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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtccaatgctctctctagtatttttgtataattgagatttggtctctaaaagtgtggtttttgtgtctgctcttggtgacagTTGATGGATATCAATGAATCTCCTGTTTATGTGCTTTTAAACCCTGCTATCAATCACACACAGAAGGATCTTCCAGTGACTATTTATGAAAGTG

Basic information

species Arabidopsis thaliana
transcript AT5G56280.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G56280.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os12g42730.4 (Oryza sativa), 3'ss of exon 4
---------gtgagtccaatgc-tctctctagtatttttg-tata-attgagatttggtctctaaaagtgtggtttttgtgtc-tgctcttggtgac-agTTGATGGATATCAATGAATCTCCTGTTTATGTGCTTTTAAACCCTGCTATCAATCACACACAGAAGGATCTTCCAGTGACTATTTATGAAAGTG
          |   || ||||  | ||| |   || | || |||| |||  |||||     ||   |      || ||   |  | || ||  |  | |||||||||||   | || | |  |  ||||| | || || || ||||| || || |   | | ||||||||| |||||||||||||||||||  |
attggaaatatttatcaaatgtatgtctgtgtgatctgtgctatacattttgattttactccttgcatgacatttcttcccttgtactatttttatccagTTGATGGATGCTAGTGGAACAACCTTTTATCTTCTATTCAATCCTGCAATGAACCTTTCCCTGAAGGATCTCCCAGTGACTATTTATGAAAAAG

upper sequence: AT5G56280.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G028089_T01 (Zea mays), 3'ss of exon 2
------------------gtgagtccaatgctctctctagtatttt-tgtataattgagatttggtctctaaaagtgtggtttttgtgtctgctcttggtgacagTTGATGGATATCAATGAATCTCCTGTTTATGTGCTTTTAAACCCTGCTATCAATCACACACAGAAGGATCTTCCAGTGACTATTTATGAAAGTG
                  |  |    |    | | | |  | | |  ||||||  |    ||   |||  | ||   |  |||   ||| |  | |      |||||||||||| | || |||   ||||||||| | || ||||| ||| ||||||| | | | ||||||||||| || |||||||||||||| ||||
agaattgagaaattgtctgccaacatagacatttgtttgatctgtgatgtatatattcatttgactctgcataaccttcttttacttgtatattatc-----cagTTGATGGATGTTAACGAAAGCCCTGTTTATCTTCTATTAAATCCTACTATCAACCTCTCCCAGAAGGATCTCCCTGTGACTATTTATGAGAGTG

upper sequence: AT5G56280.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA04G12890.1 (Glycine max), 3'ss of exon 2
------------gtgagtccaatgctctctctagtatttttgtataattgagatttggtctctaaaagtgtggtttttgtgtctgctcttg--gtgacagTTGATGGATATCAATGAATCTCCTGTTTATGTGCTTTTAAACCCTGCTATCAATCACACACAGAAGGATCTTCCAGTGACTATTTATGAAAGTG
                 | || || | | |  || | |    || | |  || |   |  |||  |  |   | || | | |   |   ||  || ||||||||||||||||||||||  ||| |||||||| ||| | || ||| ||||||||||  | ||||||||||| || || | ||||| ||||||||
ttcatctgaaattctctttcagtgatttattcagaaatcaaatacattcaagttcaagaatctttagtttctgattatatctggacctctgctgtaacagTTGATGGATATCAATGAAAGTCCAGTTTATGTTCTTCTCAATCCTTCTATCAATCATTCTCAGAAGGATCTACCTGTCAGTATTTTTGAAAGTG

upper sequence: AT5G56280.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA06G47850.1 (Glycine max), 3'ss of exon 2
------------gtgagtccaatgctctctctagtatttttgtataattgagatttggtctctaaaagtgtggtttttgtgtctgctcttg--gtgacagTTGATGGATATCAATGAATCTCCTGTTTATGTGCTTTTAAACCCTGCTATCAATCACACACAGAAGGATCTTCCAGTGACTATTTATGAAAGTG
                 |||| || | | |  || | |    || | |  |  |   ||  ||  |  |   | |||| | |   |   ||  || ||||||||||||||||||||||  ||| |||||||| ||| | || ||| ||||||| ||  | ||||||||||| || || | ||||| ||||||||
ttcatctgaaattctcttccagtgatttattcagaagtcgaatacattcaaattcaagttactttagtttctgattttatctggacctctgctgtaacagTTGATGGATATCAATGAAAGTCCAGTTTATGTTCTTCTCAATCCTTCTATCAACCATTCTCAGAAGGATCTACCTGTCAGTATTTTTGAAAGTG

upper sequence: AT5G56280.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv19s0015g01950.t01 (Vitis vinifera), 3'ss of exon 2
-----------gtgagtccaatgctctctctagtatttttgtataattga-gat---ttggtctctaaaagtgtggtttttgtgtctgctcttggtgacagTTGATGGATATCAATGAATCTCCTGTTTATGTGCTTTTAAACCCTGCTATCAATCACACACAGAAGGATCTTCCAGTGACTATTTATGAAAGTG
           |||  | || |||  | | | |  | | | |||     | |||    |  | || ||||   |  |           |||||| | ||||||||||||||| ||||||   ||||| ||||| ||| | || ||  | ||||||||  |||| |||||||| || |||||||| ||||||||||
gcgtgtgttcagtggttacactgccttattttgagtgtctatatggccaatgatgtactattttccaaaaccattataacaaacatcactcttg-taacagTTGATGGATATTAATGAAAGCCCTGTCTATGTTCTTCTCAATCCGTCAATCAATCATGCACAAAAGGATCTCCCTGTGACTATCTATGAAAGTG

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|86054010|gb|DR349767.1|DR349767
EST:     ACTCTACGGGAAGTGATGCTGAGGAATCTGATATGCATATCCATAAAGCT                         TTGATGGATATCAATGAATCTCCTGTTTATGTGCTTTTAAACCCTGCTATC
genomic: ACTCTACGGGAAGTGATGCTGAGGAATCTGATATGCATATCCATAAAGCTgtgagtccaa ... ttggtgacagTTGATGGATATCAATGAATCTCCTGTTTATGTGCTTTTAAACCCTGCTATC
EST: gi|86054007|gb|DR349764.1|DR349764
EST:     ACTCTACGGGAAGTGATGCTGAGGAATCTGATATGCATATCCATAAAGCT                         TTGATGGATATCAATGAATCTCCTGTTTATGTGCTTTTAAACCCTGCTATC
genomic: ACTCTACGGGAAGTGATGCTGAGGAATCTGATATGCATATCCATAAAGCTgtgagtccaa ... ttggtgacagTTGATGGATATCAATGAATCTCCTGTTTATGTGCTTTTAAACCCTGCTATC
EST: gi|19876192|gb|AU237023.1|AU237023
EST:     CTCTACGGGAAGTGATGCTTGAGGAATCTGATATGCATATCCATAAAGCT                         TTGATGGATATCAATGAATCTCCTGTTTATGTGCTTTTAAACCCTGCTATC
genomic: CTCTACGGGAAGTGATGC-TGAGGAATCTGATATGCATATCCATAAAGCTgtgagtccaa ... ttggtgacagTTGATGGATATCAATGAATCTCCTGTTTATGTGCTTTTAAACCCTGCTATC
EST: gi|86054009|gb|DR349766.1|DR349766
EST:     ACTCTACGGGAAGTGATGCTGAGGAATCTGATATGCATATCCATAAAGCT                         TTGATGGATATCAATGAATCTCCTGTTTATGTGCTTTTAAACCCTGCCTAT
genomic: ACTCTACGGGAAGTGATGCTGAGGAATCTGATATGCATATCCATAAAGCTgtgagtccaa ... ttggtgacagTTGATGGATATCAATGAATCTCCTGTTTATGTGCTTTTAAACCCTGC-TAT
EST: gi|86054006|gb|DR349763.1|DR349763
EST:     ACTCTACGGGAAGTGATGCTGAGGAATCTGATATGCATATCCATAAAGCT                         TTGATGGATATCAATGAATCTCCTGTTTATGTGCTTTTAAACCCTGCTATC
genomic: ACTCTACGGGAAGTGATGCTGAGGAATCTGATATGCATATCCATAAAGCTgtgagtccaa ... ttggtgacagTTGATGGATATCAATGAATCTCCTGTTTATGTGCTTTTAAACCCTGCTATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataattgagatttggtctctaaaagtgtggtttttgtgtctgctcttggtgacagTTGATGGATATCAATGAATCTCCTGTTTATGTGCTTTTAAACCCTGCTATCAATCACACACAGAAGGATCTTCCAGTGACTATTTATGAAAGTG
                ctctaaa  putative branch site (score: 3)
                                      tctgctctt  putative PPT
                 tctaaaa  TA-rich tract