACAG                         CATTATGTTTGGGCCAGATATTTGTGGCTACAGCACTAAGAAAGTACATGC
genomic: CTAAGTGATGATGTTGACCAGACGAAATTCGGAGGAGACACTCCTTACAGgtgtgttttt ... ttatctgcagCATTATGTTTGGGCCAGATATTTGTGGCTACAGCACTAAGAAAGTACATGC
EST: gi|164174507|gb|ES016214.1|ES016214
EST:     CTAAGTGATGATGTTGACCAGACGAAATTCGGAGGAGACACTCCTTACAG                         CATTATGTTTGGGCCAG
genomic: CTAAGTGATGATGTTGACCAGACGAAATTCGGAGGAGACACTCCTTACAGgtgtgttttt ... ttatctgcagCATTATGTTTGGGCCAG
EST: gi|86070954|gb|DR366711.1|DR366711
EST:     CTAAGTGATGATGTTGACCAGACGAAATTCGGAGGAGACACTCCTTACAG                         CATTATGTTTGGGCCAGATATTTGTGGCTACAGCACTAAGAAAGTACATGC
genomic: CTAAGTGATGATGTTGACCAGACGAAATTCGGAGGAGACACTCCTTACAGgtgtgttttt ... ttatctgcagCATTATGTTTGGGCCAGATATTTGTGGCTACAGCACTAAGAAAGTACATGC
EST: gi|86070959|gb|DR366716.1|DR366716
EST:     CTAAGTGATGATGTTGACCAGACGAAATTCGGAGGAGACACTCCTTACAG                         CATTATGTTTGGGCCAGATATTTGTGGCTACAGCACTAAG
genomic: CTAAGTGATGATGTTGACCAGACGAAATTCGGAGGAGACACTCCTTACAGgtgtgttttt ... ttatctgcagCATTATGTTTGGGCCAGATATTTGTGGCTACAGCACTAAG
EST: gi|86070957|gb|DR366714.1|DR366714
EST:     CTAAGTGATGATGTTGACCAGACGAAATTCGGAGGAGACACTCCTTACAG                         CATTATGTTTGGGCCAGATATTTGTGGCTACAGCACTAAGAAAGTACATGC
genomic: CTAAGTGATGATGTTGACCAGACGAAATTCGGAGGAGACACTCCTTACAGgtgtgttttt ... ttatctgcagCATTATGTTTGGGCCAGATATTTGTGGCTACAGCACTAAGAAAGTACATGC
EST: gi|86070956|gb|DR366713.1|DR366713
EST:     CTAAGTGATGATGTTGACCAGACGAAATTCGGAGGAGACACTCCTTACAG                         CATTATGTTTGGGCCAGATATTTGTGGCTACAGCACTAAGAAAGTACATGC
genomic: CTAAGTGATGATGTTGACCAGACGAAATTCGGAGGAGACACTCCTTACAGgtgtgttttt ... ttatctgcagCATTATGTTTGGGCCAGATATTTGTGGCTACAGCACTAAGAAAGTACATGC
EST: gi|164111457|gb|ES039902.1|ES039902
EST:     CACTCCTTACAG                         CATTATGTTTGGGCCAGATATTTGTGGCTACAGCACTAAGAAAGTACATGC
genomic: CACTCCTTACAGgtgtgttttt ... ttatctgcagCATTATGTTTGGGCCAGATATTTGTGGCTACAGCACTAAGAAAGTACATGC
EST: gi|116482409|gb|EG525001.1|EG525001
EST:     CTAAGTGATGATGTTGACCAGACGAAATTCGGAGGAGACACTCCTTACAG                         CATTATGTTTGGGCCAGATATTTGTGGCTACAGCACTAAGAAAGTACATGC
genomic: CTAAGTGATGATGTTGACCAGACGAAATTCGGAGGAGACACTCCTTACAGgtgtgttttt ... ttatctgcagCATTATGTTTGGGCCAGATATTTGTGGCTACAGCACTAAGAAAGTACATGC
EST: gi|116465734|gb|EG508326.1|EG508326
EST:     CTAAGTGATGATGTTGACCAGACGAAATTCGGAGGAGACACTCCTTACAG                         CATTATGTTTGGGCCAGATATTTGTGGCTACAGCACTAAGAAAGTACATGC
genomic: CTAAGTGATGATGTTGACCAGACGAAATTCGGAGGAGACACTCCTTACAGgtgtgttttt ... ttatctgcagCATTATGTTTGGGCCAGATATTTGTGGCTACAGCACTAAGAAAGTACATGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTGTCAAGCATGAGCAGAAGCTTGACTGTGGTGGTGGCTACATGAAGTTGCTAAGTGATGATGTTGACCAGACGAAATTCGGAGGAGACACTCCTTACAGgtgtgtttttcggttactttcatatcaaacttcaaacattcaaacaccaggcttatctttctttttttatctgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA