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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcttttgttttgaaataagcttatatttgagcgaatcgtacttttcttcattggtttctggctgatcagcaaagtactatcctgttttgatgcatgttttgcttctctgtttcagCTATGGTTTTTATGACGAATGCTTGAGGAAGTACGGAAATGCTAACGTCTGGAAGTATTTTACAGACCTTTTCGATTATCTTCCTCTTACCGCCCTCATA

Basic information

species Arabidopsis thaliana
transcript AT1G10430.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G10430.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G133464_T01 (Zea mays), 3'ss of exon 2
gtaagcttttgttttgaaataagcttatatttgagcgaatcgtacttttcttcattggtttctggctgatcagcaaagtactatcctgttttgatgcatgttttgcttctctgtttcagCTATGGTTTTTATGACGAATGCTTGAGGAAGTACGGAAATGCTAACGTCTGGAAGTATTTTACAGACCTTTTCGATTATCTTCCTCTTACCGCCCTCATA
                    |    || |     | |  ||  | ||    |      ||| | |   ||      ||| | | |      |  |  |   ||   |  | |||||||| ||||| || ||||| |||||||| || || || |||||||| || ||||||||||||||||||||| | || |||| | | ||||| || || || |||
------------------ggacctgtacaccgctgtgtttccaagttactctgtgaactttgtagtgtatgcctgtagtgcaaccacacagttgttgac-cttgattggtttgtttcagATATGGCTTCTATGATGAATGCTTAAGAAAATATGGAAATGCAAATGTCTGGAAGTATTTTACAGACTTGTTTGATTTTTTGCCTCTCACAGCTCTTATA

upper sequence: AT1G10430.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G038195_T01 (Zea mays), 3'ss of exon 2
gtaagcttttgttttgaaataagcttatatttgagcgaatcgtacttttcttcattggtttctggctg-atcagcaaagtactatcctgttttgatgcatgttttgcttctctgtttcagCTATGGTTTTTATGACGAATGCTTGAGGAAGTACGGAAATGCTAACGTCTGGAAGTATTTTACAGACCTTTTCGATTATCTTCCTCTTACCGCCCTCATA
       | |||||      |||||  | | ||| |   | ||| | |    |  | ||    |  || | || || |||  | |   || | ||       ||   |  | |||||||| || || || ||||| |||||||| || || || |||||||| || || |||||||||||||||||| | || |||||| | ||||| || || || |||
-------tatgtttc----caagctattctgtgaact--ttgtagtctatgcctgtagtgcaagtgtgcaacaacacagt--tgttgagtgtcgac-----cttgattgttttgtttcagGTACGGCTTCTATGATGAATGCTTAAGAAAATATGGAAATGCAAATGTATGGAAGTATTTTACAGACTTGTTTGATTATTTGCCTCTCACAGCTCTTATA

upper sequence: AT1G10430.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA08G40490.1 (Glycine max), 3'ss of exon 2
gtaagcttttgttttgaaata-agcttatatttgagcgaatcgtacttttcttcattggtttctggctgatcagcaaagtactatcctgttttgatgcatgttttgcttctctgtttcagCTATGGTTTTTATGACGAATGCTTGAGGAAGTACGGAAATGCTAACGTCTGGAAGTATTTTACAGACCTTTTCGATTATCTTCCTCTTACCGCCCTCATA
                ||||| |   | | ||| | |    |  ||   | ||  ||   ||       ||      | | || |  | |||  ||  ||  ||| | |     |||||| ||||| || ||||| ||||||||||| || || |||||||| || |||||||| || ||||||||| | || |||||| | ||||| || |||||||| 
----------------aaatagaaaatctctttaaacactacaaacaagtttttttttaattaaaa---attgttttattgctgtgttatttc-atctatcctttacctactgctttcagGTATGGCTTCTATGATGAATGCTTGAGAAAATATGGAAATGCCAATGTCTGGAAATACTTTACAGACTTGTTTGATTATTTACCTCTGACTGCCCTCATT

upper sequence: AT1G10430.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA18G17100.1 (Glycine max), 3'ss of exon 2
gtaagcttttgttttgaaataagcttatatttgagcgaatcg-tacttttcttcattggtttctggctgatcagcaaagtactatcctgttttgatgcatgttttgcttctctgtttcagCTATGGTTTTTATGACGAATGCTTGAGGAAGTACGGAAATGCTAACGTCTGGAAGTATTTTACAGACCTTTTCGATTATCTTCCTCTTACCGCCCTCATA
            ||| ||        | |    |   || |  |  |||| || |||   |  ||  | ||        | || |    ||| |||  ||  ||| | |     |||||| ||||| || ||||| ||||||||||| || || |||||||| || |||||||| || ||||||||| | || |||||| | ||||| || |||||||| 
-----------ctttaaacacgataaacaggataaaaaaccaatgttttttttaattaaataatgttttat--------tgctgtgtcattt-gatctatcctttaccttctgctttcagGTATGGCTTCTATGATGAATGCTTGAGAAAATATGGAAATGCGAATGTCTGGAAATACTTTACAGACTTGTTTGATTATTTGCCTCTGACTGCCCTCATT

upper sequence: AT1G10430.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA02G02990.1 (Glycine max), 3'ss of exon 2
gtaagcttttgttttgaaataagcttatatttgagcgaatcgtacttttcttcattggtttctggctgatcagcaaagtactatcctgttttgatgcatgttttgcttctctgtttcagCTATGGTTTTTATGACGAATGCTTGAGGAAGTACGGAAATGCTAACGTCTGGAAGTATTTTACAGACCTTTTCGATTATCTTCCTCTTACCGCCCTCATA
         | |||  | | |||  | |    |      |  || |||  |  |    | | |   | ||        | ||  ||| |||   |  ||  ||  | |     |||||| ||||| || ||||||||||||||||| ||||| |||||||| || |||||||| |  || || ||| | || |||||| | ||||| || ||||| || 
--------ctctttgaacacaagaat-tgcaaggaattttaatattttattctaagaatgttttatttatt-------tgcttacctctttgtctatatccttcacctgc---tttcagGTATGGCTTCTATGACGAATGCTTGAGAAAGTATGGAAATGCCAATGTCTGGAAATTCTTCACCGACTTGTTTGATTATTTACCTCTGACTGCCCTTATT

upper sequence: AT1G10430.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv01s0026g01080.t01 (Vitis vinifera), 3'ss of exon 2
gtaagcttttgttttgaaataagcttatatttgagcgaatcgtacttttcttcattggtttctggctgatcagcaaagtactatcctgttttgatgcatgttttgcttctctgtttcagCTATGGTTTTTATGACGAATGCTTGAGGAAGTACGGAAATGCTAACGTCTGGAAGTATTTTACAGACCTTTTCGATTATCTTCCTCTTACCGCCCTCATA
                 || | | |||   |     | || | |  ||  ||| |||  |  ||| | ||   || | |         ||||  |   |  |||    ||||  ||||| |||||||||||||||||||||||||| || || |||||||| || ||||||||||||||||| |||||||| |||||||| || ||||| |||||||| 
----------------gaaaatgattactatcatttgtataggaacttcattctttg--tattggtt-atttccatactcaaccttcattttatttgtttctttttccctcttattcagGTATGGTTTTTATGACGAATGCTTGAGAAAATATGGAAATGCCAATGTCTGGAAGTATTTTACCGACCTTTTTGATTATCTACCCCTTACAGCCCTCATT

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|116455547|gb|EG498139.1|EG498139
EST:     AGATTACTCAAGT                         CTGTGGTTTTTATGACGAATGCTTGAGGAAGTACGGAAATGCTAACGTCTG
genomic: AGATTACTCAAGTgtaagctttt ... tctgtttcagCTATGGTTTTTATGACGAATGCTTGAGGAAGTACGGAAATGCTAACGTCTG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctgatcagcaaagtactatcctgttttgatgcatgttttgcttctctgtttcagCTATGGTTTTTATGACGAATGCTTGAGGAAGTACGGAAATGCTAACGTCTGGAAGTATTTTACAGACCTTTTCGATTATCTTCCTCTTACCGCCCTCATA
                        ttttgat  putative branch site (score: 4)
                                    ttttgcttctctgttt  putative PPT
                        ttttgat  TA-rich tract