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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTTCCATTTACAGAGCTTCTTAAGTTTATTCTGTTTGCTAATTTTTCGATTGTTGGAATGAATGTTAGTCTTATGTGGAACTCTGTTGGGTTTTATCAGgtaaatgtgtttgctttttgtgttatgtaacgtttcttgttgttggttctaatggtgtcttctcttttatgcttaacag

Basic information

species Arabidopsis thaliana
transcript AT4G09810.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G09810.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: LOC_Os12g05830.1 (Oryza sativa), 5'ss of exon 3
TCTTCCATTTACAGAGCTTCTTAAGTTTATTCTGTTTGCTAATTTTTCGATTGTTGGAATGAATGTTAGTCTTATGTGGAACTCTGTTGGGTTTTATCAGgtaa-------atgtgtttgctttttgtgttatgtaacgtttcttgttgtt--ggttctaatggt--gtcttctcttttatgcttaacag
  | ||| |  |||| ||  |||| ||| |  | ||| | || || |||||||||||||||||||| ||  | |||||||||||||| |||||||||||||| |       |||  | ||||   |   ||   | | |  | |     ||   |||  ||  |          ||||| | ||   |||
CTTACCACTGCCAGATCTGATTAAATTTGTGATCTTTTCGAACTTGTCGATTGTTGGAATGAATGTGAGCTTGATGTGGAACTCTGTGGGGTTTTATCAGgttagcaaaggatggttctgctagctaaattccatcatggctttgaactttcaagtttcaaaagctaaagaatccttttgttctcttcag

upper sequence: AT4G09810.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: LOC_Os02g40090.4 (Oryza sativa), 5'ss of exon 3
TCTTCCATTTACAGAGCTTCTTAAGTTTATTCTGTTTGCTAATTTTTCGATTGTTGGAATGAATGTTAGTCTTATGTGGAACTCTGTTGGGTTTTATCAGgtaaatgtgtttgctttttgtg-ttatgtaacgtttcttgttgttg-gttctaatggtgtcttctcttttatgcttaa-cag
| | |||||  |||| ||  |||| ||  |  | ||||| || || || |||||||| |||||||||||| | ||||||||||||||||| || ||||||||        |   |||   |  || | ||     | ||    | | |  |  ||  |   ||   ||| |||| |   |||
TTTACCATTGCCAGAACTCGTTAAATTCGTCTTTTTTGCAAACTTATCAATTGTTGGGATGAATGTTAGTTTGATGTGGAACTCTGTTGGATTCTATCAGgtgggaagagtaattttaaatccttctatattcaatgttagaatggagggcacatactaattttcgtttcatgcctcttcag

upper sequence: AT4G09810.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: LOC_Os12g05780.3 (Oryza sativa), 5'ss of exon 3
TCTTCCATTTACAGAGCTTCTTAAGTTTATTCTGTTTGCTAATTTTTCGATTGTTGGAATGAATGTTAGTCTTATGTGGAACTCTGTTGGGTTTTATCAGgtaaatg--tgtttgctttttgtgttatgtaacgtttcttgttgttggttctaatggt---gtcttctcttttatgcttaacag
  | ||| |  |||| ||  |||||||| |  | ||| | || || || ||||||||||||||||| ||  | |||||||||||||| || ||||||||||| |      |   | | |    | ||  |  | |      ||     ||  ||           ||  |||| | |    |||
CTTACCAATACCAGATCTGATTAAGTTTGTGATCTTTTCGAACTTGTCAATTGTTGGAATGAATGTGAGCTTGATGTGGAACTCTGTGGGATTTTATCAGgttagcaaaggaccgttctagtagctagattccatcatggctttaaactttcaactactaaacaatcctttttcttcccttcag

upper sequence: AT4G09810.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: LOC_Os05g12490.1 (Oryza sativa), 5'ss of exon 3
TCTTCCATTTACAGAGCTTCTTAAGTTTATTCTGTTTGCTAATTTTTCGATTGTTGGAATGAATGTTAGTCTTATGTGGAACTCTGTTGGGTTTTATCAGgtaaatgtgtttgctttttgtgttatgtaacgtttcttgttgttggttctaatggtgtcttctcttttatgc--ttaacag
  | ||| |  |||| ||  | || ||| |  | ||||| ||  | || |||||||| |||||||||||| | ||||||||||||||||| || || ||||| ||     |  ||   |   |||     |  || | |   | | | |  ||  |   ||     | ||||  ||  |||
CTTACCAGTGCCAGAACTAATAAAATTTGTCTTTTTTGCAAACCTATCAATTGTTGGGATGAATGTTAGTTTGATGTGGAACTCTGTTGGATTCTACCAGgtgaagaaagtaactaagtcctttaatgttcacttttagaattggatgcatatactaatttgctcctcatgcctttttcag

upper sequence: AT4G09810.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G147446_T01 (Zea mays), 5'ss of exon 3
TCTTCCATTTACAGAGCTTCTTAAGTTTATTCTGTTTGCTAATTTTTCGATTGTTGGAATGAATGTTAGTCTTATGTGGAACTCTGTTGGGTTTTATCAGgtaaatgtgtttgctttttg--tgttatgtaacgtttctt---gttgttggttctaatggtgtcttctcttttatgcttaacag
  | ||  |  |||| ||  |||| ||| |  | ||| | || || || |||||||| |||||||| ||  | ||||||||||||||||| |||||||||||   || | ||  ||  |   || ||| | | |   | |    | |||       ||  |   ||   |    |||| |    
CTTACCCCTAGCAGATCTAGTTAAATTTGTGATATTTTCGAACTTGTCAATTGTTGGGATGAATGTGAGCTTGATGTGGAACTCTGTTGGCTTTTATCAGgttggtgagattttttagtagctgctatattatgcgaccttgaatcgttaacatctatattcattttattcccttgctcag---

upper sequence: AT4G09810.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM5G823629_T03 (Zea mays), 5'ss of exon 2
TCTTCCATTTACAGAGCTTCTTAAGTTTATTCTGTTTGCTAATTTTTCGATTGTTGGAATGAATGTTAGTCTTATGTGGAACTCTGTTGGGTTTTATCAGgtaaatgtgtttgctttttgtgttatgtaacgtttcttgttgtt----ggttctaatggtgtcttctcttttatgcttaacag
| | |||||  |||| ||  | ||||||    | ||||| ||  | ||||| || |||||||| |||||| | ||||||||||||||||| || |||||||| |  |      ||||  || || | ||| || | |||  |||    |  | || |  ||   | | | ||   |||  |||
TTTACCATTACCAGAACTAGTAAAGTTTGCCTTTTTTGCAAACCTGTCGATCGTCGGAATGAACGTTAGTTTGATGTGGAACTCTGTTGGATTCTATCAGgtgagggcagaaactttg-gtattctataa-gtatattggagttaaacgtatatactaatgctgtgtatcttgcccttttcag

upper sequence: AT4G09810.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G071378_T02 (Zea mays), 5'ss of exon 3
TCTTCCATTTACAGAGCTTCTTAAGTTTATTCTGTTTGCTAATTTTTCGATTGTTGGAATGAATGTTAGTCTTATGTGGAACTCTGTTGGGTTTTATCAGgtaaatgtgtttgctttttg-tgttatgtaacgtttcttgttgttggttctaatggtgtcttctcttttatgcttaacag
  | ||  |  |||| ||  |||| ||| |  | ||| | || || || |||||||| |||||||| ||  | |||||||||||||| || |||||||||||   ||   ||  |  | | || |||   | |   | |    ||| |   ||  |  |    ||| ||    |   |||
CTTACCCCTAGCAGATCTAGTTAAATTTGTGATATTTTCGAACTTGTCAATTGTTGGGATGAATGTGAGCTTGATGTGGAACTCTGTGGGCTTTTATCAGgttggtgaaatttttagtagctgctataatatgcaaccttaaattgttaacaactgaattcattctattcccttgctcag

upper sequence: AT4G09810.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G089630_T04 (Zea mays), 5'ss of exon 3
TCTTCCATTTACAGAGCTTCTTAAGTTTATTCTGTTTGCTAATTTTTCGATTGTTGGAATGAATGTTAGTCTTATGTGGAACTCTGTTGGGTTTTATCAGgtaaatgtgtttgctttttgtgttatgtaacgtttcttgttgttggttct----aatggtgtcttctcttttatgcttaacag
||| || ||  | || ||  | || ||     | ||||| ||  | || |||||||| |||||||| ||  | ||||||||||||||||| || ||||||||  |        |||    | || | ||| || | | |   ||     |    | ||  |   ||| | ||    ||  |||
TCTACCGTTACCTGAACTAGTAAAATTCGCCTTTTTTGCGAACCTGTCTATTGTTGGGATGAATGTAAGCTTGATGTGGAACTCTGTTGGATTCTATCAGgtgcagacagaaacttcg-atattctataa-gtatatcggaattaaacttgtatactgacgctgtctgtcttgcctttttcag

upper sequence: AT4G09810.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA02G08700.1 (Glycine max), 5'ss of exon 3
TCTTCCATTTACAGAGCTTCTTAAGTTTATTCTGTTTGCTAATTTTTCGATTGTTGGAATGAATGTTAGTCTTATGTGGAACTCTGTTGGGTTTTATCAGgtaaatgtgtttgctttttgtgttatgtaacgtttcttgttgttggttctaatggtgtcttctcttttatgcttaacag
| | || ||  |||| ||||| || ||| |||| |||||||| || || ||||||||||||||||||||||| ||||||||||| ||||| || ||||| || | |  |  ||   ||| | |  ||     ||  ||  ||        | |  | |   || |||     || ||||
TTTACCCTTGCCAGATCTTCTAAAATTTGTTCTCTTTGCTAACTTCTCTATTGTTGGAATGAATGTTAGTCTAATGTGGAACTCAGTTGGATTCTATCAAgtgagttgggctgagctttatctattggttaattcattaatgccttcagaagttatattcactttttagccattgacag

upper sequence: AT4G09810.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA10G36620.1 (Glycine max), 5'ss of exon 2
TCTTCCATTTACAGAGCTTCTTAAGTTTATTCTGTTTGCTAATTTTTCGATTGTTGGAATGAATGTTAGTCTTATGTGGAACTCTGTTGGGTTTTATCAGgtaaat-gtgtttgctttttg-tgtta-tgtaacgtttcttgttgttggttctaatggtgtcttctcttttatgcttaacag
| | || ||  |||||||||| || ||| || | |||||||| || || ||||||||||||||||| ||||| ||||||||||| ||||| || ||||| || | | || ||   ||||   | ||  |  || ||   ||  ||        | |    | ||||  || |   ||  |||
TTTACCCTTACCAGAGCTTCTAAAATTTGTTTTCTTTGCTAACTTCTCCATTGTTGGAATGAATGTCAGTCTAATGTGGAACTCAGTTGGATTCTATCAAgtgagttgtattgaattttcactattggtccaaggtccattaatgcattcagaagttaaattttcttcttaaccattggcag

upper sequence: AT4G09810.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA16G27820.1 (Glycine max), 5'ss of exon 2
TCTTCCATTTACAGAGCTTCTTAAGTTTATTCTGTTTGCTAATTTTTCGATTGTTGGAATGAATGTTAGTCTTATGTGGAACTCTGTTGGGTTTTATCAGgtaaatgtgtttgctttttgtgttatgtaacgtttcttgttgttggttctaat-ggtgtcttctcttttatgcttaacag
| | || ||  |||| ||||| || ||| ||||  ||||||| || || ||||||||||||||||||||||| ||||||||||| ||||| || ||||| || | |  |  ||   ||| | |  ||   | ||   |  ||        | |   | |   || |||     || ||||
TTTACCCTTGCCAGATCTTCTAAAATTTGTTCTCGTTGCTAACTTCTCTATTGTTGGAATGAATGTTAGTCTAATGTGGAACTCAGTTGGATTCTATCAAgtgagttgggctgagctttatctattggttcattcactaatgccttcagaagttaatattcactttttagccattgacag

upper sequence: AT4G09810.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv18s0072g00080.t01 (Vitis vinifera), 5'ss of exon 2
TCTTCCATTTACAGAGCTTCTTAAGTTTATTCTGTTTGCTAATTTTTCGATTGTTGGAATGAATGTTAGTCTTATGTGGAACTCTGTTGGGTTTTATCAGgtaaatg-tgtttgctttttgtgtt--atgtaacgtttcttgttgttggttctaatggtgtcttctcttttatgcttaacag
||| ||  || |||||||||| || ||| |  | ||||| || || || ||||||||||||||||||||| | ||||||||||| || ||||| ||||||||| ||  || ||||| | ||||||  |  | || |||  |  |  |  ||  |   ||  | |||||  | |   |  |||
TCTCCCCCTTCCAGAGCTTCTGAAATTTGTATTATTTGCGAACTTCTCTATTGTTGGAATGAATGTTAGTTTAATGTGGAACTCAGTAGGGTTCTATCAGgtatattctgattgctctgtgtgtttaagcttacattttattgtaataattgcagaagttacatctctaatttaactgtcag

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|125104185|gb|EL158345.1|EL158345
EST:     TTGTTGGAATGAATGTTAGTCTTATGTGGAACTCTGTTGGGTTTTATCAG                         ATTGCAAAGCTTAGCATGATTCCTGTATCATGCTTGTTGG
genomic: TTGTTGGAATGAATGTTAGTCTTATGTGGAACTCTGTTGGGTTTTATCAGgtaaatgtgt ... tgcttaacagATTGCAAAGCTTAGCATGATTCCTGTATCATGCTTGTTGG