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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTTCTAGATGGTATCGTACAGCTGACCGAAAAAGATGAATGTGCATATCAGGAGATGATAGCCCATCTGCCTTTATGCTCTATATCTTCCCCTAAAAATgtaatttctcaccttaaaaagtttagtctctctggtttcctatatcttgtagcctgttgcaataaatcagtcaatctaaaagtatgttcaatttgtgatg...

Basic information

species Arabidopsis thaliana
transcript AT5G53120.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G53120.4 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: LOC_Os06g33710.1 (Oryza sativa), 5'ss of exon 5
TGTTCTAGATGGTATCGTACAGCTGACCGAAAAAGATGAATGTGCATATCAGGAGATGATAGCCCATCTGCCTTTATGCTCTATATCTTCCCCTAAAAATgta-atttctcaccttaaaaagttta-gtctctctggtttcctatatcttgtagcctgttgcaataaatcagtcaatctaaaagtatgttcaatttgtgatg
 || || |||||||| || |||||||||||||| |||||||||||||| ||||| ||| |  | || || ||  | ||||| ||  | ||||| |||| ||||  ||||| | |||    |    |  | | |          | ||  || |   | |||||||  |  | |   | | | | |||        | || | 
GGTGCTTGATGGTATTGTGCAGCTGACCGAAAAGGATGAATGTGCATACCAGGAAATGGTTACTCACCTTCCACTGTGCTCGATTCCATCCCCCAAAAGTgtatgtttcttatctttgccataccatatgtttgcaaacctgaaaataatgaaagattttgcaatgcaa-aatgtttgttagattattccagtactatgtt-

upper sequence: AT5G53120.4 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: Vv16s0050g02670.t01 (Vitis vinifera), 5'ss of exon 5
TGTTCTAGATGGTATCGTACAGCTGACCGAAAAAGATGAATGTGCATATCAGGAGATGATAGCCCATCTGCCTTTATGCTCTATATCTTCCCCTAAAAATgtaatttctc-accttaaaaagtttagtctctctggtttcctatatcttgtagcctgttgcaataaatca-gtcaatctaa-aagtatgttcaatttgtgatg
||| || ||||| || || ||| ||| ||| |||||||||||||| |||||||||||||| || || || ||  | || || ||    ||||| || |  |||||||| | |  |  ||   ||     | | |    |  | |   |  |  ||| |||   |  || |  ||  ||| | ||  || || ||||||     
TGTGCTTGATGGCATTGTTCAGTTGAGCGAGAAAGATGAATGTGCCTATCAGGAGATGATTGCTCACCTTCCCCTTTGTTCAATTGAATCCCCCAAGAGAgtaatttcactatttccaagcattggagttttattccatgttgtcaatgttctccttttgacttggattatatctttctcacaaccatttttaatttgcc---
















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|47829276|gb|CK118960.1|CK118960
EST:     AGGAGATGATAGCCCATCTGCCTTTATGCTCTATATCTTCCCCTAAAAAT                         GTTCTTGTTGTTGGTGGAGGTGATGGTGGTGTTCTTCGAGAGATTTCTCGC
genomic: AGGAGATGATAGCCCATCTGCCTTTATGCTCTATATCTTCCCCTAAAAATgtaatttctc ... atatttgcagGTTCTTGTTGTTGGTGGAGGTGATGGTGGTGTTCTTCGAGAGATTTCTCGC
EST: gi|86073008|gb|DR368765.1|DR368765
EST:     AGGAGATGATAGCCCATCTGCCTTTATGCTCTATATCTTCCCCTAAAAAT                         GTTCTTGTTGTTGGTGGAGGTTGATGGTGGTGTTCTTCGAGAGATTTCTCG
genomic: AGGAGATGATAGCCCATCTGCCTTTATGCTCTATATCTTCCCCTAAAAATgtaatttctc ... atatttgcagGTTCTTGTTGTTGGTGGAGGT-GATGGTGGTGTTCTTCGAGAGATTTCTCG
EST: gi|47831735|gb|CK121419.1|CK121419
EST:     AGGAGATGATAGCCCATCTGCCTTTATGCTCTATATCTTCCCCTAAAAAT                         GTTCTTGTTGTTGGTGGAGGTGATGGTGGTGTTCTTCGAGAGATTTCTCGC
genomic: AGGAGATGATAGCCCATCTGCCTTTATGCTCTATATCTTCCCCTAAAAATgtaatttctc ... atatttgcagGTTCTTGTTGTTGGTGGAGGTGATGGTGGTGTTCTTCGAGAGATTTCTCGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTTCTAGATGGTATCGTACAGCTGACCGAAAAAGATGAATGTGCATATCAGGAGATGATAGCCCATCTGCCTTTATGCTCTATATCTTCCCCTAAAAATgtaatttctcaccttaaaaagtttagtctctctggtttcctatatcttgtagcctgttgcaataaatcagtcaatctaaaagtatgttcaatttgtgatg

- - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tctcacct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctctctgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcaataaa