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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaatcgaccttgtgctgataccttagtgataacatattctatgtcgaagatacttttgttttgtcaaagttacaaaagttgtttctctgctccatattcctaagttctctcacaatatctttcagCCTCCGTGGGATTTGTCTACCAAGGGGAAGTTTATCATTCATTACACTTATGGATGCGACTACAACATGAAG

Basic information

species Arabidopsis thaliana
transcript AT5G13500.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G13500.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA15G37490.3 (Glycine max), 3'ss of exon 6
gtaagaatcgaccttgtg-ctgataccttagtgataacatattctatgtcga-agatacttttgttttgtcaaagttacaaaagttgtttctctgctccatattcctaagttctctcacaatatctttcagCCTCCGTGGGATTTGTCTACCAAGGGGAAGTTTATCATTCATTACACTTATGGATGCGACTACAACATGAAG
||  |     || |  || ||  |    | ||  | | ||||   ||||    ||||    |||||   |||||  |   |||    |  |    ||| || |  ||   ||||   |    |  |||||||| || |||||| |    || ||   |||||  ||  | ||||||||||||||||| |||||||| ||||||
gtttggcataacatcatgtctcttgatgttgtattta-atatatgatgttatcagatcaagttgtt--atcaaatgtgacaaaaacatacccaacctcaatttagct---ttcttgtatgtgaaatttcagCCCCCATGGGATCTTGAAACTAACAAGAAGTACATTCTCCATTACACTTATGGATGTGACTACAATATGAAG

upper sequence: AT5G13500.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv13s0084g00830.t01 (Vitis vinifera), 3'ss of exon 5
gtaagaatcgaccttgtg-ctgataccttag----tgataacatattctatgtcgaagatacttt----tgttttgtcaaagttacaaaagt-tgtttctctgctccatattcct-aagttctctcacaatatc----tttcagCCTCCGTGGGATTTGTCTACCAAGGGGAAGTTTATCATTCATTACACTTATGGATGCGACTACAACATGAAG
             | |   || |||  |||     |||| | ||| |||||||   |  || |||    | |   |   |    |||  |||   | | | |     ||  |  | |||    ||   ||| |     |||||||| || ||||||||    ||      ||||||||| ||||| |||||||||||||| ||||||||| | |||
----------gtttggcatctaatattttaaattttgatgatatagtctatgttccaagtattttgcattatccagcagagacaacattagtacatgtatatagaagatgatattgaagagtccttgtaattttaaattttcagCCACCATGGGATTTAGAAACTGCAAAGAAGTTTATTATTCACTACACTTATGGATGTGACTACAACTTAAAG
















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|164060883|gb|ES151910.1|ES151910
EST:     CTGCTATACATGGGGTGCGTCACATACTTCAGAAGGATTTCATGCTTCAG                         CCTCCGTGGGATTTGTCTACCAAGGGGAAGTTTAT
genomic: CTGCTATACATGGGGTGCGTCACATACTTCGGAAGGATTTCATGCTTCAGgtaagaatcg ... tatctttcagCCTCCGTGGGATTTGTCTACCAAGGGGAAGTTTAT
EST: gi|86075298|gb|DR371055.1|DR371055
EST:     CTGCTATACATGGGGTGCGTCACATACTTCGGAAGGATTTCATGCTTCAG                         CCTCCGTGGGATTTGTCTACCAAGGGGAAGTTTATCATTCATTACACTTAT
genomic: CTGCTATACATGGGGTGCGTCACATACTTCGGAAGGATTTCATGCTTCAGgtaagaatcg ... tatctttcagCCTCCGTGGGATTTGTCTACCAAGGGGAAGTTTATCATTCATTACACTTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacaaaagttgtttctctgctccatattcctaagttctctcacaatatctttcagCCTCCGTGGGATTTGTCTACCAAGGGGAAGTTTATCATTCATTACACTTATGGATGCGACTACAACATGAAG
                                    ctctcac  putative branch site (score: 3)
                                             tatctttc  putative PPT
                                           aatatcttt  TA-rich tract