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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgatgcatctctttattattcatataccatttgattagagaaaggtttagcttgtggtttatgtactgaggtttgttttctttgcttgccctggtctttggatcatgtgtgttaatacagTTAGTCAATTCACATTATACGGATTCTTGAAAGGTAACAAACCAGATTTTCATGTCGCAATGCCACCTGATAAAGCGAAACCTTTTTACGCCTCTTTAGT

Basic information

species Arabidopsis thaliana
transcript AT4G18460.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G18460.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os01g14040.1 (Oryza sativa), 3'ss of exon 4
gtaatgatgcatctctttattattcatataccatttgattagagaaaggtttagcttgtggtttatgtactgaggtttgttttctttgcttgccctggtctttggatcatgtgtgttaatacagTTAGTCAATTCACATTATACGGATTCTTGAAAGGTAACAAACCAGATTTTCATGTCGCAATGCCACCTGATAAAGCGAAACCTTTTTACGCCTCTTTAGT
           |     || |||  ||| | |||||   |||    || |||         ||  |   |||  ||   |||  | |  ||| |   ||   |        | |  || | |||| |||||||| || ||||| ||| || |||| |||||||| |||||||||||||| || |||||||||| |||||| || || || || || ||||||||
----------gtaggagtaatata-atacagcattt--ctagtcccagatttgaa----aattcttaagctgtagtagctttgttgttattgacaccgttactaagctg-atatactatt-cagTCAGTCAATTTACCTTATATGGAATCCTGAAGGGTAACAAGCCAGATTTTCATGTGGCTATGCCACCTGCTAAAGCAAAGCCATTCTATGCTTCTTTAGT

upper sequence: AT4G18460.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G100260_T03 (Zea mays), 3'ss of exon 4
gtaatgatgcatctctttattattcatataccatttgattagagaaaggtttagcttgtggtttatgtactgaggtttgttt---tct-ttgcttgccctggtctttggatcatgtgtgttaatacagTTAGTCAATTCACATTATACGGATTCTTGAAAGGTAACAAACCAGATTTTCATGTCGCAATGCCACCTGATAAAGCGAAACCTTTTTACGCCTCTTTAGT
                                || |||| |   |    || | | ||||    || ||   ||  |   ||   ||| ||  |  ||      |||    ||||     |  | |||| ||||| ||||| ||||||||  || |||| ||||| || ||||||||||| || || ||| ||||||  ||||||||||| || || || ||| ||||
-----------------------------gtaatatgatgatgcagcctttcaccatgtgtaaaatataaatagcctccattaaatctgttattaaccactacatttctgacatgatgtcttcttcagTCAGTCAGTTCACCTTATACGGCATCCTGAAGGGTAATAAGCCAGATTTTCACGTGGCTATGTCACCTGCAAAAGCGAAACCATTCTATGCTTCTCTAGT

upper sequence: AT4G18460.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv10s0003g00640.t01 (Vitis vinifera), 3'ss of exon 5
gtaatgatgcatctctttatta-ttcatataccatttgattagagaaaggtttagcttgtggtttatgtactgaggtttgttttctttgcttgccctggtctttggatcatgtgtgttaatacagTTAGTCAATTCACATTATACGGATTCTTGAAAGGTAACAAACCAGATTTTCATGTCGCAATGCCACCTGATAAAGCGAAACCTTTTTACGCCTCTTTAGT
          |  |||  |||  ||||  || |||   |  || ||| ||   |     || | ||      |||  | |  || |    ||    || | |||||       ||||   | |||| ||||| || ||||| || ||| | ||||| |||||||| |||||||||||||| |||||||| ||  | ||||| || || ||||| || || || ||
----------agttctaaattgcttcaagtatcatgaaag-agtgaagggagaaa--aatgatatacaagtggag--tggcattttacagttctaatgctgtttgg-------gtgt---ttcagTGAGTCAGTTTACATTGTATGGAATTTTGAAGGGTAACAAGCCAGATTTTCATGTGGCAATGCCGCCCCAAAAAGCAAAGCCCTTTTATGCTTCGTTCGT

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|164074604|gb|ES181453.1|ES181453
EST:     GTAATGCAGAGGAATTATGGAGTTTTACTTG                         TTAGTCAATTCACATTATACGGATT
genomic: GTAATGCAGAGGAATTATGGAGTTTTACTTGgtaatgatgc ... gttaatacagTTAGTCAATTCACATTATACGGATT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgaggtttgttttctttgcttgccctggtctttggatcatgtgtgttaatacagTTAGTCAATTCACATTATACGGATTCTTGAAAGGTAACAAACCAGATTTTCATGTCGCAATGCCACCTGATAAAGCGAAACCTTTTTACGCCTCTTTAGT
                                            tgttaat  putative branch site (score: 3)
      tttgtttt  TA-rich tract