Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCAAAGACCACACTCCCACAGTCTGGTTTGCCGATAACGGCGAGCGTCTTGGCACTTACCGTGGCCACAGTGGTGCTGTTTGGTGCTGTGATATCTCCAgtaagtggtctcagcctctcaaattcaaatagtatatagtggatggaatggattcagtttaggatttaagtcgttgtctttgttgttttagtctttcatagcttaacgattagtgttttgtttgtgatttcttag

Basic information

species Arabidopsis thaliana
transcript AT2G46290.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G46290.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA01G03610.2 (Glycine max), 5'ss of exon 1
GCCAAAGACCACACTCCCACAGTCTGGTTTGCCGATAACGGCGAGCGTCTTGGCACTTACCGTGGCCACAGTGGTGCTGTTTGGTGCTGTGATATCTCCAgtaagtggtctcagcctctcaaattcaaatagtatatagtggatggaatggattcagtttaggatttaagtcgttgtctttgttgttttagtctttcatagcttaacgattagtgttttgtttgtgatttcttag
||||| |||||||  ||||| |||||||| ||||| |||||||| || || ||||| ||||| |||||||  || || ||||||||||| ||  |||| || |||    |||  | || |   ||  |||   || |  |  ||   || ||| | | |    ||| |  | | |     || || || ||                                            
GCCAAGGACCACAACCCCACCGTCTGGTTCGCCGACAACGGCGAACGCCTCGGCACCTACCGCGGCCACAACGGCGCCGTTTGGTGCTGCGACGTCTCAAgcaag----ctcttcatcactgttttcaatt-catctttttaataatattgatactgatagtaattaatttggattctgatgctgcttcag--------------------------------------------

upper sequence: AT2G46290.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: Vv01s0011g06630.t01 (Vitis vinifera), 5'ss of exon 1
GCCAAAGACCACACTCCCACAGTCTGGTTTGCCGATAACGGCGAGCGTCTTGGCACTTACCGTGGCCACAGTGGTGCTGTTTGGTGCTGTGATATCTCCAgtaagtggtctcagcc-tctcaaattcaaatagtatatagtggatggaatggattcagt--ttaggatttaagtcgttgtctttgttgttttagtctttcatagcttaacgattagtgttttgtttg--tgatttcttag
||||| || ||||||||||| |||||||| ||||| ||||| ||||| || ||||| || ||||| ||||  ||||| ||||||  ||| ||| ||||||||| ||  ||       | | |       ||  | | |||     | | |   ||| |     |||  ||| |   || | |  |  |   ||     |||| | | |  ||||  |   ||| |||   ||||  | ||
GCCAAGGATCACACTCCCACCGTCTGGTTCGCCGACAACGGGGAGCGCCTCGGCACCTATCGTGGACACAACGGTGCCGTTTGGACCTGCGATGTCTCCAgtatgtcttccttctgatgttattcgtccattttttttagccttggaagttatttcggcgaccaggggttagggttttctatcaggagaggta-----tcatggttaattgattgattaattggttggtcgattgttcag
















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|116426847|gb|EG469439.1|EG469439
EST:     TGGCACTTACCGTGGCCACAGTGGTGCTGTTTGGTGCTGTGATATCTCCA                         GAGACTCGTCTAGATTGATCACTGGTAGTGCTGATCAGACCGCAAAGCTGT
genomic: TGGCACTTACCGTGGCCACAGTGGTGCTGTTTGGTGCTGTGATATCTCCAgtaagtggtc ... gatttcttagGAGACTCGTCTAGATTGATCACTGGTAGTGCTGATCAGACTGCAAAGCTGT
EST: gi|86040339|gb|DR336094.1|DR336094
EST:     GGCACTTACCGTGGCCACAGTGGTCGCTGTTTGGTGSTGTGATATCTCCA                         GAGACTCGTCTAGATTGATCACTGGTAGTGCTGATCAGACTGCAAAGCTGT
genomic: GGCACTTACCGTGGCCACAGTGGT-GCTGTTTGGTGCTGTGATATCTCCAgtaagtggtc ... gatttcttagGAGACTCGTCTAGATTGATCACTGGTAGTGCTGATCAGACTGCAAAGCTGT
EST: gi|86040336|gb|DR336091.1|DR336091
EST:     TGGCACTTACCGTGGCCACAGTGGTGCTGTTTGGTGCTGTGATATCTCCA                         GAGACTCGTCTAGATTGATCACTGGTAGTGCTGATCAGACTGCAAAGCTGT
genomic: TGGCACTTACCGTGGCCACAGTGGTGCTGTTTGGTGCTGTGATATCTCCAgtaagtggtc ... gatttcttagGAGACTCGTCTAGATTGATCACTGGTAGTGCTGATCAGACTGCAAAGCTGT
EST: gi|19878991|gb|AU239822.1|AU239822
EST:     TGGCACTTACCGTGGCCACAGTGGTGCTGTTTGGTGCTGTGATATCTCCA                         GAGACTCGTCTAGATTGATCACTGGTAGTGCTGATCAGACTGCAAAGCTGT
genomic: TGGCACTTACCGTGGCCACAGTGGTGCTGTTTGGTGCTGTGATATCTCCAgtaagtggtc ... gatttcttagGAGACTCGTCTAGATTGATCACTGGTAGTGCTGATCAGACTGCAAAGCTGT
EST: gi|116426849|gb|EG469441.1|EG469441
EST:     TGGCACTTACCGTGGCCACAGTGGTGCTGTTTGGTGCTGTGATATCTCCA                         GAGACTCGTCTAGATTGATCACTGGTAGTGCTGATCAGACCGCAAAGCTGT
genomic: TGGCACTTACCGTGGCCACAGTGGTGCTGTTTGGTGCTGTGATATCTCCAgtaagtggtc ... gatttcttagGAGACTCGTCTAGATTGATCACTGGTAGTGCTGATCAGACTGCAAAGCTGT
EST: gi|86040340|gb|DR336095.1|DR336095
EST:     TGGCACTTACCGTGGCCACAGTGGTGCTGTTTGGTGCTGTGATATCTCCA                         GAGACTCGTCTAGATTGATCACTGGTAGTGCTGATCAGACTGCAAAGCTGT
genomic: TGGCACTTACCGTGGCCACAGTGGTGCTGTTTGGTGCTGTGATATCTCCAgtaagtggtc ... gatttcttagGAGACTCGTCTAGATTGATCACTGGTAGTGCTGATCAGACTGCAAAGCTGT
EST: gi|116426850|gb|EG469442.1|EG469442
EST:     TGGCACTTACCGTGGCCACAGTGGTGCTGTTTGGTGCTGTGATATCTCCA                         GAGACTCGTCTAGATTGATCACTGGTAGTGCTGATCAGACCGCAAAGCTGT
genomic: TGGCACTTACCGTGGCCACAGTGGTGCTGTTTGGTGCTGTGATATCTCCAgtaagtggtc ... gatttcttagGAGACTCGTCTAGATTGATCACTGGTAGTGCTGATCAGACTGCAAAGCTGT
EST: gi|116426846|gb|EG469438.1|EG469438
EST:     TGGCACTTACCGTGGCCACAGTGGTGCTGTTTGGTGCTGTGATATCTCCA                         GAGACTCGTCTAGATTGATCACTGGTAGTGCTGATCAGACCGCAAAGCTGT
genomic: TGGCACTTACCGTGGCCACAGTGGTGCTGTTTGGTGCTGTGATATCTCCAgtaagtggtc ... gatttcttagGAGACTCGTCTAGATTGATCACTGGTAGTGCTGATCAGACTGCAAAGCTGT
EST: gi|164114555|gb|ES175478.1|ES175478
EST:     TGATATCTCCCA                         GAGACTCGTCTAGATTGATCACTGGTAGTGCTGATCAGACTGCAAAGCTG
genomic: TGATATCT-CCAgtaagtggtc ... gatttcttagGAGACTCGTCTAGATTGATCACTGGTAGTGCTGATCAGACTGCAAAGCTG
EST: gi|86040338|gb|DR336093.1|DR336093
EST:     TGGCACTTACCGTGGCCACAGTGGTGCTGTTTGGNGCTGTGATATCTCCA                         GAGACTCGTCTAGATTGATCACTGGTAGTGCTGATCAGACTGCAAAGCTGT
genomic: TGGCACTTACCGTGGCCACAGTGGTGCTGTTTGGTGCTGTGATATCTCCAgtaagtggtc ... gatttcttagGAGACTCGTCTAGATTGATCACTGGTAGTGCTGATCAGACTGCAAAGCTGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCAAAGACCACACTCCCACAGTCTGGTTTGCCGATAACGGCGAGCGTCTTGGCACTTACCGTGGCCACAGTGGTGCTGTTTGGTGCTGTGATATCTCCAgtaagtggtctcagcctctcaaattcaaatagtatatagtggatggaatggattcagtttaggatttaagtcgttgtctttgttgttttagtctttcatagcttaacgattagtgttttgtttgtgatttcttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT