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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcctactgtcttaactaaaccagtcctttggttgtttctatttgttccaattgctgatgttgtttgcacttttttattttcaaagGTACGTTGCAACCGCAGTGACATCAGTCCATGAGATGGAGAATGGGTTCACCATATGGTCTTTCAACGGGATTATGCTTTACCGGATATTGAAGGATCAT

Basic information

species Arabidopsis thaliana
transcript AT5G27640.2
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G27640.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA03G00470.1 (Glycine max), 3'ss of exon 9
--------------------------------------------------------------------------------------------------------------gtcctactgtcttaactaaaccagtcctt-tggttgtttc--tatttgttccaattgctgatgttgtttgcacttttttattttcaaagGTACGTTGCAACCGCAGTGACATCAGTCCATGAGATGGAGAATGGGTTCACCATATGGTCTTTCAACGGGATTATGCTTTACCGGATATTGAAGGATCAT
                                                                                                               |  |     ||| ||| ||  ||| ||| | |||| ||   || || | ||||  ||| || ||| || | |||| |     |   || || |||||||| |||||||| ||||| ||||| ||||||||||| ||||  |||||||||||||| || |     || || |||||  |||||||||||
gtatatggtctatctgaatgagtaatgatattgctaataaaggcagttcataggttaatcttttgtaaaatcagtttaaaattgtatttaccttagtcattaagtgtctgatttttgccactttactgaaaaagtgcttattgttggtttgttaattatcccaa--gcttatattgctttctctttata----tggcagATATGTTGCAACTGCAGTGACTTCAGTTCATGAAATGGAGAATGGTTTCAATATATGGTCTTTCAATGGCAAGCATCTATATCGGATTCTGAAGGATCAT

upper sequence: AT5G27640.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA07G14870.1 (Glycine max), 3'ss of exon 9
--------------------------------------------------------------------------------------------------------------gtcctactgtcttaactaaaccagtcctt-tggttg--tttctatttgttccaattgctgatgttgtttgcacttttttattttcaaagGTACGTTGCAACCGCAGTGACATCAGTCCATGAGATGGAGAATGGGTTCACCATATGGTCTTTCAACGGGATTATGCTTTACCGGATATTGAAGGATCAT
                                                                                                               |  |      || ||| ||  ||| ||| ||||||  ||  || || | ||||  ||| || ||| || | |||| |  | |    || || |||||||| || ||||| ||||| ||||| ||||||||||| ||||  |||||||||||||| || |     || || |||||  |||||||||| 
gtatatggtctatctgaatgagtaatgatattgctaataaaggcagtttataggttaatcttttgtaaaatcagtttaaaattgtatttacctttgtcatcatgtgtttgataattgcaattttactgaaaaagtgcttatggttggtttcttaattatcccaa--gcttatattgctttctctttatactgt----agATATGTTGCAACTGCGGTGACTTCAGTTCATGAAATGGAGAATGGTTTCAATATATGGTCTTTCAATGGCAAGCATCTATATCGGATTCTGAAGGATCAC

upper sequence: AT5G27640.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA04G06080.1 (Glycine max), 3'ss of exon 13
---------------------------------------------------------------------------------------------------------------gtcctactgtcttaactaaaccagtcctt-tggttgttt-ctatttgttccaattgctgatgttgtttgcacttttttattttcaaagGTACGTTGCAACCGCAGTGACATCAGTCCATGAGATGGAGAATGGGTTCACCATATGGTCTTTCAACGGGATTATGCTTTACCGGATATTGAAGGATCAT--
                                                                                                               ||  |     ||| ||| ||  ||| ||| |  | ||||  || || | ||||  ||| || ||| || | |||| |      |  ||||| |||||||| || ||||| ||||| ||||| ||||||||||| ||||   ||||||||||||| || |     || || |||||  ||||||||||   
gtatatggtctatctgaatgaataatgatattgctaataaaggcagctcataggttaatcttttgtaaaatcagtctaaaattgtatttaccttagtcatcaaagtgtttggtatttgccacttcactgaaaaagtacttattatggtttgttaattatcccaa--gcttatattgctttctctttatg----ccgcagGTATGTTGCAACTGCTGTGACTTCAGTTCATGAAATGGAGAATGGTTTCA--GTATGGTCTTTCAATGGCAAACATCTATATCGGATTCTGAAGGATCACTT

upper sequence: AT5G27640.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv04s0008g07070.t01 (Vitis vinifera), 3'ss of exon 9
----------------------------------------------------------------------------------gtcctactgtct-taacta-aaccagtcctttggttgtttctatttgttccaattgctgatgttgtttgcacttttttattttcaaagGTACGTTGCAACCGCAGTGACATCAGTCCATGAGATGGAGAATGGGTTCACCATATGGTCTTTCAACGGGATTATGCTTTACCGGATATTGAAGGATCAT
                                                                                   | | | |  || |||  | ||  | |    |  ||  ||||||| | |   ||    | |||  | |  |  | |||   |    ||||| ||||||||  |||| || ||||| ||||||||||| ||||| || | ||||||||| |||||||| |   | || || |||||| | |||||||| 
gtagttttggaagaactattatattgttttgttttctaaatgaaatatcagttatcttacaatatttatcttgtccttaaaaattcgatttcctgtaatcagaaggaatttagtcatttgttctatt-gcttgtatcttggctgtgatatttaactctttgcatctttagGTATGTTGCAACTTCAGTTACTTCAGTTCATGAGATGGAAAATGGCTTTAACATATGGTCCTTCAACGGCAAGCTCCTGTATCGGATACTAAAGGATCAC

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|86060060|gb|DR355817.1|DR355817
EST:     ACAGCTGAACACTTCATGGCCACGGATATCGAATGGGACCCGACTGGAAG                         GTACGTTGCAACCGCAGTGACATCAGTCCATGAGATGGAGAATGGGTTCAC
genomic: ACAGCTGAACACTTCATGGCCACGGATATCGAATGGGACCCGACTGGAAGgtcctactgt ... attttcaaagGTACGTTGCAACCGCAGTGACATCAGTCCATGAGATGGAGAATGGGTTCAC
EST: gi|47832098|gb|CK121782.1|CK121782
EST:     ACAGCTGAACACTTCATGGCCACGGATATCGAATGGGACCCGACTGGAAG                         GTACGTTGCAACCGCAGTGACATCAGTCCATGAGATGGAGAATGGGTTCAC
genomic: ACAGCTGAACACTTCATGGCCACGGATATCGAATGGGACCCGACTGGAAGgtcctactgt ... attttcaaagGTACGTTGCAACCGCAGTGACATCAGTCCATGAGATGGAGAATGGGTTCAC
EST: gi|164009351|gb|EL996264.1|EL996264
EST:     ACAGCTGAACACTTCATGGCCACGGATATCGAATGGGACCCGACTGGAAG                         GTACGTTGCAACCGCAGTGACA
genomic: ACAGCTGAACACTTCATGGCCACGGATATCGAATGGGACCCGACTGGAAGgtcctactgt ... attttcaaagGTACGTTGCAACCGCAGTGACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttgtttctatttgttccaattgctgatgttgtttgcacttttttattttcaaagGTACGTTGCAACCGCAGTGACATCAGTCCATGAGATGGAGAATGGGTTCACCATATGGTCTTTCAACGGGATTATGCTTTACCGGATATTGAAGGATCAT
                     tgctgat  putative branch site (score: 3)
                                    cacttttttattttc  putative PPT
                                     acttttttattttcaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcctactgtcttaactaaaccagtcctttggttgtttctatttgttccaattgctgatgttgtttgcacttttttattttcaaagGTACGTTGCAACCGCAGTGACATCAGTCCATGAGATGGAGAATGGGTTCACCATATGGTCTTTCAACGGGATTATGCTTTACCGGATATTGAAGGATCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG