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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatatatataacccatagttatgttgtcgttcttggtttgtatatagctctgataatagaaatactgtttttgattgattgtctagATATGCGATCCTTGGAGATGGTTGTCAGATGGAGGGTATTTCTAATGAAGCTTGCTCTCTAGCTGGCCATTGGGGACTTGGAAAGCTCATTGCTTTCTAC

Basic information

species Arabidopsis thaliana
transcript AT3G60750.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G60750.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os06g04270.1 (Oryza sativa), 3'ss of exon 3
gtaatatatataac-ccatagttatgttgtcgttcttggtttgtatatagc--tctgataatagaaatactgtttttgattgattgtctagATATGCGATCCTTGGAGATGGTTGTCAGATGGAGGGTATTTCTAATGAAGCTTGCTCTCTAGCTGGCCATTGGGGACTTGGAAAGCTCATTGCTTTCTAC
||||| | | |     |||   ||  || | ||| |   |||   ||| |   |   |   | | || |   ||  ||  |  ||||  || ||    ||  | |||||||| || |||||||||||||| || ||||||||||||||  | |||||||||||||| ||||| ||||| ||||| ||||| 
gtaattttttttttatcatgaatacctt-tagttttcactttagttatggtggtgcaaccttggtaacatgattcatggatt-ttgtgcagCTACTGTATTTTGGGAGATGGGTGCCAGATGGAGGGTATCTCCAATGAAGCTTGCTCGTTGGCTGGCCATTGGGGTCTTGGCAAGCTGATTGCATTCTAT

upper sequence: AT3G60750.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G033208_T01 (Zea mays), 3'ss of exon 3
------------gtaat----atatataacccatagttatgttgtcgttcttggtttgtatatagctctgataatagaaatactgtttttgattgat--tgtctagATATGCGATCCTTGGAGATGGTTGTCAGATGGAGGGTATTTCTAATGAAGCTTGCTCTCTAGCTGGCCATTGGGGACTTGGAAAGCTCATTGCTTTCTAC
             |||     |  |  | |   | | | |  |  |  ||||| |||   | |   |   | | |     ||   | |||  | |||  |||  || || |  ||  | |||||||| || || |||||||||||| ||||||||||||||||  | ||||| || ||||| ||||| ||||| ||||||||||||
gtaatacttctaataacgccaacgtgcagcgtctcgcttttattacagtcttgcttttagtctgtgtggcacagttttggtaacatgtttcgtggatcctgtacagGTACGTTATTTTGGGAGATGGCTGCCAAATGGAGGGTATTGCTAATGAAGCTTGCTCCTTGGCTGGACACTGGGGTCTTGGCAAGCTGATTGCTTTCTAC

upper sequence: AT3G60750.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA10G43990.1 (Glycine max), 3'ss of exon 3
--------------------gtaatatatataacccata-gttatgttgtcgttcttggtttgtatatagctctgataatagaaatactgtttttgattgattgtct-----agATATGCGATCCTTGGAGATGGTTGTCAGATGGAGGGTATTTCTAATGAAGCTTGCTCTCTAGCTGGCCATTGGGGACTTGGAAAGCTCATTGCTTTCTAC
                     |  |    ||   |  ||  || || | |   |||||   |   |   | | |    ||   |||  | |||||  ||| ||  ||     |||||||  ||  | || ||||||||||| |||||||| ||||| |||||||| ||||| || || || || ||||| || ||||||||||||||||| || 
gtaggataattgcatcttgttttgttctcattctctctacattgtgatctacgtcttgcaattcctggtgttttacccatgagaattgtttttttctttgttttactcttgtagATATGTTATATTGGGTGATGGTTGTCAAATGGAGGGAATTTCAAATGAAGCATGCTCACTTGCCGGTCACTGGGGTCTAGGAAAGCTCATTGCTTTATAT

upper sequence: AT3G60750.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA03G03200.1 (Glycine max), 3'ss of exon 3
gtaata-tatataacccatagttatgttgtcgttcttggtttgtatatagctctgataatagaaatactgtttttgattgattgtctagATATGCGATCCTTGGAGATGGTTGTCAGATGGAGGGTATTTCTAATGAAGCTTGCTCTCTAGCTGGCCATTGGGGACTTGGAAAGCTCATTGCTTTCTAC
|||| | ||  |||  ||||   |  |||     |||   ||||   | | | || |||| |   |  ||||||          |  || ||||| || || || ||||||||||| |||||||| ||| | |||||||| ||||| || |||||||| |||||||| || ||||| || || || || 
gtaaaaataactaaatcatacacaacttgcaagactttagttgttggt-gttttgctaatggcgtt--tgtttt---------atgcagGTATGCTATTCTGGGTGATGGTTGTCAAATGGAGGGAATTGCAAATGAAGCATGCTCACTTGCTGGCCACTGGGGACTGGGGAAGCTGATAGCATTTTAT

upper sequence: AT3G60750.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA20G38720.1 (Glycine max), 3'ss of exon 3
--------------------gtaatatatataacccata-gttatgttgt-cgttcttggtttgtatatagctctgataatagaaatactgtttttgattgattgtct-----agATATGCGATCCTTGGAGATGGTTGTCAGATGGAGGGTATTTCTAATGAAGCTTGCTCTCTAGCTGGCCATTGGGGACTTGGAAAGCTCATTGCTTTCTAC
                     |  | |  ||   |  ||  || || | |  || ||||   |   |   | | |   | |   |||  | |||||  ||| ||  ||     |||||||  ||  | || ||||||||||| |||||||| ||||| |||||||| ||||| || || || || ||||| || || ||||| |||||||| || 
gtaggataactaaatcttgttttgttttcattctctctacattgtgatctatgtacttgcaattcctggtgttttaccagtgagaattgtttttttctttgttttactcttgtagATATGTTATATTGGGTGATGGTTGTCAAATGGAGGGAATTTCAAATGAAGCATGCTCACTTGCCGGTCACTGGGGTCTAGGGAAGCTTATTGCTTTATAT

upper sequence: AT3G60750.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv15s0048g00370.t01 (Vitis vinifera), 3'ss of exon 3
gtaatatatataacccatagttatgttgtcgttct-tggtttgtatatagctctgata-atagaaatactgtt------tttgattgattg-------------tctagATATGCGATCCTTGGAGATGGTTGTCAGATGGAGGGTATTTCTAATGAAGCTTGCTCTCTAGCTGGCCATTGGGGACTTGGAAAGCTCATTGCTTTCTAC
|||| | |  | | | |  ||| |  |||  |||  || | | || |||| ||||| |  ||   || || ||      ||||  | ||||               |||||| | ||| || || ||||||||||| ||||||||| || |  |||||||||| || || ||||| |||||||| ||||| ||||| || ||||| || 
gtaa-acagcttatcaaatgttgttgtgtttttcagtgctctttagatagatctgaaatgtacgtatgctcttatattgtttggctcattggtattggcatttccttagATACGTGATACTGGGGGATGGTTGTCAAATGGAGGGTGTTGCACATGAAGCTTGTTCACTTGCTGGACATTGGGGTCTTGGGAAGCTGATAGCTTTGTAT

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|86072919|gb|DR368676.1|DR368676
EST:     TTGGCTGCTAGATTCAACAAACCTGATGCTGAAGTAGTCGACCGCTGCAC                         ATATGCGATCCTTGGAGATGGTTGTCAGATGGAGGGTATTTCTAATGAAGC
genomic: TTGGCTGCTAGATTCAACAAACCTGATGCTGAAGTAGTCGACCACTACACgtaatatata ... gattgtctagATATGCGATCCTTGGAGATGGTTGTCAGATGGAGGGTATTTCTAATGAAGC
EST: gi|124948576|gb|EL024314.1|EL024314
EST:     TTGGCTGCTAGATTCAACAAACCTGATGCTGAAGTAGTCGACCACTACAC                         ATATGCGATCCTTGGA
genomic: TTGGCTGCTAGATTCAACAAACCTGATGCTGAAGTAGTCGACCACTACACgtaatatata ... gattgtctagATATGCGATCCTTGGA
EST: gi|124741668|gb|EH832830.1|EH832830
EST:     CAACAAACCTGATGCTGAAGTAGTCGACCACTACAC                         ATATGCGATCCTTGGAGATGGTTGTCAG
genomic: CAACAAACCTGATGCTGAAGTAGTCGACCACTACACgtaatatata ... gattgtctagATATGCGATCCTTGGAGATGGTTGTCAG
EST: gi|125083405|gb|EL143976.1|EL143976
EST:     TTGGCTGCTAGATTCAACAAACCTGATGCTGAAGTAGTCGACCACTACAC                         ATATGCGATCCTTGGAGATGGTTGTCAGATGGAGG
genomic: TTGGCTGCTAGATTCAACAAACCTGATGCTGAAGTAGTCGACCACTACACgtaatatata ... gattgtctagATATGCGATCCTTGGAGATGGTTGTCAGATGGAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttggtttgtatatagctctgataatagaaatactgtttttgattgattgtctagATATGCGATCCTTGGAGATGGTTGTCAGATGGAGGGTATTTCTAATGAAGCTTGCTCTCTAGCTGGCCATTGGGGACTTGGAAAGCTCATTGCTTTCTAC
                                         gattgat  putative branch site (score: 4)
                   tgataatagaaata  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatatatataacccatagttatgttgtcgttcttggtttgtatatagctctgataatagaaatactgtttttgattgattgtctagATATGCGATCCTTGGAGATGGTTGTCAGATGGAGGGTATTTCTAATGAAGCTTGCTCTCTAGCTGGCCATTGGGGACTTGGAAAGCTCATTGCTTTCTAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA