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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtaaggtcttattgatttgtataaggaatgtaaatggacatagctaatgaaatgaaattcaaaatcactgtgacagGCACTCCTGGAGACTGGAGTCACATCATAAAGCAGATTGGTATGTTTACCTTCACAGGGTTAAACCCAGCTCAAGTCTCCTTCATGACTAAAGAGTACCA

Basic information

species Arabidopsis thaliana
transcript AT5G11520.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G11520.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os01g55540.2 (Oryza sativa), 3'ss of exon 10
---------------------gtaagtaaggtct-tattgatttgtataaggaatgtaaatggacatagctaatgaaatgaaattcaaaatcactgtgacagGCACTCCTGGAGACTGGAGTCACATCATAAAGCAGATTGGTATGTTTACCTTCACAGGGTTAAACCCAGCTCAAGTCTCCTTCATGACTAAAGAGTACCA
                      | | |    ||| ||| | |     | ||| |  |     || |||  |||| |      |    | | ||   || |||  |||||||||||||||||||||||||| |||||||| || ||||| || ||||| ||| | |||   | ||||||  | |||||||   | || |||||
aggagtttttcttccctttttctgaatccattctctatggctaaaagtgaggtacattgtcagaaata-ttaatcattgttgacatgataacatcatg-cagAAACTCCTGGAGACTGGAGTCACATCATTAAGCAGATCGGAATGTTCACTTTCACTGGGCTCAACAGTGATCAAGTGGCTTTCATGAGGCAGGAATACCA
















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|301502679|gb|HO208219.1|HO208219
EST:     TCGTATCATCAGCATGAGGAAACAGCTTTTCGAGGCATTACGTACTCGAG                         GCACTCCTGGAGACTGGAGTCACATCATAAAGCAGATTGGTATGTTTACCT
genomic: TCGTATCATCAGCATGAGGAAACAGCTTTTCGAGGCATTACGTACTCGAGgtaagtaagg ... actgtgacagGCACTCCTGGAGACTGGAGTCACATCATAAAGCAGATTGGTATGTTTACCT
EST: gi|125203929|gb|EL218883.1|EL218883
EST:     AACAGCTTTTCGAGGCATTACGTACTCGAG                         GCACTCCTGGAGACTGGAGTCACATCATAAAGCAGATTGGTAT
genomic: AACAGCTTTTCGAGGCATTACGTACTCGAGgtaagtaagg ... actgtgacagGCACTCCTGGAGACTGGAGTCACATCATAAAGCAGATTGGTAT
EST: gi|125122710|gb|EL169168.1|EL169168
EST:     TTTCGAGGCATTACGTACTCGAG                         GCACTCCTGGAGACTGGAGTCACATCATAAAGCAGATTGGTATGTTTACCT
genomic: TTTCGAGGCATTACGTACTCGAGgtaagtaagg ... actgtgacagGCACTCCTGGAGACTGGAGTCACATCATAAAGCAGATTGGTATGTTTACCT
EST: gi|125272103|gb|EL286188.1|EL286188
EST:     TCGTATCATCAGCATGAGGAAACAGCTTTTCGAGGCATTACGTACTCGAG                         GCACTCCTGGAGACTGGAGTCACAT
genomic: TCGTATCATCAGCATGAGGAAACAGCTTTTCGAGGCATTACGTACTCGAGgtaagtaagg ... actgtgacagGCACTCCTGGAGACTGGAGTCACAT
EST: gi|124719994|gb|EH811396.1|EH811396
EST:     TGAGGAAACAGCTTTTCGAGGCATTACGTACTCGAG                         GCACTCCTGGAGACTGGAGTCACATCATAAAG
genomic: TGAGGAAACAGCTTTTCGAGGCATTACGTACTCGAGgtaagtaagg ... actgtgacagGCACTCCTGGAGACTGGAGTCACATCATAAAG
EST: gi|86085892|gb|DR381651.1|DR381651
EST:     TCTTATCATCAGCATGAGGAAACAGCTTTTCGAGGCATTACATACTCGAG                         GCACTCYTGGAGACTGGAGTCACATCATAAAGCAGATTGGTATGTTTACCT
genomic: TCGTATCATCAGCATGAGGAAACAGCTTTTCGAGGCATTACGTACTCGAGgtaagtaagg ... actgtgacagGCACTCCTGGAGACTGGAGTCACATCATAAAGCAGATTGGTATGTTTACCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaggaatgtaaatggacatagctaatgaaatgaaattcaaaatcactgtgacagGCACTCCTGGAGACTGGAGTCACATCATAAAGCAGATTGGTATGTTTACCTTCACAGGGTTAAACCCAGCTCAAGTCTCCTTCATGACTAAAGAGTACCA
                    agctaat  putative branch site (score: 3)
                       taatgaaatgaaattc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtaaggtcttattgatttgtataaggaatgtaaatggacatagctaatgaaatgaaattcaaaatcactgtgacagGCACTCCTGGAGACTGGAGTCACATCATAAAGCAGATTGGTATGTTTACCTTCACAGGGTTAAACCCAGCTCAAGTCTCCTTCATGACTAAAGAGTACCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA