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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtctgttatttgcttaattaccgaccagttacttcaattttcttctaatattattggtttggatatatgaatatagtgtatttcagatcattgacttgaaagaagcttgggagaactagatacagtccatgttttcttactattaaattgtttactactttttggatgtcccattattgtagATTTACATCAGACGTCAAGATCAAGAGCATATCAATTGTTGGTGGCCCTGAAGGAACAAGTCCTTCTAAGTTGAGAGT

Basic information

species Arabidopsis thaliana
transcript AT2G25950.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G25950.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os01g37832.1 (Oryza sativa), 3'ss of exon 3
gtatgtctgttatttgcttaattaccgaccagttacttcaattttcttctaatattattggtttggatatatgaatatagtgtatttcagatcattgacttgaaagaagcttgggagaactagatacagtccatgttttcttactattaaattgtttactactttttggatgtcccattattgtagATTTACATCAGACGTCAAGATCAAGAGCATATCAATTGTTGGTGGCCCTGAAGGAACAAGTCCTTCTAAGTTGAGAGT
                                                                       || ||   ||     |  | |  ||  |          |||       ||   || | | | | |        ||| ||  ||| || | ||||     |  ||  |  |||||| ||||||||||||||||||||||||||||| ||  ||||||||||  | || |||||||| |||||||   |||||| 
-----------------------------------------------------------------------tgtatgaggtaagacttgggtttttaccc---------cttctatt--ctgtttataatgcctatccagaatttataaatctgtgtaatccttt----gtaccctttggttgtagGTTTACATCAGACGTCAAGATCAAGAGCATCTCTGTTGTTGGTGGTGCAGATGGAACAAGCCCTTCTAGAATGAGAGC

upper sequence: AT2G25950.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G090647_T05 (Zea mays), 3'ss of exon 3
gtatgtctgttatttgcttaattaccgaccagttacttcaattttcttctaatattattggtttggatatatgaatatagtgtatttcagatcattgacttgaaagaagcttgggagaact--agatacagtccatgttttcttactattaaat-tgtttactactttttggatgtcccattattgtagATTTACATCAGACGTCAAGATCAAGAGCATATCAATTGTTGGTGGCCCTGAAGGAACAAGTCCTTCTAAGTTGAGAGT
                                                                                     ||  | |      ||   ||  | |||     |  |     || ||| |   |      | | |||||| ||| || | || | |   |||    |  |||||| || |||||||| || |||||||||||||| ||  ||||||||||  |||| |||||||| || || |   |||||| 
-------------------------------------------------------------------------------------tttggtttcagagctaagaaataccttcccctatttttgtctatagttctcatccaaaaaatgttaaatatgtgtaatcctgtcttcctgt----tggttgtagGTTCACATCAGATGTTAAGATCAAGAGCATTTCTGTTGTTGGTGGTGCTGATGGAACAAGCCCGTCAAGAATGAGAGC

upper sequence: AT2G25950.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA13G29400.1 (Glycine max), 3'ss of exon 3
gtatgtctgttatttgcttaattaccgaccagttacttcaattttcttctaatattattggtttggatatatgaat-atagtgtatttcagatcattgacttgaaagaagcttgggagaactagatacagtccatgttttcttactattaaattgtttactactttttggatgtcccattattgtagATTTACATCAGACGTCAAGATCAAGAGCATATCAATTGTTGGTGGCCCTGAAGGAACAAGTCCTTCTAAGTTGAGAGT
                                                                  | |    ||  |   | | | | | ||| |  | ||   |     ||  || |||| |       | ||   |||||||    || |||||   | ||| |  |          |   ||||||||| ||||| |||||||| ||||||||||| || ||||||||  |||| |||||||||||||| ||| |||||||
----------------------------------------------------------------caacaagccaacgactttatctgtaacatcttccattttcta-----tttagaaaactggtc-----ctataagttcttaccg--aacttgtta--tgcttctgtg---------caaaatagATTTACTTCAGATGTCAAGATTAAGAGCATATCCATAGTTGGTGGAGCTGATGGAACAAGTCCTTCCAAGATGAGAGT

upper sequence: AT2G25950.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv04s0008g00760.t01 (Vitis vinifera), 3'ss of exon 3
gtatgtctgttatttgcttaattaccgaccagttacttcaattttcttctaatattattggtttggatatatgaatatagtgtatttcagatcattgacttgaaagaagcttgggagaactagatacagtccatgttttcttactattaaattgtttactactttttggatgtcccattattgtagATTTACATCAGACGTCAAGATCAAGAGCATATCAATTGTTGGTGGCCCTGAAGGAACAAGTCCTTCTAAGTTGAGAGT
                                                          |  ||||    | | | |||  | |  ||   ||  ||   ||        | | |  |    | | |  || |   |||  || ||    ||||                       ||| |  ||| ||||||||||| || |||||||| || || ||| ||||||||||  |||| |||||||||||||  ||| |||||| 
----------------------------------------------------------taatttgttggtgttactatctttttatttttattgttttttttt----ttcctagaggggtgaaaaagtgttctgatttatttgctg--gaatta----------------------attgtgatagGTTTACATCAGATGTTAAGATCAAAAGTATTTCAGTTGTTGGTGGTGCTGATGGAACAAGTCCTTGCAAGATGAGAGC

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|19874521|gb|AU235352.1|AU235352
EST:     GAGCATTTGGAGAGCAATGAGGGAGACCCTGAATTGCTTGTTTTTGTACC                         ATTTACATCAGACGTCAAGATCAAGAGCATATCAATTGTTGGTGGCCCTGA
genomic: GAGCATTTGGAGAGCAATGAGGGAGACCCTGAATTGCTTGTTTTTGTACCgtatgtctgt ... attattgtagATTTACATCAGACGTCAAGATCAAGAGCATATCAATTGTTGGTGGCCCTGA
EST: gi|86080738|gb|DR376495.1|DR376495
EST:     GAGAGCAATGAGGGAGACCCTGAATTGCTTGTTTTTGTACC                         ATTTACATCAGACGTCAAGATCAAGAGCATATCAATTGTTGGTGGCCCTGA
genomic: GAGAGCAATGAGGGAGACCCTGAATTGCTTGTTTTTGTACCgtatgtctgt ... attattgtagATTTACATCAGACGTCAAGATCAAGAGCATATCAATTGTTGGTGGCCCTGA
EST: gi|164206460|gb|ES095000.1|ES095000
EST:     GAGCATTTGGAGAGCAATGAGGGAGACCCTGAATTGCTTGTTTTTGTACC                         ATTTACATCAGACGTCAAGATCAAGAGCATATCAATTG
genomic: GAGCATTTGGAGAGCAATGAGGGAGACCCTGAATTGCTTGTTTTTGTACCgtatgtctgt ... attattgtagATTTACATCAGACGTCAAGATCAAGAGCATATCAATTG
EST: gi|125221275|gb|EL235360.1|EL235360
EST:     GAGCATTTGGAGAGCAATGAGGGAGACCCTGAATTGCTTGTTTTTGTACC                         ATTTACATCAG
genomic: GAGCATTTGGAGAGCAATGAGGGAGACCCTGAATTGCTTGTTTTTGTACCgtatgtctgt ... attattgtagATTTACATCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catgttttcttactattaaattgtttactactttttggatgtcccattattgtagATTTACATCAGACGTCAAGATCAAGAGCATATCAATTGTTGGTGGCCCTGAAGGAACAAGTCCTTCTAAGTTGAGAGT
      ttcttac  putative branch site (score: 2)
                                         tcccatt  putative PPT
         ttactattaaattgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtctgttatttgcttaattaccgaccagttacttcaattttcttctaatattattggtttggatatatgaatatagtgtatttcagatcattgacttgaaagaagcttgggagaactagatacagtccatgttttcttactattaaattgtttactactttttggatgtcccattattgtagATTTACATCAGACGTCAAGATCAAGAGCATATCAATTGTTGGTGGCCCTGAAGGAACAAGTCCTTCTAAGTTGAGAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA