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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatccctcaagaattcacattactaaaacattagcaagaccagtgaactggagagaatccagaacttgactctcttttttccctgactaaaatttttagGTCTTTGGTGCTCTGGCAATAGCAAAAATGCTATCTGTACCAATAGTAATGTCTTACCACACACACGTCCCTGT

Basic information

species Arabidopsis thaliana
transcript AT5G01220.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G01220.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G117153_T01 (Zea mays), 3'ss of exon 4
gtaaatccctcaagaattcacattactaaaacattagcaagaccagtgaactggagagaatccagaacttgactctcttttttccctgactaaaatttttagGTCTTTGGTGCTCTGGCAATAGCAAAAATGCTATCTGTACCAATAGTAATGTCTTACCACACACACGTCCCTGT
                      | |  ||  ||| | |   |  | |  |||      |||   |   ||| ||  ||  || || |   | |   ||  ||||  | ||||||||||| ||||| |||||| |||| || |||||| | |||||||| ||||||||  | || | 
---------------------gtaatcaatgcat-acccgaagtattatactacttcaaat---gtttttgccttgctcattaccttatgtga---ttacagGTTCTCGGTGCTCTGGCTATAGCTAAAATGATATCGGTTCCAATATTGATGTCTTATCACACACATCTTCCAGC
















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|116409173|gb|EG451765.1|EG451765
EST:     TTGCACGGTTTAAGCCTGACATTATACGCGCTTCATCTCCCGGAGTTATG                         GTCTTTGGTGCTCTGGCAATAGCAAAAATGCTATCTGTACCAATAGTAATG
genomic: TTGCACGGTTTAAGCCTGACATTATACACGCTTCATCTCCCGGAGTTATGgtaaatccct ... aaatttttagGTCTTTGGTGCTCTGGCAATAGCAAAAATGCTATCTGTACCAATAGTAATG
EST: gi|116431123|gb|EG473715.1|EG473715
EST:     CATCTCCCGGAGTTATG                         GTCTTTGGTGCTCTGGCAATAGCAAAAATGCTATCTGTACCAATAGTAATG
genomic: CATCTCCCGGAGTTATGgtaaatccct ... aaatttttagGTCTTTGGTGCTCTGGCAATAGCAAAAATGCTATCTGTACCAATAGTAATG
EST: gi|86057508|gb|DR353265.1|DR353265
EST:     TTGCACGGTTTAAGCCTGACATTATACACGCTTCATCTCCCGGAGTTATG                         GTCTTTGGTGCTCTGGCAATAGCAAAAATGCTATCTGTACCAATAGTAATG
genomic: TTGCACGGTTTAAGCCTGACATTATACACGCTTCATCTCCCGGAGTTATGgtaaatccct ... aaatttttagGTCTTTGGTGCTCTGGCAATAGCAAAAATGCTATCTGTACCAATAGTAATG
EST: gi|116409166|gb|EG451758.1|EG451758
EST:     TTGCACGGTTTAAGCCTGACATTATACGCGCTTCATCTCCCGGAGTTATG                         GTCTTTGGTGCTCTGGCAATAGCAAAAATGCTATCTGTACCAATAGTAATG
genomic: TTGCACGGTTTAAGCCTGACATTATACACGCTTCATCTCCCGGAGTTATGgtaaatccct ... aaatttttagGTCTTTGGTGCTCTGGCAATAGCAAAAATGCTATCTGTACCAATAGTAATG
EST: gi|116409154|gb|EG451746.1|EG451746
EST:     TTGCACGGTTTAAGCCTGACATTATACGCGCTTCATCTCCCGGAGTTATG                         GTCTTTGGTGCTCTGGCAATAGCAAAAATGCGATCTGTACCAATAGTAATG
genomic: TTGCACGGTTTAAGCCTGACATTATACACGCTTCATCTCCCGGAGTTATGgtaaatccct ... aaatttttagGTCTTTGGTGCTCTGGCAATAGCAAAAATGCTATCTGTACCAATAGTAATG
EST: gi|116409155|gb|EG451747.1|EG451747
EST:     TTGCACGGTTTAAGCCTGACATTATACGCGCTTCATCTCCCGGAGTTATG                         GTCTTTGGTGCTCTGGCAATAGCAAAAATGCGATCTGTACCAATAGTAATG
genomic: TTGCACGGTTTAAGCCTGACATTATACACGCTTCATCTCCCGGAGTTATGgtaaatccct ... aaatttttagGTCTTTGGTGCTCTGGCAATAGCAAAAATGCTATCTGTACCAATAGTAATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaactggagagaatccagaacttgactctcttttttccctgactaaaatttttagGTCTTTGGTGCTCTGGCAATAGCAAAAATGCTATCTGTACCAATAGTAATGTCTTACCACACACACGTCCCTGT
                                        gactaaa  putative branch site (score: 2)
                                                ttttt  CT-rich tract
                                       tgactaaaattttta  TA-rich tract