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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtcaagtttggagttggaaatatagcttgagtttcttgttacctttttgctgagacctctttttatcttaagGTTATCAAGAGAAGTTTTATTTCAATCCTGGAGATACTGGCTTTAAG

Basic information

species Arabidopsis thaliana
transcript AT2G27450.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G27450.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os02g33080.2 (Oryza sativa), 3'ss of exon 3
-------gtgagtcaagtttggagttgga--aatatagcttgagtttcttgttacct--ttttgctgag--acctctttttatctta---agGTTATCAAGAGAAGTTTTATTTCAATCCTGGAGATACTGGCTTTAAG
           ||  |||||      |    | |||||  | |||       || ||  |||     ||  | || |||   | ||    ||||||||||||||| ||||||||||||||||| || || ||||| |||
gtattgcccatgtatagtttatgacagattcactatagact-agtcatggactatctgatttaaacaagttagctatttcctttttggctagGTTATCAAGAGAAATTTTATTTCAATCCTGGTGACACCGGCTTCAAG

upper sequence: AT2G27450.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G073950_T01 (Zea mays), 3'ss of exon 4
gtgagtcaagtttggagttggaaatatagcttgagtttcttgttacctttttgctgagacctctttttatcttaagGTTATCAAGAGAAGTTTTATTTCAATCCTGGAGATACTGGCTTTAAG
|| ||   | |  |   ||     | |  | |   ||    |||| ||  |   | |  || ||| |  |  | ||| ||||||||||||||||||||||| || || || ||||||||||||
gtaaggtcaataggcttttcctgttctgccatacattgg--gttatctcatctataaagccgcttctgtttgtcagGATATCAAGAGAAGTTTTATTTCAACCCCGGTGACACTGGCTTTAAG
















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|125216416|gb|EL230499.1|EL230499
EST:     ATTCCTGATGGACCTG                         GTTATCAAGAGAAG-TTTATTTCAATCCTGGAGATACTGGCTTTAAG
genomic: ATTCCTGATGGACCTGgtgagtcaag ... ttatcttaagGTTATCAAGAGAAGTTTTATTTCAATCCTGGAGATACTGGCTTTAAG
EST: gi|125210028|gb|EL224982.1|EL224982
EST:     TGGAACTGACTTGGGAATTTATAGGAAGTCTCATATTCCTGATGGACCTG                         GTTATCAAGAGAAGTTTTATTTCAATCCTGGAGATACTGGCTTT
genomic: TGGAACTGACTTGGGAATTTATAGGAAGTCTCATATTCCTGATGGACCTGgtgagtcaag ... ttatcttaagGTTATCAAGAGAAGTTTTATTTCAATCCTGGAGATACTGGCTTT
EST: gi|125159389|gb|EL187494.1|EL187494
EST:     TAGGAAGTCTCATATTCCTGATGGACCTG                         GTTATCAAGAGAAGTTTTATTTCAATCCTGGAGATACTGGCTTTTAAGG
genomic: TAGGAAGTCTCATATTCCTGATGGACCTGgtgagtcaag ... ttatcttaagGTTATCAAGAGAAGTTTTATTTCAATCCTGGAGATACTGGCTTT-AAGG
EST: gi|125037175|gb|EL109444.1|EL109444
EST:     TATTCCTGATGGACCTG                         GTTATCAAGAGAAGTTTTATTTCAATCCTGGAGATACTGGCTTTAAG
genomic: TATTCCTGATGGACCTGgtgagtcaag ... ttatcttaagGTTATCAAGAGAAGTTTTATTTCAATCCTGGAGATACTGGCTTTAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaatatagcttgagtttcttgttacctttttgctgagacctctttttatcttaagGTTATCAAGAGAAGTTTTATTTCAATCCTGGAGATACTGGCTTTAAG
                                      cctctttttatctt  CT-rich tract
                                        tctttttatcttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtcaagtttggagttggaaatatagcttgagtttcttgttacctttttgctgagacctctttttatcttaagGTTATCAAGAGAAGTTTTATTTCAATCCTGGAGATACTGGCTTTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT