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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAAGAGCTTCACTCTTATGAGAAAGAAGTTGAGAGAGAAGCGGCTAAGACTGCTGATATGAAGGACAAAGGTGCTGATCCCTACGACCTTAAACAACAGgtacagatttcattgtttatctctctgtattcgaagattcggagcccgtctttgttcgtcagaatctagaaatgctgtgttgtgctgtgtttagacttggtttttcctaatctgtgtatgtggtgatgcag

Basic information

species Arabidopsis thaliana
transcript AT2G30410.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G30410.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: LOC_Os02g57150.1 (Oryza sativa), 5'ss of exon 2
GAAAGAGCTTCACTCTTATGAGAAAGAAGTTGAGAGAGAAGCGGCTAAGACTGCTGATATGAAGGACAAAGGTGCTGATCCCTACGACCTTAAACAACAGgtacagatttcattgtttatctctctgtattcgaagattcggagcccgtctttgttcgtcagaatctagaaatg-ctgtgttgtgctgtgtttagacttggtttttcctaatctgtgtatgtggtgatgcag
 || ||||| | ||| || ||||| || || ||||  || ||||| ||||||||||| |||||||| ||||| || || |||||||| || || ||||||||  |||        | | | |   || | | | |         |||  ||||  |   | |  | |  |  || |||  || | |||    || | |     |                            
CAAGGAGCTCCGCTCCTACGAGAAGGAGGTGGAGAAGGAGGCGGCCAAGACTGCTGACATGAAGGAGAAAGGCGCCGACCCCTACGATCTCAAGCAACAGgtgaagaag-----atctttgtgcttgcaattgcaagcctttttcccccctttactaacctgcctgttaatttgtctgcattattctggtagtaaattgcaagtg---------------------------

upper sequence: AT2G30410.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA12G34820.1 (Glycine max), 5'ss of exon 2
GAAAGAGCTTCACTCTTATGAGAAAGAAGTTGAGAGAGAAGCGGCTAAGACTGCTGATATGAAGGACAAAGGTGCTGATCCCTACGACCTTAAACAACAGgtacagatttcattgtttatctctctgtattcgaagattcggagcccgtctttgttcgtcagaatctagaa-atgctgtgttgtgctgtgtttagacttggtttttcctaatctgtgtatgtggtgatgcag
||| ||||| || ||||||||||| ||||||||||||||||| || || || |||||||||||||| ||||| || |||||||| || || || ||||||||| |   | |||| ||||  || ||||  |   || ||   | | | | |||  |  ||    |  | || |   | ||                                                    
GAAGGAGCTGCATTCTTATGAGAAGGAAGTTGAGAGAGAAGCTGCCAAAACAGCTGATATGAAGGAAAAAGGAGCCGATCCCTATGATCTCAAGCAACAGgtatat-ctccattctttaa-tcactgtgctttcaggtt---atctcttatttacttttctctgttcaaaacaaattttgacag------------------------------------------------

upper sequence: AT2G30410.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA13G35770.1 (Glycine max), 5'ss of exon 2
GAAAGAGCTTCACTCTTATGAGAAAGAAGTTGAGAGAGAAGCGGCTAAGACTGCTGATATGAAGGACAAAGGTGCTGATCCCTACGACCTTAAACAACAGgtacagatt-----tcattgtttatctctctgt-attcgaagattcggagcccgtctttgttcgtcagaatctagaaatgctgtgttgtgctgtgtttagacttggtttttcctaatctgtgtatgtggtgatgcag
||| ||||| || ||||||||||| ||||||||||||||||| || || || |||||||||| ||| ||||| ||||| ||| | || || || ||||||||| |  ||     ||    |||   |    || ||| |     ||||     || ||  ||        |||   ||       || |||  | || |   |   ||||    |     | |   |  |||     
GAAGGAGCTGCATTCTTATGAGAAGGAAGTTGAGAGAGAAGCTGCCAAAACAGCTGATATGACGGAAAAAGGAGCTGACCCCCATGATCTCAAGCAACAGgtatatcttctccctctgcatttgctttcaggtgatttgccacatcgggttatgtgtt-atttacttttctctgttaaaaaaaaattatgcaat-ttgatggtaaattttgttgagctgatttgcattttgacag--

upper sequence: AT2G30410.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: Vv15s0021g01180.t01 (Vitis vinifera), 5'ss of exon 2
GAAAGAGCTTCACTCTTATGAGAAAGAAGTTGAGAGAGAAGCGGCTAAGACTGCTGATATGAAGGACAAAGGTGCTGATCCCTACGACCTTAAACAACAGgtacagatttcattgtttatctctctgtattcgaagattcggagcccgtctttgttcgtcagaatctagaaatgctgtgttgtgctgtgtttagacttggtttttcctaatctgtgtatgtggtgatgcag
 || ||| | || || ||||||||||| ||||| |||||||| || || ||||| ||||||||||| || || ||||| || || ||||||||||||||||||       |   | |   || |   | ||| ||   | | | |  |   ||| |  |    ||||  |  |  ||| | || |  ||   ||  ||   |      ||                     
TAAGGAGTTCCATTCCTATGAGAAAGAGGTTGAAAGAGAAGCTGCAAAAACTGCGGATATGAAGGAGAAGGGAGCTGACCCTTATGACCTTAAACAACAGgtatg-----cccaggtc--cttttcattttccaaa--tagcatcatgaaattggtgttatatatcttaaggttatgtttggttcc-tggaaagtattaagtaaaaaaaa---------------------

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|124720338|gb|EH811740.1|EH811740
EST:     CTGATATGAAGGACAAAGGTGCTGATCCCTACGACCTTAAACAACAG                         GAAAATGTGTTGGGTGAGTCTAGGATGATGATTCCGGATTGCCACAAACGT
genomic: CTGATATGAAGGACAAAGGTGCTGATCCCTACGACCTTAAACAACAGgtacagattt ... ggtgatgcagGAAAATGTGTTGGGTGAGTCTAGGATGATGATTCCGGATTGCCACAAACGT
EST: gi|164124514|gb|ES017761.1|ES017761
EST:     TGCTGATATGAAGGACAAAGGTGCTGATCCCTACGACCTTAAACAACAG                         GAAA-TGTGTTGGGT
genomic: TGCTGATATGAAGGACAAAGGTGCTGATCCCTACGACCTTAAACAACAGgtacagattt ... ggtgatgcagGAAAATGTGTTGGGT
EST: gi|47831397|gb|CK121081.1|CK121081
EST:     CTGCTGATATGAAGGACAAAGGTGCTGATCCCTACGACCTTAAACAACAG                         GAAAATGTGTTGGGTGAGTCTAGGATGATGATTCCGGATTGCCACAAACGT
genomic: CTGCTGATATGAAGGACAAAGGTGCTGATCCCTACGACCTTAAACAACAGgtacagattt ... ggtgatgcagGAAAATGTGTTGGGTGAGTCTAGGATGATGATTCCGGATTGCCACAAACGT
EST: gi|125014068|gb|EL086337.1|EL086337
EST:     CTGCTGATATGAAGGACAAAGGTGCTGATCCCTACGACCTTAAACAACAG                         GAAAATGTGTTGGGTGAGT
genomic: CTGCTGATATGAAGGACAAAGGTGCTGATCCCTACGACCTTAAACAACAGgtacagattt ... ggtgatgcagGAAAATGTGTTGGGTGAGT
EST: gi|125013737|gb|EL086006.1|EL086006
EST:     CTGCTGATATGAAGGACAAAGGTGCTGATCCCTACGACCTTAAACAACAG                         GAAAATGTGTTGGGTGAGTCTAGGAT
genomic: CTGCTGATATGAAGGACAAAGGTGCTGATCCCTACGACCTTAAACAACAGgtacagattt ... ggtgatgcagGAAAATGTGTTGGGTGAGTCTAGGAT
EST: gi|125099750|gb|EL155449.1|EL155449
EST:     CTGCTGATATGAAGGACAAAGGTGCTGATCCCTACGACCTTAAACAACAG                         GAAAATGTGTTGGGTGAGTCTAGGATGATGATTCCG
genomic: CTGCTGATATGAAGGACAAAGGTGCTGATCCCTACGACCTTAAACAACAGgtacagattt ... ggtgatgcagGAAAATGTGTTGGGTGAGTCTAGGATGATGATTCCG
EST: gi|124864196|gb|EH948633.1|EH948633
EST:     CTTAAACAACAG                         GAAAATGTGTTGGGTGAGTCTAGGATGATGATTCCGGATTGCCACAAACG
genomic: CTTAAACAACAGgtacagattt ... ggtgatgcagGAAAATGTGTTGGGTGAGTCTAGGATGATGATTCCGGATTGCCACAAACG
EST: gi|124908815|gb|EH982895.1|EH982895
EST:     TGCTGATCCCTACGACCTTAAACAACAG                         GAAAATGTGTTGGGTGAGTCTAGGATGATGATTCCGGATTGCCACAAACGT
genomic: TGCTGATCCCTACGACCTTAAACAACAGgtacagattt ... ggtgatgcagGAAAATGTGTTGGGTGAGTCTAGGATGATGATTCCGGATTGCCACAAACGT
EST: gi|164217100|gb|ES037804.1|ES037804
EST:     TGCTGATATGAAGGACAAAGGTGCTGATCCCTACGACCTTAAACAACAG                         GAAAATGTGTTGGGT
genomic: TGCTGATATGAAGGACAAAGGTGCTGATCCCTACGACCTTAAACAACAGgtacagattt ... ggtgatgcagGAAAATGTGTTGGGT
EST: gi|86074489|gb|DR370246.1|DR370246
EST:     CTGCTGATATGAAGGACAAAGGTGCTGATCCCTACGACCTTAAACAACAG                         GAAAATGTGTTGGGTGAGTCTAGGATGATGATTCCGGATTGCCACAAACGT
genomic: CTGCTGATATGAAGGACAAAGGTGCTGATCCCTACGACCTTAAACAACAGgtacagattt ... ggtgatgcagGAAAATGTGTTGGGTGAGTCTAGGATGATGATTCCGGATTGCCACAAACGT
EST: gi|124837160|gb|EH921599.1|EH921599
EST:     TGAAGGACAAAGGTGCTGATCCCTACGACCTTAAACAACAG                         GAAGATGTGTTGGGTGAGTCTAGGATGATGATTCCGGATTGCCACAAACGT
genomic: TGAAGGACAAAGGTGCTGATCCCTACGACCTTAAACAACAGgtacagattt ... ggtgatgcagGAAAATGTGTTGGGTGAGTCTAGGATGATGATTCCGGATTGCCACAAACGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAAGAGCTTCACTCTTATGAGAAAGAAGTTGAGAGAGAAGCGGCTAAGACTGCTGATATGAAGGACAAAGGTGCTGATCCCTACGACCTTAAACAACAGgtacagatttcattgtttatctctctgtattcgaagattcggagcccgtctttgttcgtcagaatctagaaatgctgtgttgtgctgtgtttagacttggtttttcctaatctgtgtatgtggtgatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT