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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgggtgtcttcttctgtcctaagtttctgcacgagacaagttttgagacttgatttgtcaaaatatctttgattttcagGTTGTTTTGGAGGCAGATGGTTATCAACCTTATCTTATATCTCCAGAGAAAGGGTTGAGATCGTTGATAAAGATTGTCCTTGAGTTGGCTAAAGACCCGG

Basic information

species Arabidopsis thaliana
transcript AT1G10290.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G10290.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os06g13820.1 (Oryza sativa), 3'ss of exon 9
----gtgggtgtcttcttctgtcctaagtttctgcacgagacaagttttgagacttgatttgt-caaaata----tctttgat-tttcagGTTGTTTTGGAGGCAGATGGTTATCAACCTTATCTTATATCTCCAGAGAAAGGGTTGAGATCGTTGATAAAGATTGTCCTTGAGTTGGCTAAAGACCCGG
    |   |  ||   ||      | |||      |  || ||  ||   |   || ||     |  || |    ||| |||  ||  || |||| ||||| || |||||||||||||| || || ||||||||||||||||||||||| || ||||||||||| ||  | ||  |||| || || ||  
gtaagattggatccagtttcaggattagtgctactatcaggcattttcccatcttttatgaacactgaacagtattctctgacattctagATTGTCTTGGAAGCCGATGGTTATCAACCGTACCTGATATCTCCAGAGAAAGGGTTGAGGTCCTTGATAAAGATAGTATTGGATATGGCAAAGGAGCCAT

upper sequence: AT1G10290.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os02g50550.1 (Oryza sativa), 3'ss of exon 9
----gtgggtgtcttcttctgtcctaagtttctgcacgagacaagttttgagacttgatttgtcaaaatatctttgattttcagGTTGTTTTGGAGGCAGATGGTTATCAACCTTATCTTATATCTCCAGAGAAAGGGTTGAGATCGTTGATAAAGATTGTCCTTGAGTTGGCTAAAGACCCGG
     |         |||||    | | |||  |   | | ||   ||||     ||||   |     |||||||   ||  || ||||  |||| || |||||||||||||| ||| | ||||||||||||||||| || | ||| || |||||    || |||||  |||| || || ||  
gtaaattcaaaagcccttctagaattaattttagagtggg-cacactttgct-tatgatgattactgttatctttatattctagATTGTCCTGGAAGCCGATGGTTATCAACCATATTTGATATCTCCAGAGAAAGGTTTAAAATCCTTAATAAAAGGAGTACTTGAAATGGCAAAGGAGCCAT

upper sequence: AT1G10290.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G157462_T01 (Zea mays), 3'ss of exon 9
gtgggtgtcttcttctgtcctaagtttctgcacgagacaagttttgagacttgatttgtca-aaatatctttgattttcagGTTGTTTTGGAGGCAGATGGTTATCAACCTTATCTTATATCTCCAGAGAAAGGGTTGAGATCGTTGATAAAGATTGTCCTTGAGTTGGCTAAAGACCCGG
  |  ||    ||||     | |  ||  || |  |       ||   || |||||   || |  | |||         || |||| ||||| ||||||||||||||||| ||| | |||||||||||||||||||||||||| || ||||| || || || ||  |||| || || ||  
--gtatgatcacttccaattttacattgagctctggttggcagttagcacatgattaaacacatttctctccacacaatagATTGTCTTGGAAGCAGATGGTTATCAACCATATTTGATATCTCCAGAGAAAGGGTTGAGATCCTTAATAAAAATAGTACTGGAAATGGCAAAGGAGCCAT

upper sequence: AT1G10290.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA07G40300.1 (Glycine max), 3'ss of exon 9
--------------gtgggtgtcttcttctgtcc---taagtttctgcacgagacaag-ttttgagacttga----tttgtcaaaatatc-----tttgatt---ttcagGTTGTTTTGGAGGCAGATGGTTATCAACCTTATCTTATATCTCCAGAGAAAGGGTTGAGATCGTTGATAAAGATTGTCCTTGAGTTGGCTAAAGACCCGG
               ||  | | |  |  |||     ||   ||  |  |     |   | |||| ||||||     |||     ||||      ||||  |   ||||| ||||  | || |||||||| ||||||||||||||||| |||||||||||||| |||||||| || || ||    || |||||  |||| || || ||  
gtaaaccttctcccttgaatttgtcatattgtttaggtagaatttagttcattttattctcttgacacttgaggtgcttgcttctatattcccattttggcttatttcagATTGTCCTTGAAGCAGATGGATATCAACCTTATCTTATCTCTCCAGAGAAAGGTTTGAGATCCTTAATTAAAGGCGTTCTTGAACTGGCAAAGGAGCCAT

upper sequence: AT1G10290.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA17G00480.1 (Glycine max), 3'ss of exon 9
gtgggtgtcttct------tctgtcctaa-gtttctgcacgagacaagtt-----------ttgagacttga----tttgtcaaaatatc-----tttgattttcagGTTGTTTTGGAGGCAGATGGTTATCAACCTTATCTTATATCTCCAGAGAAAGGGTTGAGATCGTTGATAAAGATTGTCCTTGAGTTGGCTAAAGACCCGG
||   | |  ||       | |||| ||  ||||  | |  | | |  |            |||| |||||      |||     ||||      ||||  |||||| ||||  | || |||||||| |||||||||||||| || |||||||||||||| |||||||| || || ||    || |||||  |||| || || ||  
gtaaatcttctcccttgaatttgtcatattgtttaggtagaatatagttcatcttattctgttgacacttggggtgcttgcttctatattctcattttggctttcagATTGTCCTAGAAGCAGATGGATATCAACCTTATCTGATCTCTCCAGAGAAAGGTTTGAGATCCTTAATTAAAGGCGTTCTTGAACTGGCGAAGGAGCCAT

upper sequence: AT1G10290.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv12s0035g01740.t01 (Vitis vinifera), 3'ss of exon 9
--gtgggtgtcttcttct---gtcctaagtttc-tgcacg--agacaagtttt----gagacttgatttgtcaaaatatc---tttgattt----tcagGTTGTTTTGGAGGCAGATGGTTATCAACCTTATCTTATATCTCCAGAGAAAGGGTTGAGATCGTTGATAAAGATTGTCCTTGAGTTGGCTAAAGACCCGG
   ||| | |||| |  |    | | || |||  |||     | | | ||| |      | ||| |||  |   ||| |    ||| | ||     ||| ||||  | || ||||||||||||||||||||||||||||||||||| ||||| || || ||  | ||||| |||||||| ||| |||| ||||| ||  
gtatggttctcttttattcacattccaacttttgtgccttttaaatatgttgttgtaaggcctttattgtttgcaatgttccttttcaattgataccagATTGTGCTAGAAGCAGATGGTTATCAACCTTATCTTATATCTCCAGAAAAAGGTTTAAGGTCTCTAATAAAAATTGTCCTGGAGCTGGCGAAAGAGCCAT

upper sequence: AT1G10290.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv18s0089g00350.t01 (Vitis vinifera), 3'ss of exon 9
------gtgggtgtcttcttctgtcctaagtttctgcacga-----gacaagttttgagacttgatttgtcaaaatatctttg----atttt----cagGTTGTTTTGGAGGCAGATGGTTATCAACCTTATCTTATATCTCCAGAGAAAGGGTTGAGATCGTTGATAAAGATTGTCCTTGAGTTGGCTAAAGACCCGG
           ||| || ||| |||  || ||| | |   |     ||  | |||||||   | |||  |   | |   |||     ||||     ||| |||| || || || |||||||||||||| |||||||||||||| |||||||| ||||||||||| |||||   |||| | ||| | || ||||| ||  
gtatctaccattgtgttgttcggtctcaattttatactatattttggattatttttgaggtctaattactttgagtgattttcccccatttggtcacagATTGTGTTAGAAGCTGATGGTTATCAACCATATCTTATATCTCCTGAGAAAGGTTTGAGATCGTTAATAAAAGGTGTCTTGGAGCTTGCAAAAGAGCCAT

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|164237558|gb|ES093240.1|ES093240
EST:     ACCTGAACAATGTTAAAAGG                         GTTGTTTTGGAGGCAGATGGTTATCAACCTTACCTTATATCTCCAGAGAAA
genomic: ACCTGAACAATGTTAAAAGGgtgggtgtct ... tgattttcagGTTGTTTTGGAGGCAGATGGTTATCAACCTTATCTTATATCTCCAGAGAAA
EST: gi|47831974|gb|CK121658.1|CK121658
EST:     TCAAGCAGCTTCCATTGGATAGACATTTTGACCTGAACAATGTTAAAAGG                         GTTGTTTTGGAGGCAGATGGTTATCAACCTTATCTTATATCTCCAGAGAAA
genomic: TCAAGCAGCTTCCATTGGATAGACATTTTGACCTGAACAATGTTAAAAGGgtgggtgtct ... tgattttcagGTTGTTTTGGAGGCAGATGGTTATCAACCTTATCTTATATCTCCAGAGAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctgcacgagacaagttttgagacttgatttgtcaaaatatctttgattttcagGTTGTTTTGGAGGCAGATGGTTATCAACCTTATCTTATATCTCCAGAGAAAGGGTTGAGATCGTTGATAAAGATTGTCCTTGAGTTGGCTAAAGACCCGG
                                          ctttgat  putative branch site (score: 5)
                                       tatcttt  CT-rich tract
                                   aaaatatctttgattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgggtgtcttcttctgtcctaagtttctgcacgagacaagttttgagacttgatttgtcaaaatatctttgattttcagGTTGTTTTGGAGGCAGATGGTTATCAACCTTATCTTATATCTCCAGAGAAAGGGTTGAGATCGTTGATAAAGATTGTCCTTGAGTTGGCTAAAGACCCGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC