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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttttacttcttctgttcacgcatttcttttttcgacatgtcgtagtaaaatcgttgataccaaactgaaaatattgcagACAAACAATCTTCTTGCTCCTATCATCACACATGGTATATACTCAGCCGTTGTATTGGGTAATGGTCTCTGGAAACTACACCATCATCAGCAAAGACTCC

Basic information

species Arabidopsis thaliana
transcript AT4G17840.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G17840.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv02s0012g01220.t01 (Vitis vinifera), 3'ss of exon 8
-------------------gtttttacttcttctgttcacgcatttcttttttcgacatgtcg-----tagtaaaatc-gttgataccaaactgaaaatattg-cagACAAACAATCTTCTTGCTCCTATCATCACACATGGTATATACTCAGCCGTTGTATTGGGTAATGGTCTCTGGAAACTACACCATCATCAGCAAAGACTCC
                    ||| |  || ||    | ||   |  |||      | |  |||     |  |||| |  | ||  |     ||||    | || |||||||| ||| |||||||||| ||||||||||| |||||||||||  | ||| || ||||  | || || |||||  | ||| | || |    |||||| |
gtaaccctggttacctactctttgtgattattaaactaactgctggcttaacgtcagagatcgaaacctgataaattttgctgtaatttttctgatgcaaatgtcagACAAATAATATTCTTGCTCCCATCATCACACACGGTATATACTCCACTGTTATACTGGGACACGGCCTTTGGAAGATTCACGACCACCGCAGAAGACTGC
















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|86080454|gb|DR376211.1|DR376211
EST:     CTCTTCTTGAAGGGCTTTTGGGTCTATACCTCGGCTTTGAATGGATTCAG                         ACAAACAATCTTCTTGCTCCTATCATCACACATGGTATATACTCAGCCGTT
genomic: CTCTTCTTGAAGGGCTTTTGGGTCTATACCTCGGCTTTGAATGGATTCAGgtttttactt ... aatattgcagACAAACAATCTTCTTGCTCCTATCATCACACATGGTATATACTCAGCCGTT
EST: gi|116444842|gb|EG487434.1|EG487434
EST:     CTCTTCTTGAAGGGCTTTTGGGTCTATACCTCGGCTTTGAATGGATTCAG                         ACAAACAATCTTCTTGCTCCTATCATCACACATGGTATATACTCAGCCGTT
genomic: CTCTTCTTGAAGGGCTTTTGGGTCTATACCTCGGCTTTGAATGGATTCAGgtttttactt ... aatattgcagACAAACAATCTTCTTGCTCCTATCATCACACATGGTATATACTCAGCCGTT
EST: gi|19799440|gb|AU230730.1|AU230730
EST:     CTCTTCTTGAAGGGCTTTTGGGTCTATACCTCGGCTTTGAATGGATTCAG                         ACAAACAATCTTCTTGCTCCTATCATCACACATGGTATATAGCTCAGCCGT
genomic: CTCTTCTTGAAGGGCTTTTGGGTCTATACCTCGGCTTTGAATGGATTCAGgtttttactt ... aatattgcagACAAACAATCTTCTTGCTCCTATCATCACACATGGTATATA-CTCAGCCGT
EST: gi|116444840|gb|EG487432.1|EG487432
EST:     CTCTTCTTGAAGGGCTTTTGGGTCTATACCTCGGCTTTGAATGGATTCAG                         ACAAACAATCTTCTTGCTCCTATCATCACACATGGTATATACTCAGCCGTT
genomic: CTCTTCTTGAAGGGCTTTTGGGTCTATACCTCGGCTTTGAATGGATTCAGgtttttactt ... aatattgcagACAAACAATCTTCTTGCTCCTATCATCACACATGGTATATACTCAGCCGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttttttcgacatgtcgtagtaaaatcgttgataccaaactgaaaatattgcagACAAACAATCTTCTTGCTCCTATCATCACACATGGTATATACTCAGCCGTTGTATTGGGTAATGGTCTCTGGAAACTACACCATCATCAGCAAAGACTCC
                           cgttgat  putative branch site (score: 5)
                                     aaactgaaaatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttttacttcttctgttcacgcatttcttttttcgacatgtcgtagtaaaatcgttgataccaaactgaaaatattgcagACAAACAATCTTCTTGCTCCTATCATCACACATGGTATATACTCAGCCGTTGTATTGGGTAATGGTCTCTGGAAACTACACCATCATCAGCAAAGACTCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG