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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaacataagtttaatctggcttagttttggtgcaatgctcggtactcttactaaattacactgcttcacgcttacatattatgttcaattgcagGTGGATGAAGCTCTGATGAAGTTGGCGGGTCAAAAAGCCTATTTCATGCATTGTTTGCCTGCAGAGAGAGGAGTTGAGGTGACCAATGGAGTCGTAGAGG

Basic information

species Arabidopsis thaliana
transcript AT1G75330.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G75330.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os02g47590.1 (Oryza sativa), 3'ss of exon 4
---------------------------------------gtaaacataagtttaatctg-gcttagttttggtgcaatgctcggtactcttactaaattac-----------actgcttcacgcttacatattatgttcaattg------cagGTGGATGAAGCTCTGATGAAGTTGGCGGGTCAAAAAGCCTATTTCATGCATTGTTTGCCTGCAGAGAGAGGAGTTGAGGTGACCAATGGAGTCGTAGAGG
                                       ||   || ||  | | | |   | || | |    | | | |||   ||| |||      ||            | | ||| |  || | ||| | ||||   |||      ||||||||||||||| ||||| || |||| || | ||| ||||   | ||||||||||||||||||||||||||  | ||||| ||  | || | | | || |
gttagaatacctccttttatgctcttgttccgatgttctgtctgcacaaactcattttacacataatatctcagtagtcctctccactattatctgcatatgggatctggctaatactttattctca-atactttgtttctttgttcctgcagGTGGATGAAGCTATGATGGAGATGGCTGGGCCAAATGCCTTCCTTATGCATTGTTTGCCTGCAGAGAGAGGGATAGAGGTAACAGACGGCGCCATTGAAG

upper sequence: AT1G75330.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G046748_T02 (Zea mays), 3'ss of exon 5
--------gtaaacataagtttaatctggcttagttttggtgcaatgctcggtactcttactaaattacactgcttcacgcttacatattatgttcaattgcagGTGGATGAAGCTCTGATGAAGTTGGCGGGTCAAAAAGCCTATTTCATGCATTGTTTGCCTGCAGAGAGAGGAGTTGAGGTGACCAATGGAGTCGTAGAGG
        | ||   |     |    ||  ||    ||  |    | |   ||   | | | |  | ||||| ||      ||  |   |||  |  |||||||||||||||||| |||||| || | || || | | | |||||  | ||||| |||||||| |||||||||||||| ||||||||| | || | | | ||||
cctccatagcaactgttgcaatgtcttgttttgaccttcatagcttacgttgttggccttc-agctaacacttctgt---tttttaccctatactatattgcagGTGGATGAAGCCCTGATGGAGATTGCTGGCCCACAGGCCTACCTTATGCACTGTTTGCCCGCAGAGAGAGGAGTGGAGGTGACCGACGGTGCCATCGAGG

upper sequence: AT1G75330.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G050371_T01 (Zea mays), 3'ss of exon 4
----gtaaacataagtttaatctggcttagttttggt-gcaatgctcggtactcttactaaattacactgcttcacgcttacatattatgttcaattgcagGTGGATGAAGCTCTGATGAAGTTGGCGGGTCAAAAAGCCTATTTCATGCATTGTTTGCCTGCAGAGAGAGGAGTTGAGGTGACCAATGGAGTCGTAGAGG
     |      | || | || |   |   | |  || | |||  | | |    ||  ||   | ||      |||   |   | ||||  |  ||||||||||||||| || |||||| || | || || | | | |||||  | ||||| ||||||||||||||||||||||| ||||||||  | || | | | ||||
gaccattgctcaatgtcttatttctgtgtttctcagtagtaattatagctcacattgttagccttcagc-taacacttctgttttttatcctatattgcagGTGGATGAGGCCCTGATGGAGATTGCTGGCCCACAGGCCTACCTTATGCACTGTTTGCCTGCAGAGAGAGGAGTGGAGGTGACTGACGGCGCCATTGAGG

upper sequence: AT1G75330.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G062142_T01 (Zea mays), 3'ss of exon 6
-----gtaaacataagtttaatctggcttagttttggt-gcaatgctcggtactcttactaaattacactgcttcacgcttacatatt-atgttcaattgcagGTGGATGAAGCTCTGATGAAGTTGGCGGGTCAAAAAGCCTATTTCATGCATTGTTTGCCTGCAGAGAGAGGAGTTGAGGTGACCAATGGAGTCGTAGAGG
     ||      | || | || |   |   | |  || | |||  | | |    ||  ||   | ||     | || |||  || || ||  |  ||||||||| |||||| | |||||| || | || || | | |||||||  | ||||| ||||||||||||||||||||||| |||||||   |||| | | | ||||
caaccgttgctcaatgtcttatttctgtgtttctcagtcgtaattatagcttacattgttagccttcagc---taacacttctatttttatcctatattgcagGTAGATGAAACACTGATGGAGATTGCTGGCCCACAAGCCTACCTTATGCACTGTTTGCCTGCAGAGAGAGGAGTGGAGGTGATTGATGGCGCCATTGAGG

upper sequence: AT1G75330.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv18s0001g12780.t01 (Vitis vinifera), 3'ss of exon 4
--gtaaacataa--gtttaatctggctt--agttttggtgcaatgctcggtactcttactaaattacactgcttcacgctta-catattatgttcaattgcagGTGGATGAAGCTCTGATGAAGTTGGCGGGTCAAAAAGCCTATTTCATGCATTGTTTGCCTGCAGAGAGAGGAGTTGAGGTGACCAATGGAGTCGTAGAGG
  || |   | |    |||| |   |||  ||||||  |   ||  |    | ||| |  |  |||   |    ||  | ||  | || || ||    |||||||||||||| | || |||||||| || || | |||||||||||||||||||||||| || || || ||||| || ||||||||  |||| ||  | || |
tagtcagtctcataacttaagcaacctttgagttttatttttattgttaagagtctca--agtttatgttctgacatccatagtacataat-ttattctgcagGTGGATGAACCCCTTATGAAGTTAGCCGGGCCAAAAGCCTATTTCATGCATTGTTTACCGGCTGAAAGAGGCGTGGAGGTGACTGATGGGGTTCTTGAAG

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|164093412|gb|EL981290.1|EL981290
EST:     GGAAAGCATTCCAAGGATTCCAG                         GTGGATGAAGCTCTGATGAAGTTGGCGGGTCAAAAAGCCTATTTCATGCAT
genomic: GGAAAGCATTCCAAGGATTCCAGgtaaacataa ... tcaattgcagGTGGATGAAGCTCTGATGAAGTTGGCGGGTCAAAAAGCCTATTTCATGCAT
EST: gi|86080147|gb|DR375904.1|DR375904
EST:     GTCAAAAGGATGAAGCCGAAGCTCGCCGGAAAGCATTCCAAGGATTCCAG                         GTGGATGAAGCTCTGATGAAGTTGGCGGGTCAAAAAGCCTATTTCATGCAT
genomic: GTCAAAAGGATGAAGCCGAAGCTCGCCGGAAAGCATTCCAAGGATTCCAGgtaaacataa ... tcaattgcagGTGGATGAAGCTCTGATGAAGTTGGCGGGTCAAAAAGCCTATTTCATGCAT
EST: gi|86074354|gb|DR370111.1|DR370111
EST:     GTCAAAAGGATGAAGCCGAAGCTCGCCGGAAAGCATTCCAAGGATTCCAG                         GTGGATGAAGCTCTGATGAAGTTGGCGGGTCAAAAAGCCTATTTCATGCAT
genomic: GTCAAAAGGATGAAGCCGAAGCTCGCCGGAAAGCATTCCAAGGATTCCAGgtaaacataa ... tcaattgcagGTGGATGAAGCTCTGATGAAGTTGGCGGGTCAAAAAGCCTATTTCATGCAT
EST: gi|125314592|gb|EL328677.1|EL328677
EST:     GTCAAAAGGATGAAGCCGAAGCTCGCCGGAAAGCATTCCAAGGATTCCAG                         GTGGATAGAAGCTCTGATGAAGTTGGCGGGTCAAA
genomic: GTCAAAAGGATGAAGCCGAAGCTCGCCGGAAAGCATTCCAAGGATTCCAGgtaaacataa ... tcaattgcagGTGGAT-GAAGCTCTGATGAAGTTGGCGGGTCAAA
EST: gi|125212292|gb|EL227246.1|EL227246
EST:     GTCAAAAGGATGAAGCCGAAGCTCGCCGGAAAGCATTCCAAGGATTCCAG                         GTGGATGAAGCTCTGATGAAGTTGGCGGGT
genomic: GTCAAAAGGATGAAGCCGAAGCTCGCCGGAAAGCATTCCAAGGATTCCAGgtaaacataa ... tcaattgcagGTGGATGAAGCTCTGATGAAGTTGGCGGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cggtactcttactaaattacactgcttcacgcttacatattatgttcaattgcagGTGGATGAAGCTCTGATGAAGTTGGCGGGTCAAAAAGCCTATTTCATGCATTGTTTGCCTGCAGAGAGAGGAGTTGAGGTGACCAATGGAGTCGTAGAGG
                                    atattatgttcaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaacataagtttaatctggcttagttttggtgcaatgctcggtactcttactaaattacactgcttcacgcttacatattatgttcaattgcagGTGGATGAAGCTCTGATGAAGTTGGCGGGTCAAAAAGCCTATTTCATGCATTGTTTGCCTGCAGAGAGAGGAGTTGAGGTGACCAATGGAGTCGTAGAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG