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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttactaccatgctgtcttgtgggtttaacaattcatctggtatcctgcttattaatatgttgtttatgtttttcttgtagTCGATATCCTGAAGCTCCTTTTACCAGATCCCTGGAAAGAAATACCGTACTTCAAGAAATTGGATAAATTAGTTGGAGTACCAGTTATTAATGTTCATAT

Basic information

species Arabidopsis thaliana
transcript AT4G14210.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G14210.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA11G36810.1 (Glycine max), 3'ss of exon 8
---------------gtttactaccatgctgtcttgtgggtttaacaattcatctggtatcctgcttattaatatgtt-gtttatgtttttcttg----tagTCGATATCCTGAAGCTCCTTTTACCAGATCCCTGGAAAGAAATACCGTACTTCAAGAAATTGGATAAATTAGTTGGAGTACCAGTTATTAATGTTCATAT
                ||| | |   |  |   |  | | ||| |  |      |  | | |      |||| || || |    | |||||||||     ||| ||||| |||||||| ||| |||||||   ||||||||  || ||||| ||| ||| | ||||||||||||||||||| ||||| || |||||||| ||
gtatttttcttcttattttcccaatgtattaattaattgttttcatgacattcttaatcttc-ataccttaacatttttgaggttctttttcttgaaaacagTGGATATTCTGAAGCTTCTTCTACCAGACAACTGGAAAGGGATTCCGTATTTCCAGAGACTGGATAAATTAGTTGGAGTCCCAGTCATAAATGTTCACAT

upper sequence: AT4G14210.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA18G00720.2 (Glycine max), 3'ss of exon 4
-------------------gtttactaccatgctgtcttgtgggtttaacaattcatctggtatcctgcttattaatatgttgtttatg-tttttcttg----tagTCGATATCCTGAAGCTCCTTTTACCAGATCCCTGGAAAGAAATACCGTACTTCAAGAAATTGGATAAATTAGTTGGAGTACCAGTTATTAATGTTCATAT
                    ||||| |   |  |   |  | | ||| |  |      |  | | |  ||  |||| || || |   |  |||||||||     ||| ||||| |||||||| ||| ||||||||  ||||||||  || || || ||| ||| |||||||||||||||||| || ||||| || |||||||| ||
gtgttttttcttcttcttattttacgaatgtaataattaattgttttcatgacattcttaatcttc-actccttaacattttttaggttctttttcttgaaaacagTGGATATTCTGAAGCTTCTTCTACCAGATAACTGGAAAGGGATTCCATATTTCCAGAGATTGGATAAATTAGTTGGCGTCCCAGTCATAAATGTTCACAT

upper sequence: AT4G14210.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv09s0002g00100.t01 (Vitis vinifera), 3'ss of exon 9
gtttactaccatgctgtcttgtgggtttaacaatt-----catctg-gtatcct--gcttattaatatgttgtttatg---tttttcttg--tagTCGATATCCTGAAGCTCCTTTTACCAGATCCCTGGAAAGAAATACCGTACTTCAAGAAATTGGATAAATTAGTTGGAGTACCAGTTATTAATGTTCATAT
|| | |       || |||  | | ||  ||| ||     ||| ||  || |||  |||| |  || ||||| || ||   ||| | ||    ||| |||||||||||||| ||||| || |    ||||||||| || || ||||||| || ||||||||||||||||||||| ||||| || |||||||||||
gtatgcattttaactctctctttgattgtacatttttcttcatgtgtataacctcagcttctctat-tgttgcttttgaaatttgttttaatcagTTGATATCCTGAAGCTTCTTTTGCCGGGAGACTGGAAAGAGATTCCATACTTCAGGAGATTGGATAAATTAGTTGGAGTTCCAGTGATCAATGTTCATAT

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|86074019|gb|DR369776.1|DR369776
EST:     CACTAATGGAAGCACTGTCGAGGGAGACGCTTATGTGTTTGCCGCTCCAG                         TCGATATCCTGAAGCTCCTTTTACCAGATCCCTGGAAAGAAATACCGTACT
genomic: CACTAATGGAAGCACTGTCGAAGGAGACGCTTATGTGTTTGCCGCTCCAGgtttactacc ... tttcttgtagTCGATATCCTGAAGCTCCTTTTACCAGATCCCTGGAAAGAAATACCGTACT
EST: gi|86074018|gb|DR369775.1|DR369775
EST:     CACTAATGGAAGCACTGTCGAGGGAGACGCTTATGTGTTTGCCGCTCCAG                         TCGATATCCTGAAGCTCCTTTTACCAGATCCCTGGAAAGAAATACCGTACT
genomic: CACTAATGGAAGCACTGTCGAAGGAGACGCTTATGTGTTTGCCGCTCCAGgtttactacc ... tttcttgtagTCGATATCCTGAAGCTCCTTTTACCAGATCCCTGGAAAGAAATACCGTACT
EST: gi|86074021|gb|DR369778.1|DR369778
EST:     CACTAATGGAAGCACTGTCGAGGGAGACGCTTATGTGTTTGCCGCTCCAG                         TCGATATCCTGAAGCTCCTTTTACCAGATCCCTGGAAAGAAATACCGTACT
genomic: CACTAATGGAAGCACTGTCGAAGGAGACGCTTATGTGTTTGCCGCTCCAGgtttactacc ... tttcttgtagTCGATATCCTGAAGCTCCTTTTACCAGATCCCTGGAAAGAAATACCGTACT
EST: gi|124753441|gb|EH843571.1|EH843571
EST:     CACTGTCGAAGGAGACGCTTATGTGTTTGCCGCTCCAG                         TCGATATCCTGAAGCTCCTTTTACCAGATCCCTGGAAAAGAAATACCGTAC
genomic: CACTGTCGAAGGAGACGCTTATGTGTTTGCCGCTCCAGgtttactacc ... tttcttgtagTCGATATCCTGAAGCTCCTTTTACCAGATCCCTGGAAA-GAAATACCGTAC
EST: gi|116473797|gb|EG516389.1|EG516389
EST:     CACTAATGGAAGCACTGTCGAAGGAGACGCTTATGTGTTTGCCGCTCCAG                         TCGATATCCTGAAGCTCCTTTTACCAGATCCCTGGAAAGAAATACCGTACT
genomic: CACTAATGGAAGCACTGTCGAAGGAGACGCTTATGTGTTTGCCGCTCCAGgtttactacc ... tttcttgtagTCGATATCCTGAAGCTCCTTTTACCAGATCCCTGGAAAGAAATACCGTACT
EST: gi|86074020|gb|DR369777.1|DR369777
EST:     CACTAATGGAAGCACTGTCGAGGGAGACGCTTATGTGTTTGCCGCTCCAG                         TCGATATCCTGAAGCTCCTTTTACCAGATCCCTGGAAAGAAATACCGTACT
genomic: CACTAATGGAAGCACTGTCGAAGGAGACGCTTATGTGTTTGCCGCTCCAGgtttactacc ... tttcttgtagTCGATATCCTGAAGCTCCTTTTACCAGATCCCTGGAAAGAAATACCGTACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taacaattcatctggtatcctgcttattaatatgttgtttatgtttttcttgtagTCGATATCCTGAAGCTCCTTTTACCAGATCCCTGGAAAGAAATACCGTACTTCAAGAAATTGGATAAATTAGTTGGAGTACCAGTTATTAATGTTCATAT
                        tattaat  putative branch site (score: 2)
                                     tttatgtttttctt  putative PPT
                       ttattaatatgttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttactaccatgctgtcttgtgggtttaacaattcatctggtatcctgcttattaatatgttgtttatgtttttcttgtagTCGATATCCTGAAGCTCCTTTTACCAGATCCCTGGAAAGAAATACCGTACTTCAAGAAATTGGATAAATTAGTTGGAGTACCAGTTATTAATGTTCATAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG