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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaactaactaacttaaactgttcttttgtgggactcaccattctttttggtttgggaatgctaaaattgttgtgttcgttgttcctacagTGTTCTTGGGGAAGCAAGCCAACTCCAGCAGGAACAGCTTCAAACCCGCTTCCTCCACCAGCTCCTGCACCAATCCCGGGATTCTCAGCGAGTGATCTCT

Basic information

species Arabidopsis thaliana
transcript AT1G17370.2
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G17370.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: LOC_Os11g40510.2 (Oryza sativa), 3'ss of exon 11
gtaaaac-taactaacttaaactgttcttttgtgg----gactcaccattctttttggtttgggaatgcta--aaattgttgtgttcgttgttcctacagTGTTCTTGGGGAAGCAAGCCAACTCCAGCAGGAACAGCTTCAAACCCGCTTCCTCCACCAGCTCCTGCACCAATC---CCGGGATTCTCAGCGAGTGATCTCT
| ||    |   |      |  | || |  |  ||    ||   |   |  || | | | | | ||| |    ||| | |  | ||  |  | | | |||||||| ||||||||||||||||||||| |||| ||||| ||    || || || || ||||| || |||||| ||   || ||  | || ||||  || |   
gcaagttatgttttcaccgagtttttatcgtaaggagaggatgtagtctagttatggttcttgcaattcagctaaactttaatcttgttcctacttgcagTGTTCCTGGGGAAGCAAGCCAACTCCACCAGGGACAGCATCCGCGCCCCTACCCCCTCCAGCACCAGCACCATTCAATCCTGGCATGTCGGCGACCGACC---

upper sequence: AT1G17370.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: Vv09s0002g00880.t01 (Vitis vinifera), 3'ss of exon 11
------gtaaaactaactaacttaa--actgttcttttgtgggactcaccattcttt-ttggtttgggaatgctaaaattgttgtgttcgttgttcctacagTGTTCTTGGGGAAGCAAGCCAACTCCAGCAGGAACAGCTTCAAACCCGCTTCCTCCACCAGCTCCTGCACCAATCCCGGGATTCTCAGCGAGTGATCTCT
       | |||  ||   |   |   ||  || ||   |   | |    ||    | |||| |||   ||    ||  || |   ||   || |  |  |||| || ||||| ||||||||||||||| ||||||||  ||||||||| || || ||||| ||  |||||||  | || ||  | ||||| |  || ||| 
tctgtgatgaaagcaatacatcgatccaccttttttccataatattggtgatctaatgttggattgaccata--gaatatgcttccttttatgctgttgtagTGCTCATGGGGTAGCAAGCCAACTCCACCAGGAACAAGTTCAAACCCACTCCCCCCACCTGCAGCTGCACCTCTGCCAGGTCTTTCAGCCACGGACCTCC
















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|163975430|gb|ES022466.1|ES022466
EST:     CTATTCAGATGGGAAACACACATTCCTACCTTAGTGGCAGGCAAATGAAG                         TGTTCTTGGGGAAGCAAGCCAACTCCAGCAGG
genomic: CTATTCAGATGGGAAACACACATTCCTACCTTAGTGGCAGGCAAATGAAGgtaaaactaa ... gttcctacagTGTTCTTGGGGAAGCAAGCCAACTCCAGCAGG
EST: gi|124784149|gb|EH873913.1|EH873913
EST:     ATTCCTACCTTAGTGGCAGGCAAATGAAG                         TGTTCTTGGGGAAGCAAGCCAACTCCAGCAGGAACAGCTTCAAACCCGCTT
genomic: ATTCCTACCTTAGTGGCAGGCAAATGAAGgtaaaactaa ... gttcctacagTGTTCTTGGGGAAGCAAGCCAACTCCAGCAGGAACAGCTTCAAACCCGCTT
EST: gi|125305517|gb|EL319602.1|EL319602
EST:     CTATTCAGATGGGAAACACACATTCCTACCTTAGTGGCAGGCAAATGAAG                         TGTTCTTGGGGAAGCAAGCCAACTCCAG
genomic: CTATTCAGATGGGAAACACACATTCCTACCTTAGTGGCAGGCAAATGAAGgtaaaactaa ... gttcctacagTGTTCTTGGGGAAGCAAGCCAACTCCAG
EST: gi|164221781|gb|ES147385.1|ES147385
EST:     TTCCTACCTTAGTGGCAGGCAAATGAAG                         TGTTCTTGGGGAAGCAAGCCAACTCCAGCAGGAACAGCTTCAAACCCGCT-
genomic: TTCCTACCTTAGTGGCAGGCAAATGAAGgtaaaactaa ... gttcctacagTGTTCTTGGGGAAGCAAGCCAACTCCAGCAGGAACAGCTTCAAACCCGCTT
EST: gi|163996643|gb|ES055971.1|ES055971
EST:     TATTCAGATGGGAAACAACACATTCCTACCTTAGTGGCAGGCAAATGAAG                         TGTTCTTGGGGAAGCAAGCCAAC
genomic: TATTCAGATGGGAAAC-ACACATTCCTACCTTAGTGGCAGGCAAATGAAGgtaaaactaa ... gttcctacagTGTTCTTGGGGAAGCAAGCCAAC
EST: gi|125044329|gb|EL116598.1|EL116598
EST:     CTATTCAGATGGGAAACACACATTCCTACCTTAGTGGCAGGCAAATGAAG                         TGTTCTTGGGGAAGCAAG
genomic: CTATTCAGATGGGAAACACACATTCCTACCTTAGTGGCAGGCAAATGAAGgtaaaactaa ... gttcctacagTGTTCTTGGGGAAGCAAG
EST: gi|124837223|gb|EH921662.1|EH921662
EST:     CTATTCAGATGGGAAACACACATTCCTACCTTAGTGGCAGGCAAATGAAG                         TGTTCTTGGGGAAGCAAGCCAACTCCAGC
genomic: CTATTCAGATGGGAAACACACATTCCTACCTTAGTGGCAGGCAAATGAAGgtaaaactaa ... gttcctacagTGTTCTTGGGGAAGCAAGCCAACTCCAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caccattctttttggtttgggaatgctaaaattgttgtgttcgttgttcctacagTGTTCTTGGGGAAGCAAGCCAACTCCAGCAGGAACAGCTTCAAACCCGCTTCCTCCACCAGCTCCTGCACCAATCCCGGGATTCTCAGCGAGTGATCTCT
                       tgctaaa  putative branch site (score: 2)
                                           ttgttcct  putative PPT
                          taaaattgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaactaactaacttaaactgttcttttgtgggactcaccattctttttggtttgggaatgctaaaattgttgtgttcgttgttcctacagTGTTCTTGGGGAAGCAAGCCAACTCCAGCAGGAACAGCTTCAAACCCGCTTCCTCCACCAGCTCCTGCACCAATCCCGGGATTCTCAGCGAGTGATCTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC