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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatacactgccttctcgtccacctttaaatatcgcttaaactaattgtactctactcatttgaatttagtgcagtagaggttgaattgtgatgagttttgttcatacagGTACCAAAGAAGGATGTCCAACATCATTGATGATGTCCTTGAGTGGTCACCAAAGCTAGCACTTTCTGGTTTGATGGAGAATCAGCAACCTGTAAACATC

Basic information

species Arabidopsis thaliana
transcript AT3G20920.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G20920.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os02g23890.2 (Oryza sativa), 3'ss of exon 5
-gtatacactgccttctcgtccacctttaaatatcgcttaaactaattgtactctactcatttgaatttagtgcagtagaggttgaattgtgatgagttttgttcatacagGTACCAAAGAAGGATGTCCAACATCATTGATGATGTCCTTGAGTGGTCACCAAAGCTAGCACTTTCTGGTTTGATGGAGAATCAGCAACCTGTAAACATC
 | |   | ||   |   |      |  ||||      ||   |     | || || |||| |    | |||  ||||     | | || |  |   |  ||||  ||  ||||||| |  | | | || ||||| ||||||||||| ||||||||||| |||||| ||||  | |||||  ||||||| || ||          ||    
tgcacggagtgtgctgaagcttgtgtgcaaatga----tatgttctccattctata-tcatattctatcagttgagtaa----tcatttctcttttttcctgttacta--gGTACCAGAAGAAGGTTTCGAACATAATTGATGATGTTCTTGAGTGGTCTCCAAAGTTAGCTTTGTCTGGGATGATGGAAAAACATACTGGGACTAATGCA
















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|125155418|gb|EL185559.1|EL185559
EST:     CTGCTTAGGCGTCATGCCCCTGATGAANCTGCTCGGGCCAG                         GTACCAAAGAAGGATGTCCAACATCATTGATGATGTCCTTGAGTGGTCACC
genomic: CTGCTTAGGCGTCATGCCCCTGATGAAGCTGCTCGGGCCAGgtatacactg ... gttcatacagGTACCAAAGAAGGATGTCCAACATCATTGATGATGTCCTTGAGTGGTCACC
EST: gi|164111878|gb|ES178104.1|ES178104
EST:     CGTCATGCCCCTGATGAAGCTGCTCGGGCCAG                         GTACCAAAGAAGGATGTCCAACATCATTGATGATGTCCTTGAGTGGTCACC
genomic: CGTCATGCCCCTGATGAAGCTGCTCGGGCCAGgtatacactg ... gttcatacagGTACCAAAGAAGGATGTCCAACATCATTGATGATGTCCTTGAGTGGTCACC
EST: gi|47830302|gb|CK119986.1|CK119986
EST:     GTTGTCATGCTGCTTAGGCGTCATGCCCCTGATGAAGCTGCTCGGGCCAG                         GTACCAAAGAAGGATGTCCAACATCATTGATGATGTCCTTGAGTGGTCACC
genomic: GTTGTCATGCTGCTTAGGCGTCATGCCCCTGATGAAGCTGCTCGGGCCAGgtatacactg ... gttcatacagGTACCAAAGAAGGATGTCCAACATCATTGATGATGTCCTTGAGTGGTCACC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcatttgaatttagtgcagtagaggttgaattgtgatgagttttgttcatacagGTACCAAAGAAGGATGTCCAACATCATTGATGATGTCCTTGAGTGGTCACCAAAGCTAGCACTTTCTGGTTTGATGGAGAATCAGCAACCTGTAAACATC
                                         ttttgttc  CT-rich tract
     ttgaattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatacactgccttctcgtccacctttaaatatcgcttaaactaattgtactctactcatttgaatttagtgcagtagaggttgaattgtgatgagttttgttcatacagGTACCAAAGAAGGATGTCCAACATCATTGATGATGTCCTTGAGTGGTCACCAAAGCTAGCACTTTCTGGTTTGATGGAGAATCAGCAACCTGTAAACATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA