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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcaaatttggcttataaagataattcttcaaaactttttggtttctcattttcttaatatgctttgttttggtttcagCTTGCTAAAGATATGGAACATGAACAAGTACACTGGAGTTCTTGGCGTGTATAACTGCCAAGGAGCAGCTTGGAGCAGCACAGAGAGAAAAAACATTTTC

Basic information

species Arabidopsis thaliana
transcript AT5G20250.3
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G20250.3 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os06g07600.1 (Oryza sativa), 3'ss of exon 4
------------------------gtaagcaaatttggc-ttataaagataattcttcaaaactttttggtttctcattttcttaatatgctttgttttggtttcagCTTGCTAAAGATATGGAACATGAACAAGTACACTGGAGTTCTTGGCGTGTATAACTGCCAAGGAGCAGCTTGGAGCAGCACAGAGAGAAAAAACATTTTC
                         |   | |  |   | || |    ||   ||||  |     ||||  |   || |     | | || |   |  | | |  |||||||| ||||| |||||||||||||||| ||| ||||| || || || || || ||||| || || || ||||||      ||||  || ||||| |||
gtgaattcgaccccctttgctcgaattgtcgagctgcacgttgtgccaatgcatcttggag--catttgtctgaacaatgctgaactgtgttgcttggttgctgtagCTTGCTGAAGATTTGGAACATGAACAAGTTCACCGGAGTGCTCGGAGTCTACAATTGCCAGGGCGCGGCATGGAGCTCTGTGGAGAAGAAGAACATCTTC

upper sequence: AT5G20250.3 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G127147_T01 (Zea mays), 3'ss of exon 5
---------gtaagcaaatttggcttataaagataattctt--caaaactttttggtttctcattttcttaata-tgctttgttttggtttcagCTTGCTAAAGATATGGAACATGAACAAGTACACTGGAGTTCTTGGCGTGTATAACTGCCAAGGAGCAGCTTGGAGCAGCACAGAGAGAAAAAACATTTTC
         | | ||     ||  || |     |  ||     ||| |    |  |       || |   |  | |||  ||  |  |   |||| |||| ||||| |||||||||||||||| ||| || || || |||||||| |||||||| || || || |||| |  |   ||||  || ||||  |||
gtgccatttgcaggcgctgctgtttttttttttttttttggagcaagagcaataagcagtgtgttctaacaccaatgccatgcatgtg---cagCCTGCTCAAGATCTGGAACATGAACAAGTTCACCGGCGTGCTGGGCGTGTACAACTGCCAGGGCGCGGCGTGGAACTCCGTGGAGAAGAAGAACACCTTC

upper sequence: AT5G20250.3 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv11s0016g05770.t01 (Vitis vinifera), 3'ss of exon 3
----------------------gtaagcaaatttggcttataaagataattcttcaaaactttttggtttctcattttcttaatatgctttgttttggtttcagCTTGCTAAAGATATGGAACATGAACAAGTACACTGGAGTTCTTGGCGTGTATAACTGCCAAGGAGCAGCTTGGAGCAGCACAGAGAGAAAAAACATTTTC
                      ||||  |||||   || || ||  |      || ||  ||||    | || | | | ||     |||||| |   ||||||| ||| | ||||||||||||||||| ||||||||||||||  |||| ||||| ||||||||||| ||||| |||| |||| | || ||||| ||||  |||
gtatatttaacatacaatttttgtaaagaaatt-aactaatgaaattggagaatccaatattttcttgtgcttaatgtgttgcctggctttggt---gtttcagTTTGTTGAAGATATGGAACATGAATAAGTACACTGGAGTGATTGGAGTGTACAACTGCCAAGGTGCAGCCTGGAACAGCGCTGAAAGAAAGAACACATTC

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|86055200|gb|DR350957.1|DR350957
EST:     AGACCAACTCGCGATTGTTTGTTCGCTGATCCTGCCCGTGATGGTGTCAG                         CTTGCTAAAGATATGGAACATGAACAAGTACACTGGAGTTCTTGGCGTGTA
genomic: AGACCAACTCGCGATTGTTTGTTCGCTGATCCTGCCCGTGATGGTGTCAGgtaagcaaat ... ttggtttcagCTTGCTAAAGATATGGAACATGAACAAGTACACTGGAGTTCTTGGCGTGTA
EST: gi|86055199|gb|DR350956.1|DR350956
EST:     AGACCAACTCGCGATTGTTTGTTCGCTGATCCTGCCCGTGATGGTGTCAG                         CTTGCTAAAGATATGGAACATGAACAAGTACACTGGAGTTCTTGGCGTGTA
genomic: AGACCAACTCGCGATTGTTTGTTCGCTGATCCTGCCCGTGATGGTGTCAGgtaagcaaat ... ttggtttcagCTTGCTAAAGATATGGAACATGAACAAGTACACTGGAGTTCTTGGCGTGTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcttcaaaactttttggtttctcattttcttaatatgctttgttttggtttcagCTTGCTAAAGATATGGAACATGAACAAGTACACTGGAGTTCTTGGCGTGTATAACTGCCAAGGAGCAGCTTGGAGCAGCACAGAGAGAAAAAACATTTTC
                            tcttaat  putative branch site (score: 3)
                                      ctttgtttt  putative PPT
                      tcattttcttaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcaaatttggcttataaagataattcttcaaaactttttggtttctcattttcttaatatgctttgttttggtttcagCTTGCTAAAGATATGGAACATGAACAAGTACACTGGAGTTCTTGGCGTGTATAACTGCCAAGGAGCAGCTTGGAGCAGCACAGAGAGAAAAAACATTTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG