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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaataactcgtagcaccctttttattttcatactcatgatttgaaatctttgtatcattggggtctaattgggtgttgtgtggtagTGTCGTACTCTTTCCTGTAGCTGTTACATTCCTCATCACTTGGTGGTTTATCCAGTTCGTTGATGGTTTCTTCAGTCCGATATACGAGAACCTTGGTGTT

Basic information

species Arabidopsis thaliana
transcript AT1G43130.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G43130.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os05g36110.4 (Oryza sativa), 3'ss of exon 2
gtaaataactcgtagcaccctttttattttcatactcatgatttgaaatctttg--------tatcattggggtctaattgggtgttgtgtggtagTGTCGTACTCTTTCCTGTAGCTGTTACATTCCTCATCACTTGGTGGTTTATCCAGTTCGTTGATGGTTTCTTCAGTCCGATATACGAGAACCTTGGTGTT
|||  |   |   | ||     | ||     || | || ||  | ||   | |         ||| |    | | ||      | |||  | | || || || || || ||||| |||||||||||| ||||||| ||||||||| |  |||| |||||||| || ||||||||  | || |  || |||||  ||
gtatgtttttt-caacaattaatctagacatat-cacaagagctaaagattatatccaagcctattaacctgttttatccctcttttgatttgcagCGTAGTTCTTTTCCCTGTTGCTGTTACATTCTTCATCACCTGGTGGTTTGTTAAGTTTGTTGATGGATTTTTCAGTCCACTGTATGCAAAGCTTGGATTT

upper sequence: AT1G43130.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os01g64780.4 (Oryza sativa), 3'ss of exon 2
gtaaataactcgtagcacccttttta------ttttcatactcatgatttgaaatctttgtatcattggggtctaattgggtgttgtgtggtagTGTCGTACTCTTTCCTGTAGCTGTTACATTCCTCATCACTTGGTGGTTTATCCAGTTCGTTGATGGTTTCTTCAGTCCGATATACGAGAACCTTGGTGTT
||| ||   |   || | ||   |||      ||  || ||  |   |   ||||| | | ||  ||    |    ||   | || | | | || ||||| || |||||||| ||||| || ||| ||||||| ||||||||||| || || |||||||| || ||||| ||  |||| |  || |||||  | 
gtacatctttgacaggaaccaagttaagcatgttaccaaacaaaaagtaaaaaatcat-gcattgttcttcttccctt---tttttttttgcagCGTCGTTCTGTTTCCTGTTGCTGTCACGTTCTTCATCACATGGTGGTTTATTCAATTTGTTGATGGCTTTTTCAGCCCACTATATGCAAAACTTGGGATC

upper sequence: AT1G43130.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G052855_T01 (Zea mays), 3'ss of exon 2
--------------------gtaaataactcgtagcaccctttttattttcatactcatgatttga-aatctttgtatcat-tggggtctaattgggtgttgtgtggtagTGTCGTACTCTTTCCTGTAGCTGTTACATTCCTCATCACTTGGTGGTTTATCCAGTTCGTTGATGGTTTCTTCAGTCCGATATACGAGAACCTTGGTGTT
                     | | ||| ||  ||   | ||   ||    | |   |  || |    ||  |  |||| | |   ||||   |   | || | ||  ||||| || || || ||  | ||||| |||||| |||||||||||||||||||||| || ||||||||||| ||||| ||  | || |  || || ||  ||
gtatgcttcacaagttcacaatgactaattc--agacactttgcaatggctacaactacaatatattgatgctaatatcttcttttgtctccctactttttctttg-cagTGTAGTTCTTTTGCCAATTGCTGTCACATTCTTCATCACTTGGTGGTTTATCCAATTTGTTGATGGTTTTTTCAGCCCACTCTATGCAAAACTGGGGTTT

upper sequence: AT1G43130.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv07s0031g02010.t01 (Vitis vinifera), 3'ss of exon 2
---------gtaaataactcgtagcaccctttttattttcatactcatgatttgaaatctttgtatcattggggtctaattgggtgttgtgtggtagTGTCGTACTCTTTCCTGTAGCTGTTACATTCCTCATCACTTGGTGGTTTATCCAGTTCGTTGATGGTTTCTTCAGTCCGATATACGAGAACCTTGGTGTT
          ||  ||   | ||  |   | |  || ||  |||||||  |||   || ||     |  |    |  | |||  | |    | | ||||| || || ||||| || || ||||||||  |  | || ||||||||||| ||||||||||||||||||||||||||  |||| ||    |||||  | 
gtaatatgcttacctatgccttaatatattctagatgtt--tactcattttttattattttccagcc--taacattgagttgattttgaaattgcagTGTTGTTCTTTTTCCAGTTGCAGTTACATTTTTTGTTACATGGTGGTTTATTCAGTTCGTTGATGGTTTCTTCAGTCCATTATATGAACGGCTTGGCATC

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|164222479|gb|ES110134.1|ES110134
EST:     TGTTATGGGGTTCTACAGAGTTGGGTGTCTAAGAAGTTTATGACTGGATT                         TGTCGTACTCTTTCCTGTAGCTGTTACATTCCTCATCACTTGGTGGTTTAT
genomic: TGTTATGGGGTTCTACAGAGTTGGGTGTCTAAGAAGTTTATGACTGGATTgtaaataact ... tgtgtggtagTGTCGTACTCTTTCCTGTAGCTGTTACATTCCTCATCACTTGGTGGTTTAT
EST: gi|116447062|gb|EG489654.1|EG489654
EST:     TGTTATGGGGTTCTACAGAGTTGGGTGTCTAAGAAGTTTATGACTGGATT                         TGTCGTACTCTTTCCTGTAGCTGTTACATTCCTCATCACTTGGTGGTTTAT
genomic: TGTTATGGGGTTCTACAGAGTTGGGTGTCTAAGAAGTTTATGACTGGATTgtaaataact ... tgtgtggtagTGTCGTACTCTTTCCTGTAGCTGTTACATTCCTCATCACTTGGTGGTTTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actcatgatttgaaatctttgtatcattggggtctaattgggtgttgtgtggtagTGTCGTACTCTTTCCTGTAGCTGTTACATTCCTCATCACTTGGTGGTTTATCCAGTTCGTTGATGGTTTCTTCAGTCCGATATACGAGAACCTTGGTGTT
                               gtctaat  putative branch site (score: 3)
       atttgaaat  TA-rich tract