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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttatctgctgcctgtgcgtctcttcttcttcttatcccgtaccattctgatttggatcttttaaattgactgcttaactgtttcacacagACCGATGCATTCTTCAAAACAAGTGTTCCAGATGTTTACGCTGTTGGTGACGTTGCTACTTTCCCTTTGAAAATGTACGGAGACGTGAGAAGGGTCGAGC

Basic information

species Arabidopsis thaliana
transcript AT3G52880.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G52880.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G134708_T01 (Zea mays), 3'ss of exon 8
gtatttatctgctgcctgtgcgtctcttct-------------tcttcttatcccg-taccattctgatttggatcttttaaattgactgcttaactgtttcacacagACCGATGCATTCTTCAAAACAAGTGTTCCAGATGTTTACGCTGTTGGTGACGTTGCTACTTTCCCTTTGAAAATGTACGGAGACGTGAGAAGGGTCGAGC
   |   |   || | ||    |||  ||              | |||   || || |    |||||  |     ||  ||   ||    | |   ||||     |||||||||||||||||| ||||||||||  | |  || |||||  | || ||||| || || |||||| ||||  | |||   ||   ||| || || ||||
--gtcagttcacttcttgcttttcttctcaaaaaaagaagaaatgttcgagtctcgatgagcttctgtgtcttgcctgatattgtgctaacgtttttgttatgt-cagACCGATGCATTCTTCGAAACAAGTGTAGCCGGGGTATACGCGATCGGCGACGTGGCCACCTTCCCTCTGAAGCTCTACAACGAGCAGAGGAGAGTTGAGC

upper sequence: AT3G52880.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA0169S00210.1 (Glycine max), 3'ss of exon 8
----------------gtatttatctg-----ctgcctgtgcgtctcttcttcttcttatcccgtacc----attctgatttggatcttttaaattgactgc-ttaactgtttca--cacagACCGATGCATTCTTCAAAACAAGTGTTCCAGATGTTTACGCTGTTGGTGACGTTGCTACTTTCCCTTTGAAAATGTACGGAGACGTGAGAAGGGTCGAGC
                    ||||| |      ||       |        | || |||||||    |    ||  |||||    || |  |  |  |       |  |||||      ||||||||||| ||||||||||| | | || | ||||| || ||||||||||| ||||||||||||||||||||| | ||||| ||  ||||||| || || |
gtcagtgataccatatccgattatccggaggcttgttaacaggctataaaatgttgttatcccaagtcgggaatagtgattcttgtcatcaatgtcaatgatgccatttgttttggttgcagACCGATGCTTTCTTCAAAACTAATCTTTCCGATGTATATGCTGTTGGTGATGTTGCTACTTTCCCTTTGAAATTATACGGTGAATTGAGAAGAGTTGAAC

upper sequence: AT3G52880.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA10G07820.1 (Glycine max), 3'ss of exon 8
------------gtatttatctgctgcctgtgcgtctcttct-tcttcttatcccgtacc----attctgatttggatcttttaaattgactgct--taactgtttca--cacagACCGATGCATTCTTCAAAACAAGTGTTCCAGATGTTTACGCTGTTGGTGACGTTGCTACTTTCCCTTTGAAAATGTACGGAGACGTGAGAAGGGTCGAGC
             ||| |    |||   ||   | || |    | || | |||| |        ||  |||||    |  |  ||  | | || |   |  |||||      ||||||||||| ||||||||||| | | |  | ||||| || ||||||||||| ||||||||||||||||||||| | ||||| ||  ||||||| || || |
gtcagtgataccatatctggaggcttgttgacaggctataaaatgttgtcatccggagtagtgaatagtgattcttgttatcaaatatcaatgatgccatttgttttggttgcagACCGATGCTTTCTTCAAAACTAATCTCTCCGATGTATATGCTGTTGGTGATGTTGCTACTTTCCCTTTGAAATTATACGGTGAATTGAGAAGAGTTGAAC

upper sequence: AT3G52880.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv08s0007g03610.t01 (Vitis vinifera), 3'ss of exon 8
--------gtatttatctgctgcctgtgcgtctcttcttcttcttatcccgtaccattctgatttggatcttttaaattgactgcttaactgtttcacacagACCGATGCATTCTTCAAAACAAGTGTTCCAGATGTTTACGCTGTTGGTGACGTTGCTACTTTCCCTTTGAAAATGTACGGAGACGTGAGAAGGGTCGAGC
          | | ||  | |     |   | |       ||  | ||  | |      |  |||| |   || |  |   |    | |   ||     ||||| |||| ||||||||||||||||||||| ||||| || ||||| || || ||||||||||||||  ||||| |||||   ||  | ||||| || || |
gtcgtcccaaaataatgagttatacatatctatagctagtttgatgtcttggatagcatt--tttgaaaacttgaggtcatcactctgatctttgactgcagACTGATGAATTCTTCAAAACAAGTGTTCCTGATGTATATGCTGTGGGAGATGTTGCTACTTTCCCACTGAAATTGTACAATGAAATTAGAAGAGTTGAAC

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|124931203|gb|EL008581.1|EL008581
EST:     TGACATCCTTATTCAAGGGACAGGTCGAGGAAGATAAAGGTGGAATTAAG                         ACCGATGCATTCTTCAAAACAAGTGTTCCAG
genomic: TGACATCCTTATTCAAGGGACAGGTCGAGGAAGATAAAGGTGGAATTAAGgtatttatct ... tttcacacagACCGATGCATTCTTCAAAACAAGTGTTCCAG
EST: gi|47828341|gb|CK118025.1|CK118025
EST:     TGACATCCTTATTCAAGGGACAGGTCGAGGAAGATAAAGGTGGAATTAAG                         ACCGATGCATTCTTCAAAACAAGTGTTCCAGATGTTTACGCTGTTGGTGAC
genomic: TGACATCCTTATTCAAGGGACAGGTCGAGGAAGATAAAGGTGGAATTAAGgtatttatct ... tttcacacagACCGATGCATTCTTCAAAACAAGTGTTCCAGATGTTTACGCTGTTGGTGAC
EST: gi|164238115|gb|ES059181.1|ES059181
EST:     TGACATCCTTATTCAAGGGACAGGTCGAGGAAGATAAAGGTGGAATTAAG                         ACCGATGCATTC
genomic: TGACATCCTTATTCAAGGGACAGGTCGAGGAAGATAAAGGTGGAATTAAGgtatttatct ... tttcacacagACCGATGCATTC
EST: gi|47828077|gb|CK117761.1|CK117761
EST:     TGACATCCTTATTCAAGGGACAGGTCGAGGAAGATAAAGGTGGAATTAAG                         ACCGATGCATTCTTCAAAACAAGTGTTCCAGATGTTTACGCTGTTGGTGAC
genomic: TGACATCCTTATTCAAGGGACAGGTCGAGGAAGATAAAGGTGGAATTAAGgtatttatct ... tttcacacagACCGATGCATTCTTCAAAACAAGTGTTCCAGATGTTTACGCTGTTGGTGAC
EST: gi|125017288|gb|EL089557.1|EL089557
EST:     TCAAGGGACAGGTCGAGGAAGATAAAGGTGGAATTAAG                         ACCGATGCATTCTTCAAAACAAGTGTTCCAGATGTTTACGCTGTTGGTGA
genomic: TCAAGGGACAGGTCGAGGAAGATAAAGGTGGAATTAAGgtatttatct ... tttcacacagACCGATGCATTCTTCAAAACAAGTGTTCCAGATGTTTACGCTGTTGGTGA
EST: gi|125125613|gb|EL171048.1|EL171048
EST:     AAGGTGGAATTAAG                         ACCGATGCATTCTTCAAAACAAGTGTTCCAGATGTTTACGCTGTTGGTGAC
genomic: AAGGTGGAATTAAGgtatttatct ... tttcacacagACCGATGCATTCTTCAAAACAAGTGTTCCAGATGTTTACGCTGTTGGTGAC
EST: gi|47830852|gb|CK120536.1|CK120536
EST:     GTGGAATTAAG                         ACCGATGCATTCTTCAAAACAAGTGTTCCAGATGTTTACGCTGTTGGTGAC
genomic: GTGGAATTAAGgtatttatct ... tttcacacagACCGATGCATTCTTCAAAACAAGTGTTCCAGATGTTTACGCTGTTGGTGAC
EST: gi|125286687|gb|EL300772.1|EL300772
EST:     GTCGAGGAAGATAAAGGTGGAATTAAG                         ACCGATGCATTCTTCAAAACAAGTGTTCCAGATGTTTACGCTGTTGGTGAC
genomic: GTCGAGGAAGATAAAGGTGGAATTAAGgtatttatct ... tttcacacagACCGATGCATTCTTCAAAACAAGTGTTCCAGATGTTTACGCTGTTGGTGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cccgtaccattctgatttggatcttttaaattgactgcttaactgtttcacacagACCGATGCATTCTTCAAAACAAGTGTTCCAGATGTTTACGCTGTTGGTGACGTTGCTACTTTCCCTTTGAAAATGTACGGAGACGTGAGAAGGGTCGAGC
                                    gcttaac  putative branch site (score: 3)
                                          ctgtttc  CT-rich tract
                    atcttttaaattga  TA-rich tract