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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagcatttcttcttctgaattatacttcacctattgtttgtttggatcttcttcaatgactctgtaacttactctcttaattagGGGTCGCAAGAGAGCTTCTATCACCTACTGTATCACCTACATTCTCAGCTGTATCACCAAACATTCTCCCCAGTACAAAGTTTTGATGGTCGGTCGTGTT

Basic information

species Arabidopsis thaliana
transcript AT1G64650.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G64650.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os03g02380.2 (Oryza sativa), 3'ss of exon 2
gtcagcatttcttcttc--tgaattatacttcacctattgtttgtttggatcttcttcaatgactctgtaacttactctcttaattagGGGTCGCAAGAGAGCTTCTATCACCTACTGTATCACCTACATTCTCAGCTGTATCACCAAACATTCTCCCCAGTACAAAGTTTTGATGGTCGGTCGTGTT
     | ||||||||||   || ||   || |   | |      ||  |  |  |    |         ||    || | |   | |||||  | ||||| || |  ||||||||||| |||| |||||| |||||||| |||||||| || || ||| |||||||  |  | ||| |||| || || 
--gtacgtttcttcttcatcgatttcctctccgattgtcacagattgtgccccgcgctgagactgacagaaaaatctgtgtgtttcagGGGGAGGAAGAGGGCGTGCATCACCTACTGCATCAGCTACATCCTCAGCTGCATCACCAAGCACTCCCCCGAGTACAAGATCCTCATGATCGGCCGCGTG

upper sequence: AT1G64650.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G067638_T01 (Zea mays), 3'ss of exon 2
-------gtcagcatttcttcttctgaattatacttcacctattg---tttgtttggat--cttcttcaatgactctgtaacttactctcttaattagGGGTCGCAAGAGAGCTTCTATCACCTACTGTATCACCTACATTCTCAGCTGTATCACCAAACATTCTCCCCAGTACAAAGTTTTGATGGTCGGTCGTGTT
       |    |   ||  | |  |   |  | |    | |||    | ||||| | |   | |  | | ||  |||     |  || | |  | ||||| || ||||| || | | |||| ||||| ||||||||||| |||||||| |||||||| || |||||||||||||||||| | ||| | || ||||| 
gtgcgttgcgccctcctccgccttgggggtgaattcagtcgatttcgttctgttttggtggatacggcgacgaggctgatggattttc-cgtggtcagGGGGCGGAAGAGGGCGTGTGTCACGTACTGCATCACCTACATCCTCAGCTGCATCACCAAGCACTCTCCCCAGTACAAAGTTCTTATGATTGGGCGTGTC

upper sequence: AT1G64650.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G077669_T01 (Zea mays), 3'ss of exon 2
----gtcagcatttcttcttctgaattatacttcacctattgtttgtttggatcttcttcaatgactctg-taacttactctcttaattagGGGTCGCAAGAGAGCTTCTATCACCTACTGTATCACCTACATTCTCAGCTGTATCACCAAACATTCTCCCCAGTACAAAGTTTTGATGGTCGGTCGTGTT
    | | ||   |    |||     | ||| |   | | |     |   |  |  ||       | |||   | |    ||       || || |||||||| || |  ||||||||||| |||| |||||| |||||||| |||||||| || || ||| ||||||  ||  | ||| |||| ||  | 
gtacgcccgcccctgccattccttcctttacgtattccaatcccgatccagtgcgcctctcgcctccctgacgaatcgtgcttccctccagAGGCCGCAAGAGGGCCTGCATCACCTACTGCATCAGCTACATCCTCAGCTGCATCACCAAGCACTCCCCCGAGTACAGGGTCCTCATGATCGGCCGCATC

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|86062549|gb|DR358306.1|DR358306
EST:     GGATCTTCCATGTTGTTTGGCACCATTGTTGGATCTCTTGCCGACAAACA                         GGGTCGCAAGAGAGCTTCTATCACCTATTGTATCACCTACATTCTCAGCTG
genomic: GGATCTTCCATGTTGTTTGGCACCATTGTTGGATCTCTTGCCGACAAACAgtcagcattt ... tcttaattagGGGTCGCAAGAGAGCTTCTATCACCTACTGTATCACCTACATTCTCAGCTG
EST: gi|86062544|gb|DR358301.1|DR358301
EST:     GGATCTTCCATGTTGTTTGGCACCATTGTTGGATCTCTTGCCGACAAACA                         GGGTCGCAAGAGAGCTTCTATCACNTATTGTATCACSTASATTCTCAGCTG
genomic: GGATCTTCCATGTTGTTTGGCACCATTGTTGGATCTCTTGCCGACAAACAgtcagcattt ... tcttaattagGGGTCGCAAGAGAGCTTCTATCACCTACTGTATCACCTACATTCTCAGCTG
EST: gi|163974400|gb|ES175130.1|ES175130
EST:     ACCATTGTTGGATCTCTTGCCGACAAACA                         GGGTCGCAAGAGAGCTTCTATCACCTACTGTATCACCTACATTCTCAGCTG
genomic: ACCATTGTTGGATCTCTTGCCGACAAACAgtcagcattt ... tcttaattagGGGTCGCAAGAGAGCTTCTATCACCTACTGTATCACCTACATTCTCAGCTG
EST: gi|86051061|gb|DR346816.1|DR346816
EST:     GGATCTTCCATGTTGTTTGGCACCATTGTTGGATCTCTTGCCGACAAACA                         GGGTCGCAAGAGAGCTTCTATCACCTATTGTATCACCTACATTCTCAGCTG
genomic: GGATCTTCCATGTTGTTTGGCACCATTGTTGGATCTCTTGCCGACAAACAgtcagcattt ... tcttaattagGGGTCGCAAGAGAGCTTCTATCACCTACTGTATCACCTACATTCTCAGCTG
EST: gi|86062548|gb|DR358305.1|DR358305
EST:     GGATCTTCCATGTTGTTTGGCACCATTGTTGGATCTCTTGCCGACAAACA                         GGGTCGCAAGAGAGCTTCTATCACCTATTGTATCACCTACATTCTCAGCTG
genomic: GGATCTTCCATGTTGTTTGGCACCATTGTTGGATCTCTTGCCGACAAACAgtcagcattt ... tcttaattagGGGTCGCAAGAGAGCTTCTATCACCTACTGTATCACCTACATTCTCAGCTG
EST: gi|19876555|gb|AU237386.1|AU237386
EST:     GGATCTTCCATGTTGTTTGGCACCATTGTTGGATCTCTTGCCGACAAACA                         GGGTCGCAAGAGAGCTTCTATCACCTACTGTATCACCTACATTCTCAGCTG
genomic: GGATCTTCCATGTTGTTTGGCACCATTGTTGGATCTCTTGCCGACAAACAgtcagcattt ... tcttaattagGGGTCGCAAGAGAGCTTCTATCACCTACTGTATCACCTACATTCTCAGCTG
EST: gi|125000617|gb|EL072886.1|EL072886
EST:     CTTCCATGTTGTTTGGCACCATTGTTGGATCTCTTGCCGACAAACA                         GGGTCGCAAGAGAGCTTCTATCACCTACTGTATCACCTACATT
genomic: CTTCCATGTTGTTTGGCACCATTGTTGGATCTCTTGCCGACAAACAgtcagcattt ... tcttaattagGGGTCGCAAGAGAGCTTCTATCACCTACTGTATCACCTACATT
EST: gi|116485730|gb|EG528322.1|EG528322
EST:     GGATCTTCCATGTTGTTTGGCACCATTGTTGGATCTCTTGCCGACAAACA                         GGGTCGCAAGAGAGCTTCTATCACCTACTGTATCACCTACATTCTCAGCTG
genomic: GGATCTTCCATGTTGTTTGGCACCATTGTTGGATCTCTTGCCGACAAACAgtcagcattt ... tcttaattagGGGTCGCAAGAGAGCTTCTATCACCTACTGTATCACCTACATTCTCAGCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctattgtttgtttggatcttcttcaatgactctgtaacttactctcttaattagGGGTCGCAAGAGAGCTTCTATCACCTACTGTATCACCTACATTCTCAGCTGTATCACCAAACATTCTCCCCAGTACAAAGTTTTGATGGTCGGTCGTGTT
                                    aacttac  putative branch site (score: 2)
                                      cttactctctt  CT-rich tract
                                             tcttaatta  TA-rich tract