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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactgcagttttttcctgcttctcttaactatattttttccccaatagacagaatcatgagtgtggttgttctgaaaacagGTAACTCCATGTGAACATTTCTTTCACTCGGGATGCTTACAGAGATGGATGGATATAAAAATGGAGTGTCCAACTTGTCGGCGGTCTCTTCCTCCAGCAT

Basic information

species Arabidopsis thaliana
transcript AT4G28370.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G28370.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA12G33270.1 (Glycine max), 3'ss of exon 12
----------------gtactgcagttttttcctgc-ttctcttaactatattt----tttccccaatagacagaatcatgagtgt-ggttgttctgaaaacagGTAACTCCATGTGAACATTTCTTTCACTCGGGATGCTTACAGAGATGGATGGATATAAAAATGGAGTGTCCAACTTGTCGGCGGTCTCTTCCTCCAGCAT
                 || |  |  | |  |||   || | | ||||  | ||    ||| |   ||  |   | ||    |    |  ||||    | |||||| || || ||||| |||||||| ||||| || || || || ||||||||||||||||| |||||||| |||||||| |||||  | || || || || |
ggagtgtcaatgtaatttaatctaaatataacctttgttttgtcaactcaaattgaagtttacaatatgaattaagtctaatgcacagactgtt----acacagGTGACACCTTGTGATCATTTCTTCCACTCTGGCTGTTTGCAAAGATGGATGGATATAAAGATGGAGTGCCCAACTTGCCGGCGCCCGCTACCCCCCGCTT

upper sequence: AT4G28370.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA13G37150.1 (Glycine max), 3'ss of exon 13
---------------gtac-tgcagttttttcctgcttctcttaactatattttttccccaatagacagaatcatgagtg-tggttgttctga-aaacagGTAACTCCATGTGAACATTTCTTTCACTCGGGATGCTTACAGAGATGGATGGATATAAAAATGGAGTGTCCAACTTGTCGGCGGTCTCTTCCTCCAGCAT
               || | |  |  | |  |||  || | ||| | |    ||       | |    |||| | |  |  ||      |||  | |||||| || || ||||| |||||||| ||||| || || || || ||||||||||||||||| |||||||| |||||||| |||||  | || || || || |
aagaaaccacaaggagtgcctctaaatataaccttttttttttatcaactcattaaattttacaatatgaattaagtctaatgcacaaactgttacacagGTGACACCTTGTGATCATTTCTTCCACTCTGGCTGTTTGCAAAGATGGATGGATATAAAGATGGAGTGCCCAACTTGCCGGCGCCCACTACCCCCTGCCT

upper sequence: AT4G28370.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA06G44530.1 (Glycine max), 3'ss of exon 13
gtactgcagttttttcctgcttctcttaactatattttttccccaatagacagaatcatgagtgtg----gttgttctgaaaacagGTAACTCCATGTGAACATTTCTTTCACTCGGGATGCTTACAGAGATGGATGGATATAAAAATGGAGTGTCCAACTTGTCGGCGGTCTCTTCCTCCAGCAT
| |    | | |   | || |    | || | ||| ||| |     |  ||| |||| | ||| |     |           |||||| || || ||||| ||||| || ||||| || || || || ||||||||||||||||| |||||||| || ||||| || ||  ||||||| || ||||
gcatgtgaatgtaaccttggtctattcaaatttatctttacaatc-tgaacataatc-taagtctaatacgccaactcttccacagGTGACCCCTTGTGACCATTTTTTCCACTCTGGCTGTTTGCAAAGATGGATGGATATAAAGATGGAGTGCCCTACTTGCCGACGCCCTCTTCCACCTGCAT

upper sequence: AT4G28370.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA12G13220.1 (Glycine max), 3'ss of exon 13
----gt-actgcagttttttcctgcttctcttaactatattttttccccaatagacagaatcatgagtgtggttgttctgaaaacagGTAACTCCATGTGAACATTTCTTTCACTCGGGATGCTTACAGAGATGGATGGATATAAAAATGGAGTGTCCAACTTGTCGGCGGTCTCTTCCTCCAGCAT
    || | || |   |||  ||  |    ||||   |           ||||  |  | ||    |  |  |   |   |   ||||| || || ||||| ||||| || ||||| || || || || ||||||||||||||||| |||||||| || ||||| ||| |  ||||||| || ||||
gcatgtgaatgtaacctttggctattcaaattaatctttacaacctgaaaataacctaagtctaatgcatcatctcttcca---cagGTGACCCCTTGTGATCATTTTTTCCACTCTGGCTGTTTGCAAAGATGGATGGATATAAAGATGGAGTGCCCTACTTGCCGGGGCCCTCTTCCACCTGCAT

upper sequence: AT4G28370.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: Vv12s0028g03410.t01 (Vitis vinifera), 3'ss of exon 13
-----------------gtactgcagttttttcctgcttctcttaactatattttttccccaatagacagaatcatgagtgtggttgttctgaaaacagGTAACTCCATGTGAACATTTCTTTCACTCGGGATGCTTACAGAGATGGATGGATATAAAAATGGAGTGTCCAACTTGTCGGCGGTCTCTTCCTCCAGCAT
                  |  |   ||  |||| || |  | |      |||||  |      | |||   |   | |      || |  |     ||||| || |||||||| ||||| || || || || || ||||| || |||||||||||||||||||| || ||||| || |||||  | || || ||||| |
gtatttattggaagatgtttatcttgtaatttcttgttgatatgggggttatttgctttgtcctggactcgaatctaatcaacattttcttt----cagGTGACGCCATGTGATCATTTTTTCCATTCTGGTTGTTTACAAAGGTGGATGGATATAAAAATGGAATGCCCAACATGCCGGCGTCCACTGCCACCAGCCT

upper sequence: AT4G28370.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: EFJ33128 (Selaginella moellendorffii), 3'ss of exon 12
gtactgcagttttttcctgcttctcttaactatattttttccccaatagacagaatcatgagtgtggttgttctgaaaacagGTAACTCCATGTGAACATTTCTTTCACTCGGGATGCTTACAGAGATGGATGGATATAAAAATGGAGTGTCCAACTTGTCGGCGGTCTCTTCCTCCAGCAT
                                ||     | |    |   |  | ||    |     ||  | |     ||||| || || || || ||| | |||||||| || ||  | ||| |||||||||| || |||||||| |||||||||||||| || ||| | |||||    |
-------------------------------gtaaggcattcaagctctgcgcattctcaggctcacttcgtttctt--cagGTTACGCCTTGCGACCATGTTTTTCACTCTGGCTGTCTCCAGCGATGGATGGACATCAAAATGGAATGTCCAACTTGTCGTCGATCTTTACCTCCGCTGT

upper sequence: AT4G28370.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: EFJ27372 (Selaginella moellendorffii), 3'ss of exon 11
gtactgcagttttttcctgcttctcttaactatattttttccccaatagacagaatcatgagtgtggttgttctgaaaacagGTAACTCCATGTGAACATTTCTTTCACTCGGGATGCTTACAGAGATGGATGGATATAAAAATGGAGTGTCCAACTTGTCGGCGGTCTCTTCCTCCAGCAT
                                ||     | |    |   |  | ||    |  |   | |  |     ||||| || || || || ||| | |||||||| || ||  | ||| |||||||||| || |||||||| |||||||||||||| || ||| | |||||    |
-------------------------------gtaaggcattcaagttctgcgcagtctcaggcttcact-tcgtttcttcagGTTACGCCTTGCGACCATGTTTTTCACTCTGGCTGTCTCCAGCGATGGATGGACATCAAAATGGAATGTCCAACTTGTCGTCGATCTTTACCTCCGCTGT

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|19878061|gb|AU238892.1|AU238892
EST:     TTATCTGCATGACCGCTATTGATCTCAGACAGCATACCAGTGATTGCATG                         GTAACTCCATGTGAACATTTNTTTTCACTCGGGATGCTTACAGAGATGGAT
genomic: TTATCTGCATGACCGCTATTGATCTCAGACAGCATACCAGTGATTGCATGgtactgcagt ... ctgaaaacagGTAACTCCATGTGAACATTTCTTT-CACTCGGGATGCTTACAGAGATGGAT
EST: gi|19798850|gb|AU230140.1|AU230140
EST:     TTATCTGCATGACCGCTATTGATCTCAGACAGCATACCAGTGATTGCAT-                         GTAACTCCATGTGAACATTTCTTTCACTCGGGATGCTTACAGAGATGGATG
genomic: TTATCTGCATGACCGCTATTGATCTCAGACAGCATACCAGTGATTGCATGgtactgcagt ... ctgaaaacagGTAACTCCATGTGAACATTTCTTTCACTCGGGATGCTTACAGAGATGGATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aactatattttttccccaatagacagaatcatgagtgtggttgttctgaaaacagGTAACTCCATGTGAACATTTCTTTCACTCGGGATGCTTACAGAGATGGATGGATATAAAAATGGAGTGTCCAACTTGTCGGCGGTCTCTTCCTCCAGCAT
 tcttaac  putative branch site (score: 2)
                                        ttgttct  putative PPT
     tatttttt  TA-rich tract