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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttctgtctaaaaaaccttgctctttaatgcctactacttgaagattttatttatattgcttctattttaagagttctttcctcgttcaaagttattattgctcttaagatgcattggtttcttctcagGTTGCTAGGAAGTTCACTAACAAAGTTGAAGGGAAGATGGGGTATGAGGACTTTGTCTATTTCATTCTTGCGGAAGAAGATAAATCGTCAGTGCCTAGCC

Basic information

species Arabidopsis thaliana
transcript AT5G28900.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G28900.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: PP1S147_62V6.2 (Physcomitrella patens), 3'ss of exon 8
-------------------------------gttctgtctaaaaaaccttgc-------tctttaatgcctactacttgaagattttatttatattgcttctattttaagagttctttcctcgttcaaagttattattgctcttaagatgcattggtttct--------tctcagGTTGCTAGGAAGTTCACTAACAAAGTTGAAGGGAAGATGGGGTATGAGGACTTTGTCTATTTCATTCTTGCGGAAGAAGATAAATCGTCAGTGCCTAGCC
                                |   || |   |||| | ||       |    ||||  |  |  ||||||     ||    | |  |||| | |    | |   |   ||    |||   | || | |      | ||  |  | |  |        | ||||||| | || |||||||| | |||||| || ||||||||||| ||||||||||| || |  ||||||||| | ||||| || || || ||||  |||||| 
gtgcattctaatatccgacttgaatttcaaaatctagtttgggaaacttagcatggatgtaagaaatgtttcatgattgaagtgaagatcatgactatttctgtctagtaattcgctatttcaaagaaaaagaataattcctgagggttggttctgataatgtggtggatttcagGTTCCAAGAAAGTTCACCAGCAAAGTAGAGGGGAAGATGGGTTATGAGGACTTCGTGTGGTTCATTCTTTCAGAAGAGGACAAGTCTTCAGAACCTAGCT

upper sequence: AT5G28900.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: PP1S68_31V6.1 (Physcomitrella patens), 3'ss of exon 8
gttctgtctaaaaaaccttgctctttaatgcctactacttgaagattttatttatattgcttctattttaagagttctttcctcgttcaaagttattattgctcttaagatgcattggtttcttctcagGTTGCTAGGAAGTTCACTAACAAAGTTGAAGGGAAGATGGGGTATGAGGACTTTGTCTATTTCATTCTTGCGGAAGAAGATAAATCGTCAGTGCCTAGCC
                     | |  | ||||| |     |   |  | ||     |||  |   | ||  | ||| | |  |  || |  |      ||||       | |||     |   |   ||||| | |||| ||| |  | |   |||||||| |||||||||||||||||||| || |  || ||  |  | ||||| || || || || | | | ||||
---------------------tttagattgcctgca----ggcaacctaatgcgc-ttgaattagtgttgggcgttttcttttgctttaccg--gacgttgccaacggta-gcaccttgtgaatgatagGTTCCAAGGAGGTTTAGAAGCGGCGTTGAAGGAAAGATGGGGTATGAGGACTTCGTTTGGTTTATATTATCAGAAGAGGACAAGTCATCGGAGACCAGCC
















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|116434984|gb|EG477576.1|EG477576
EST:     ATGGAAACCATGCTCTTACCTACCGGATTGTCGACAGAATATTCTCCCAG                         GTTGCTAGGAAGTTCACTAGCAAAGTTGAAGGGAAGATGGGGTATGAAGAC
genomic: ATGGAAACCATGCTCTTACCTACCGGATTGTCGACAGAATATTCTCCCAGgttctgtcta ... ttcttctcagGTTGCTAGGAAGTTCACTAACAAAGTTGAAGGGAAGATGGGGTATGAGGAC
EST: gi|116435329|gb|EG477921.1|EG477921
EST:     ATGGAAACCATGCTCTTACCTACCGGATTGTCGACAGAATATTCTCCCAG                         GTTGCTAGGAAGTTCACTAGCAAAGTTGAAGGGAAGATGGGGTATGAAGAC
genomic: ATGGAAACCATGCTCTTACCTACCGGATTGTCGACAGAATATTCTCCCAGgttctgtcta ... ttcttctcagGTTGCTAGGAAGTTCACTAACAAAGTTGAAGGGAAGATGGGGTATGAGGAC
EST: gi|125016152|gb|EL088421.1|EL088421
EST:     ATGGAAACCATGCTCTTACCTACCGGATTGTCGACAGAATATTCTCCCAG                         GTTGCTAGGAAGTTCACTAACAA
genomic: ATGGAAACCATGCTCTTACCTACCGGATTGTCGACAGAATATTCTCCCAGgttctgtcta ... ttcttctcagGTTGCTAGGAAGTTCACTAACAA
EST: gi|164038356|gb|EL993532.1|EL993532
EST:     ACCATGCTCTTACCTACCGGATTGTCGACAGAATATTCTCCCAG                         GTTGCTAGGAAGTTCACTAGCAAAGTTGAAGGGAAGATGGGGTATGAAGAC
genomic: ACCATGCTCTTACCTACCGGATTGTCGACAGAATATTCTCCCAGgttctgtcta ... ttcttctcagGTTGCTAGGAAGTTCACTAACAAAGTTGAAGGGAAGATGGGGTATGAGGAC
EST: gi|164209234|gb|ES063761.1|ES063761
EST:     CCGGATTGTCGACAGAATATTCTCCCAG                         GTTGCTAGGAAGTTCACTAGCAAAGTTGAAGGGAAGATGGGGTATGAAGAC
genomic: CCGGATTGTCGACAGAATATTCTCCCAGgttctgtcta ... ttcttctcagGTTGCTAGGAAGTTCACTAACAAAGTTGAAGGGAAGATGGGGTATGAGGAC
EST: gi|116435322|gb|EG477914.1|EG477914
EST:     ATGGAAACCATGCTCTTACCTACCGGATTGTCGACAGAATATTCTCCCAG                         GTTGCTAGGAAGTTCACTAGCAAAGTTGAAGGGAAGATGGGGTATGAAGAC
genomic: ATGGAAACCATGCTCTTACCTACCGGATTGTCGACAGAATATTCTCCCAGgttctgtcta ... ttcttctcagGTTGCTAGGAAGTTCACTAACAAAGTTGAAGGGAAGATGGGGTATGAGGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctttcctcgttcaaagttattattgctcttaagatgcattggtttcttctcagGTTGCTAGGAAGTTCACTAACAAAGTTGAAGGGAAGATGGGGTATGAGGACTTTGTCTATTTCATTCTTGCGGAAGAAGATAAATCGTCAGTGCCTAGCC
                                            tttcttctc  CT-rich tract
           ttcaaagttattatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttctgtctaaaaaaccttgctctttaatgcctactacttgaagattttatttatattgcttctattttaagagttctttcctcgttcaaagttattattgctcttaagatgcattggtttcttctcagGTTGCTAGGAAGTTCACTAACAAAGTTGAAGGGAAGATGGGGTATGAGGACTTTGTCTATTTCATTCTTGCGGAAGAAGATAAATCGTCAGTGCCTAGCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG