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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggccatgagaccaattcctctgtctagagttcaaaccagcttatccatatgactgtttataccacaaatattctttgagttgtcctctgaaatagctggtgttacatttttccagCTTGCAGATGTATGGTCTTGCGGTGTAACATTATATGTAATGTTGGTTGGAGCTTATCCATTCGAGGATCCACAGGAGCCACGAGATTATCGAAAGACAA

Basic information

species Arabidopsis thaliana
transcript AT3G50500.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G50500.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: PP1S218_59V6.1 (Physcomitrella patens), 3'ss of exon 6
----------------------------------gtaa---ggccatgagaccaattcctctgtctagagttcaaaccagcttatccatatgactgtttataccacaaatattctttgagttgtcctctgaaatagctggtgttacatttt-tccagCTTGCAGATGTATGGTCTTGCGGTGTAACATTATATGTAATGTTGGTTGGAGCTTATCCATTCGAGGATCCACAGGAGCCACGAGATTATCGAAAGACAA
                                   |||   ||   |  ||| ||| |   | ||  | |   ||   |   |||   |      | | |    |||| |   |      |||||  || ||   |||| | |  | |  | | ||| |||||||||| |||||||||||||| || || || || |||||||||||||| ||||| |||||||||||  | || ||| |  |||   | || || |
gtaagtttttcggaagcgtgttggttttagtggaataaattggttcttggac-aatgctattatcatgcgg--aactgaagctatttttggtgtcggtgaggttacaagtgcacggctctttgtcagctaaagaggctgatttgccgtgatatacagATTGCAGATGTGTGGTCTTGCGGTGTTACCTTGTACGTGATGTTGGTTGGAGCATATCCTTTCGAGGATCCTGAAGACCCAAGGAATTTCAGGAAAACCA

upper sequence: AT3G50500.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: PP1S116_98V6.1 (Physcomitrella patens), 3'ss of exon 6
-------------gtaaggccatgagacc--aattcctctgtctagagttcaaaccagctt---atccatatgactgtttataccacaaatattctttgagttgtcctctgaaatagctggtg----ttacatttttc------cagCTTGCAGATGTATGGTCTTGCGGTGTAACATTATATGTAATGTTGGTTGGAGCTTATCCATTCGAGGATCCACAGGAGCCACGAGATTATCGAAAGACAA
               ||||   |  ||||  ||    |  |  |    ||||      |||   |   |    | ||| |        | ||   ||  ||    | | |     | |||  |      || |  |||      ||| |||| ||||| ||||| |||||||| || || || || |||||||| ||||| || ||||||||||||||  | || ||| |  |||   | || || |
gtacgtggtttgcacaagggtttttgaccgcaaggattggggtttcgcttcatgatgtctttctactgaatcaagtgtgttagtgtttactaaagttcaaggcaccttatcggggaactgaaggaacccacttgcttcgagatgcagATTGCGGATGTGTGGTCGTGCGGTGTGACCTTGTACGTCATGTTGGTGGGAGCATACCCATTCGAGGATCCCTATGACCCAAGGAATTTCAGGAAAACCA
















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|124768642|gb|EH858772.1|EH858772
EST:     ATTGCACCAGAGATTCTTCTTCGACAGGAATATGATGGCAAG                         CTTGCAGATGTATGGTCTTGCGGTGTAACATTATATGTAATGTTGGTTGG
genomic: ATTGCACCAGAGATTCTTCTTCGACAGGAATATGATGGCAAGgtaaggccat ... atttttccagCTTGCAGATGTATGGTCTTGCGGTGTAACATTATATGTAATGTTGGTTGG
EST: gi|116422506|gb|EG465098.1|EG465098
EST:     CTGCATACATTGCACCAGAGATTCTTCTTCGACAGGAATATGATGGCAAG                         CTTGCAGATGTATGGTCTTGCGGTGTAACATTATATGTAATGTTGGTTGGA
genomic: CTGCATACATTGCACCAGAGATTCTTCTTCGACAGGAATATGATGGCAAGgtaaggccat ... atttttccagCTTGCAGATGTATGGTCTTGCGGTGTAACATTATATGTAATGTTGGTTGGA
EST: gi|124912723|gb|EH986714.1|EH986714
EST:     CTGCATACATTGCACCAGAGATTCTTCTTCGACAGGAATATGATGGCAAG                         CTTGCAGATGTATGGTCTTGCGGTGTAACATTA
genomic: CTGCATACATTGCACCAGAGATTCTTCTTCGACAGGAATATGATGGCAAGgtaaggccat ... atttttccagCTTGCAGATGTATGGTCTTGCGGTGTAACATTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

accacaaatattctttgagttgtcctctgaaatagctggtgttacatttttccagCTTGCAGATGTATGGTCTTGCGGTGTAACATTATATGTAATGTTGGTTGGAGCTTATCCATTCGAGGATCCACAGGAGCCACGAGATTATCGAAAGACAA
                                            catttttcc  CT-rich tract
     aaatattcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaggccatgagaccaattcctctgtctagagttcaaaccagcttatccatatgactgtttataccacaaatattctttgagttgtcctctgaaatagctggtgttacatttttccagCTTGCAGATGTATGGTCTTGCGGTGTAACATTATATGTAATGTTGGTTGGAGCTTATCCATTCGAGGATCCACAGGAGCCACGAGATTATCGAAAGACAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT