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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATGATGACTTCTGGATTCTTCCGTTTGCTTCCCGATCTGCCAAAGGTTTTCTGGCGCTACCCGATTTCCTTCATGAGTTATGGTTCTTGGGCTATTCAGgtatttttttttgctttattgatcacaagaaccattcaatacaattgttgtagcgtttagcttgtaactattgcatatctcacattaaaggaaatatagt...

Basic information

species Arabidopsis thaliana
transcript AT1G51500.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G51500.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: LOC_Os05g13520.1 (Oryza sativa), 5'ss of exon 7
CATGATGACTTCTGGATTCTTCCGTTTGCTTCCCGATCTGCCAAAGGTTTTCTGGCGCTACCCGATTTCCTTCATGAGTTATGGTTCTTGGGCTATTCAGgtatttttttttgctttattgatcacaagaaccattcaatacaattgttgtagcgttt-agcttgtaactattgcatatctcacattaaaggaaatatagt-----
 ||| |||||||||||||||||||  ||||||| || || |||||| | |||||||| |||||| | |||| |||    || || || |||| | |  | ||| ||   ||  ||  ||   | || |    |||||     | ||| || || |    |  ||   || || |      ||||  ||   | | |  | |     
GATGCTGACTTCTGGATTCTTCCGGCTGCTTCCGGAACTTCCAAAGATCTTCTGGCGATACCCGGTGTCCTACATTGTCTACGGCTCGTGGGGTTTGAAAgtaattgactt--ctgaatgacttaccatgtgcattct---tacttggtgcagagaccgaagttacgacaatggtgctaatcactctacctgcattggaattgcag
















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|125106584|gb|EL159973.1|EL159973
EST:     CTGGCGCTACCCGATTTCCTTCATGAGTTATGGTTCTTGGGCTAATTCAG                         GGAGCATACAAGAATGATTTTC
genomic: CTGGCGCTACCCGATTTCCTTCATGAGTTATGGTTCTTGGGCTA-TTCAGgtattttttt ... tatattgcagGGAGCATACAAGAATGATTTTC
EST: gi|124950938|gb|EL026356.1|EL026356
EST:     TGGCGCTACCCGATTTCCTTCATGAGTTATGGTTCTTGGGCTAAATTCAG                         GGAGCATACAAGAATGATTT
genomic: TGGCGCTACCCGATTTCCTTCATGAGTTATGGTTCTTGGGCTA--TTCAGgtattttttt ... tatattgcagGGAGCATACAAGAATGATTT
EST: gi|124780448|gb|EH870391.1|EH870391
EST:     ATTTCCTTCATGAGTTATGGTTCTTGGGCTATTCAG                         GGAACATACAAGAATGATTTTCTTGGTCTAGAGTTTGACCCGATGTTTGCG
genomic: ATTTCCTTCATGAGTTATGGTTCTTGGGCTATTCAGgtattttttt ... tatattgcagGGAGCATACAAGAATGATTTTCTTGGTCTAGAGTTTGACCCGATGTTTGCG
EST: gi|124862166|gb|EH946603.1|EH946603
EST:     TCTGGCGCTACCCGATTTCCTTCATGAGTTATGGTTCTTGGGCTATTCAG                         GGAGCATACAAGAATGATTTTCTTGGTCTAGAGTTTGACCCGATGTT
genomic: TCTGGCGCTACCCGATTTCCTTCATGAGTTATGGTTCTTGGGCTATTCAGgtattttttt ... tatattgcagGGAGCATACAAGAATGATTTTCTTGGTCTAGAGTTTGACCCGATGTT
EST: gi|116460257|gb|EG502849.1|EG502849
EST:     TCTGGCGCTACCCGATTTCCTTCATGAGTTATGGTTCTTGGGCTATTCAG                         GGAGCATACAAGAATGATTTTCTTGGTCTAGAGTTTGACCCGATGTTTGCG
genomic: TCTGGCGCTACCCGATTTCCTTCATGAGTTATGGTTCTTGGGCTATTCAGgtattttttt ... tatattgcagGGAGCATACAAGAATGATTTTCTTGGTCTAGAGTTTGACCCGATGTTTGCG

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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CATGATGACTTCTGGATTCTTCCGTTTGCTTCCCGATCTGCCAAAGGTTTTCTGGCGCTACCCGATTTCCTTCATGAGTTATGGTTCTTGGGCTATTCAGgtatttttttttgctttattgatcacaagaaccattcaatacaattgttgtagcgtttagcttgtaactattgcatatctcacattaaaggaaatatagt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cacaagaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caatacaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tatctcac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaggaaa