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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgcgacacgttcagcttcacattagttatgctggagcctgatgataagtttgatcttttactagttgatgaaactgagtgtttgagactgttgaatatttttactttgcagATGGTAACAACATTTGGAATGTCTGATATTGGACCATGGTCTTTGATGGATTCTTCGGCACAAAGCGATGTCATCATGAGAATGATGGCAAGAAACTCCA

Basic information

species Arabidopsis thaliana
transcript AT2G30950.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G30950.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os06g45820.1 (Oryza sativa), 3'ss of exon 4
gtacgcgacacgttcagc-ttcacattagttatgctggagcctgatgataagtttgatcttttactagttgatgaaactgagtgtttgagactgttgaatatttttactttgcagATGGTAACAACATTTGGAATGTCTGATATTGGACCATGGTCTTTGATGGATTCTTCGGCACAAAG---CGATGTCATCATGAGAATGATGGCAAGAAACTCCA
    |  | ||   |||| || ||||    |||  |  |      |  | |||     |  || ||   |  ||  | | |     || |       |||  || |     |||||||||    ||||| || ||||| || ||||| || |||||  | ||||| ||    || || ||   ||||||||||||||| ||||||||||| ||||   
----gaaaaactgacagcatttacata---tatattaaacatctgttcttagtccttcccctttctttcttttgctaatta-cacctggggtcac--aatgcttct-----gcagATGGTGGTTACATTCGGTATGTCGGACATTGGTCCGTGGTCGCTAATGGACTCAGGAGCTCAGAGCGGCGATGTCATCATGAGGATGATGGCAAGGAACT---

upper sequence: AT2G30950.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA15G17070.1 (Glycine max), 3'ss of exon 4
gtacgcgacacgttcagcttcacattagttatgctggagcctgatgataagtttgatcttttactagttgatgaaactgagtgtttgagactgttgaatatttttactttgcagATGGTAACAACATTTGGAATGTCTGATATTGGACCATGGTCTTTGATGGATTCTTCGGCACAAAGCGATGTCATCATGAGAATGATGGCAAGAAACTCCA
             |||   ||| |  | |  | ||  |   |  |     |         |||| | ||  | | ||    || ||   |    || | ||  |    |||||||||||||| ||||||||||||||||||||||| || |||||  | ||||| || || || ||||| ||||| |||||||||||||||||||||||||| |
------------ctcattgtcaaaagaatctttctt-attttcctaccttgcccttctaattacaactttgtcacacctc-tgcttctaataaatgtaaatgatactcttgcagATGGTAACCACATTTGGAATGTCTGATATTGGTCCTTGGTCACTCATGGACTCATCAGCTCAAAGTGATGTTATCATGAGAATGATGGCAAGAAACTCAA

upper sequence: AT2G30950.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA09G05820.2 (Glycine max), 3'ss of exon 3
gtacgcgacacgttcagcttcacattagttatgctggagcctgatgataagtttgatcttttactagttgatgaaactgagtgtttgagactgttgaatatttttactttgcagATGGTAACAACATTTGGAATGTCTGATATTGGACCATGGTCTTTGATGGATTCTTCGGCACAAAGCGATGTCATCATGAGAATGATGGCAAGAAACTCCA
             ||    ||| |  | |  | ||  |   |  |     |         |||| | ||    | ||    || ||   | |  || | ||  |    | |||||||||||| ||||||||||||||||||||||| || |||||  |  |||| || || || ||||| ||||| |||||||||||||||||||||||||| |
------------ctcgttgtcaaaaaaatctttctt-attttcctacgttgcccttctgattacaactttgccacacctc-tgcttctaattaatgtaaatgatactctagcagATGGTAACCACATTTGGAATGTCTGATATTGGTCCTTGGTCACTCGTGGACTCATCAGCTCAAAGTGATGTTATCATGAGAATGATGGCAAGAAACTCAA

upper sequence: AT2G30950.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA09G05820.1 (Glycine max), 3'ss of exon 4
gtacgcgacacgttcagcttcacattagttatgctggagcctgatgataagtttgatcttttactagttgatgaaactgagtgtttgagactgttgaatatttttactttgcagATGGTAACAACATTTGGAATGTCTGATATTGGACCATGGTCTTTGATGGATTCTTCGGCACAAAGCGATGTCATCATGAGAATGATGGCAAGAAACTCCA
         |   ||    ||| |  | |  | ||  |   |  |     |         |||| | ||    | ||    || ||   | |  || | ||  |    | |||||||||||| ||||||||||||||||||||||| || |||||  |  |||| || || || ||||| ||||| |||||||||||||||||||||||||   
---------atactcgttgtcaaaaaaatctttctt-attttcctacgttgcccttctgattacaactttgccacacctc-tgcttctaattaatgtaaatgatactctagCAGATGGTAACCACATTTGGAATGTCTGATATTGGTCCTTGGTCACTCGTGGACTCATCAGCTCAAAGTGATGTTATCATGAGAATGATGGCAAGAAACT---

upper sequence: AT2G30950.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA05G26230.1 (Glycine max), 3'ss of exon 4
gtacgcgacacgttcagcttcacattagttatgctggagcctgatgataagtttgatcttttactagttgatgaaactgagtgtttga-gactgttgaatatttttactttgcagATGGTAACAACATTTGGAATGTCTGATATTGGACCATGGTCTTTGATGGATTCTTCGGCACAAAGCG---ATGTCATCATGAGAATGATGGCAAGAAACTCCA
         | ||||| ||    |  |   |   |  |   |  | ||||     |  | || | | ||     |  ||  | ||  |  | |||| |||  || |   |||||||||||||| ||||||||||||||||||||||| || |||||  | |||||  | || |||||||| |   ||||||||||||||||||||||||| ||||   
-------taatgttca-ctctgaaggatgaacttttaatttttcttataaa---aaaatctttccatttagccta--tgtttcttcaataattgttaaatgattct--cttgcagATGGTAACCACATTTGGAATGTCTGATATTGGTCCTTGGTCACTTATGGAAGCATCAGCACAAAGTGGGGATGTCATCATGAGAATGATGGCAAGGAACT---

upper sequence: AT2G30950.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA08G09160.1 (Glycine max), 3'ss of exon 4
gtacgcgacacgttcagcttcacattagttatgctggagcctgatgat-aagtttgatcttttactagttgatgaaactgagtgtttgagactgttgaatatttttactt--tgcagATGGTAACAACATTTGGAATGTCTGATATTGGACCATGGTCTTTGATGGATTCTTCGGCACAAAGCG---ATGTCATCATGAGAATGATGGCAAGAAACTCCA
               |     | | | || ||| |    |   | ||| || ||| |  | |||  |    |  |||   |   |||       || |     | |  ||  |||||||||| || ||||||||||||||||||||||| || |||||  | |||||  | || |||||| | |   ||||||||||||||||||||||||| ||||   
---------------attgaaagaatggtaatgatcagtctgaaggatgaacttttaattcttataaaaaaaaaaaa--aatcattttcattccttaacctcctatgtttcttgcagATGGTGACCACATTTGGAATGTCTGATATTGGTCCTTGGTCACTTATGGAACCATCAGCACAAGGTGGGGATGTCATCATGAGAATGATGGCAAGGAACT---

upper sequence: AT2G30950.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv12s0028g01600.t01 (Vitis vinifera), 3'ss of exon 4
gtacgcgacacgttcagcttcacattagttatgctggagcctgatgataagtttgatcttttactagttg-atgaaactgagtgtttgagactg-ttgaatatttttactttgcagATGGTAACAACATTTGGAATGTCTGATATTGGACCATGGTCTTTGATGGATTCTTCGGCACAAAGCG---ATGTCATCATGAGAATGATGGCAAGAAACTCCA
            ||   |||   | || ||  |||  |  |  || | || ||   ||   || || ||| |  ||  | | ||  |  ||| | || ||||  ||   |||||||||||| || |||||||| |||||||| || || ||||||||  | |||||  | ||||| || || |   ||||||||||||||||||||||||| || |   
-----------cttgctcttttaactaatt--gcttaa--caaataacaatttccctcacctattatttggacaaatttaactgaatttgacgggtttaataaattcg-tttgcagATGGTGACCACATTTGGGATGTCTGACATCGGCCCATGGTCGCTTATGGACACCTCGGCTCAGAGTGCTGATGTCATCATGAGAATGATGGCAAGGAATT---

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|86060903|gb|DR356660.1|DR356660
EST:     CTACTGGCGCAGTTGGTGACTTACAACAGATCACCGGTTTGGCTAGACAG                         ATGGTAACAACATTTGGAATGTCTGATATTGGACCATGGTCTTTGATGGAT
genomic: CTACTGGCGCAGTTGGTGACTTACAACAGATCACCGGTTTGGCTAGACAGgtacgcgaca ... tactttgcagATGGTAACAACATTTGGAATGTCTGATATTGGACCATGGTCTTTGATGGAT
EST: gi|125066491|gb|EL133346.1|EL133346
EST:     TCACCGGTTTGGCTAGACAG                         ATGGTAACAACATTTGGAATGTCTGATATTGGACCATGGTCTTTCGATGGA
genomic: TCACCGGTTTGGCTAGACAGgtacgcgaca ... tactttgcagATGGTAACAACATTTGGAATGTCTGATATTGGACCATGGTCTTT-GATGGA
EST: gi|125104918|gb|EL158850.1|EL158850
EST:     CAACAGATCACCGGTTTGGCTAGACAG                         ATGGTAACAACATTTGGAATGTCTGATATTGGACCATGGTCTTTGATGGAT
genomic: CAACAGATCACCGGTTTGGCTAGACAGgtacgcgaca ... tactttgcagATGGTAACAACATTTGGAATGTCTGATATTGGACCATGGTCTTTGATGGAT
EST: gi|163966545|gb|ES084070.1|ES084070
EST:     CTACTGGCGCAGTTGGTGACTTACAACAGATCACCGGTTTGGCTAGACAG                         ATGGTAACAACATTTGGAATGTCTGATATTGGACCATGGTCTTTGATGG
genomic: CTACTGGCGCAGTTGGTGACTTACAACAGATCACCGGTTTGGCTAGACAGgtacgcgaca ... tactttgcagATGGTAACAACATTTGGAATGTCTGATATTGGACCATGGTCTTTGATGG
EST: gi|124735162|gb|EH826564.1|EH826564
EST:     CAGTTGGTGACTTACAACAGATCACCGGTTTGGCTAGACAG                         ATGGTAACAACATTTGGAATGTCTGATAT
genomic: CAGTTGGTGACTTACAACAGATCACCGGTTTGGCTAGACAGgtacgcgaca ... tactttgcagATGGTAACAACATTTGGAATGTCTGATAT
EST: gi|125281835|gb|EL295920.1|EL295920
EST:     CTACTGGCGCAGTTGGTGACTTACAACAGATCACCGGTTTGGCTAGACAG                         ATGGTAACAACATTTGGAATGTCTGATATTGGACCATGGTCTTT
genomic: CTACTGGCGCAGTTGGTGACTTACAACAGATCACCGGTTTGGCTAGACAGgtacgcgaca ... tactttgcagATGGTAACAACATTTGGAATGTCTGATATTGGACCATGGTCTTT
EST: gi|116411694|gb|EG454286.1|EG454286
EST:     CTACTGGCGCAGTTGGTGACTTACAACAGATCACCGGTTTGGCTAGACAG                         ATGGTAACAACATTTGGAATGTCTGATATTGGACCATGGTCTTTGATGGAT
genomic: CTACTGGCGCAGTTGGTGACTTACAACAGATCACCGGTTTGGCTAGACAGgtacgcgaca ... tactttgcagATGGTAACAACATTTGGAATGTCTGATATTGGACCATGGTCTTTGATGGAT
EST: gi|124927513|gb|EL005245.1|EL005245
EST:     TCACCGGTTTGGCTAGACAG                         ATGGTAACAACATTTGGAATGTCTGATATTGGACCATGGTCTTTGATGGAT
genomic: TCACCGGTTTGGCTAGACAGgtacgcgaca ... tactttgcagATGGTAACAACATTTGGAATGTCTGATATTGGACCATGGTCTTTGATGGAT
EST: gi|125304546|gb|EL318631.1|EL318631
EST:     GCAGTTGGTGACTTACAACAGATCACCGGTTTGGCTAGACAG                         ATGGTAACAACATTTGGAATGT
genomic: GCAGTTGGTGACTTACAACAGATCACCGGTTTGGCTAGACAGgtacgcgaca ... tactttgcagATGGTAACAACATTTGGAATGT
EST: gi|125199131|gb|EL214085.1|EL214085
EST:     CTACTGGCGCAGTTGGTGACTTACAACAGATCACCGGTTTGGCTAGACAG                         ATGGTAACAACATTTGGAATGTCTGA
genomic: CTACTGGCGCAGTTGGTGACTTACAACAGATCACCGGTTTGGCTAGACAGgtacgcgaca ... tactttgcagATGGTAACAACATTTGGAATGTCTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttactagttgatgaaactgagtgtttgagactgttgaatatttttactttgcagATGGTAACAACATTTGGAATGTCTGATATTGGACCATGGTCTTTGATGGATTCTTCGGCACAAAGCGATGTCATCATGAGAATGATGGCAAGAAACTCCA
      agttgat  putative branch site (score: 5)
                                         tttttacttt  putative PPT
                                  ttgaatatttttactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgcgacacgttcagcttcacattagttatgctggagcctgatgataagtttgatcttttactagttgatgaaactgagtgtttgagactgttgaatatttttactttgcagATGGTAACAACATTTGGAATGTCTGATATTGGACCATGGTCTTTGATGGATTCTTCGGCACAAAGCGATGTCATCATGAGAATGATGGCAAGAAACTCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA