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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGCTTCAGGAGGTTGTGTTCTATGCAAGAAAATGTGGTATCTGTTGCAACTCCACGCTCGGGCCTGCAAGGAATCCGAGTGTGATGTACCTCGATGCGGgtaatctctttaacttctgtccctgtctaacattttgcaatcgatctcttaacgggatcattcagtatttgccttttctttcaacaagtaaaaacgtaaa...

Basic information

species Arabidopsis thaliana
transcript AT1G16710.2
intron # 17
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G16710.1 (Arabidopsis thaliana), 5'ss of exon 16
lower sequence: LOC_Os02g04490.1 (Oryza sativa), 5'ss of exon 16
GTGCTTCAGGAGGTTGTGTTCTATGCAAGAAAATGTGGTATCTGTTGCAACTCCACGCTCGGGCCTGCAAGGAATCCGAGTGTGATGTACCTCGATGCGGgta-----atctctttaacttctgtccctgtctaacattttgcaatcgatctcttaacgggatcattcagtatttgccttttct-ttcaacaagtaaaaacgtaaa
||||||||||||| |||||||| |||||||||||||||||  || | || ||||| || || || |||| ||| || |  ||  | || ||  ||||| |||       |   | | |||| ||| ||           |||   | |||||   ||    | |  | |  | || |     || | ||  | | |          
GTGCTTCAGGAGGGTGTGTTCTTTGCAAGAAAATGTGGTACATGCTCCAGCTCCATGCCCGAGCTTGCAGGGACTCAGGATGCAACGTGCCGAGATGCAGgtgtgttggtgcttctcacttttgttccgtcaccttgccttgtgcttgatctgg-aataacacc-ctgaccacttacggaaactatacactatgcag---------

upper sequence: AT1G16710.1 (Arabidopsis thaliana), 5'ss of exon 16
lower sequence: GRMZM2G139977_T01 (Zea mays), 5'ss of exon 15
GTGCTTCAGGAGGTTGTGTTCTATGCAAGAAAATGTGGTATCTGTTGCAACTCCACGCTCGGGCCTGCAAGGAATCCGAGTGTGATGTACCTCGATGCGGgtaatctctttaacttctgtccctgtcta---acat------tttgcaatcgatctcttaacgggatcattcagtatttgccttttctttcaacaagtaaaaacgtaaa---
||||||||||||| ||||| || |||||||||||||||||  || | |||||||| || || || |||||||| || || ||  |||| || || ||| |||    | |    | ||      |||  |   ||||      | ||   ||  |    || |     | |     ||   |||  | |  |     |  |||   |  |   
GTGCTTCAGGAGGGTGTGTCCTTTGCAAGAAAATGTGGTACATGCTTCAACTCCATGCCCGAGCTTGCAAGGATTCAGACTGCAATGTGCCGCGGTGCAGgtttgttgtcgtccctcctcttttgtgcacatacatatggtttctgtgttcacttgtatagcattgccgtctgcgatagacctgatttacctgtgtggtaaactatgcacag

upper sequence: AT1G16710.1 (Arabidopsis thaliana), 5'ss of exon 16
lower sequence: GLYMA15G00250.1 (Glycine max), 5'ss of exon 16
GTGCTTCAGGAGGTTGTGTTCTATGCAAGAAAATGTGGTATCTGTTGCAACTCCACGCTCGGGCCTGCAAGGAATCCGAGTGTGATGTACCTCGATGCGGgtaatctctttaacttctgtccctgtctaacattttgcaatcgatctcttaacgggatcattcagtatttgccttttct-ttcaacaagtaaaaacgtaaa
|||| || ||||||||||||||||||||||||||||||||| || | |||||||| ||||| || ||||||||||| || ||  ||||||| || ||| |||       | |      | |  ||       ||  |  |  | |    ||    |    |  |  |||| | ||||   || ||  ||            
GTGCCTCTGGAGGTTGTGTTCTATGCAAGAAAATGTGGTATTTGCTTCAACTCCATGCTCGTGCTTGCAAGGAATCTGAATGCCATGTACCACGTTGCAGgtttgtgggtcaggcataggcattgcaattacttaagtcactgtttatatattttgcgtgtataacattttctttttgggttaaatcag------------

upper sequence: AT1G16710.1 (Arabidopsis thaliana), 5'ss of exon 16
lower sequence: GLYMA07G00230.1 (Glycine max), 5'ss of exon 16
GTGCTTCAGGAGGTTGTGTTCTATGCAAGAAAATGTGGTATCTGTTGCAACTCCACGCTCGGGCCTGCAAGGAATCCGAGTGTGATGTACCTCGATGCGGgtaatctctttaacttctgtccctgtctaacattttgcaatcgatctcttaacgggatcattca-gtatttgccttttctttcaacaagtaaaaacgtaaa
| ||||| |||||||||||||| |||||||||||||||||| || | ||||| || ||||| || ||||| ||||| || ||  ||||||| || ||| |||       | |     || |  | |      |  ||  | |  | | |||    |||  | || |||||     | | | |       ||||   |    
GAGCTTCTGGAGGTTGTGTTCTTTGCAAGAAAATGTGGTATTTGCTTCAACTTCATGCTCGTGCTTGCAAAGAATCTGAATGCCATGTACCACGTTGCAGgtttgtagatcaggcattgccattattc----tcgtgttaacactattttat--agattttgcatgtattaatactgtttatttgggtttaaatcag----

upper sequence: AT1G16710.1 (Arabidopsis thaliana), 5'ss of exon 16
lower sequence: GLYMA08G24290.1 (Glycine max), 5'ss of exon 18
GTGCTTCAGGAGGTTGTGTTCTATGCAAGAAAATGTGGTATCTGTTGCAACTCCACGCTCGGGCCTGCAAGGAATCCGAGTGTGATGTACCTCGATGCGGgtaatctctttaacttctgtccctgtctaacattttgcaatcgatc--tcttaacgggatcattcagtatttgccttttctttcaacaagtaaaaacgtaaa
| ||||| |||||||||||||| |||||||||||||||||| |  | ||||| || ||||| || ||||| ||||| || ||  | ||||| || ||| |||      ||  |  || | |  || | || ||| |  | |  |    | || |  |  |   |  |||||  |  | | | |      || ||| |     
GGGCTTCTGGAGGTTGTGTTCTTTGCAAGAAAATGTGGTATTTACTTCAACTTCATGCTCGTGCTTGCAAAGAATCTGAATGCCACGTACCACGTTGCAGgt------ttgtagatcaggcattgcc-aatattctcgagttaactcttttttatagattttgtatgtattaacactgtttatt--tgggttaaatcag---

upper sequence: AT1G16710.1 (Arabidopsis thaliana), 5'ss of exon 16
lower sequence: Vv09s0054g01780.t01 (Vitis vinifera), 5'ss of exon 15
GTGCTTCAGGAGGTTGTGTTCTATGCAAGAAAATGTGGTATCTGTTGCAACTCCACGCTCGGGCCTGCAAGGAATCCGAGTGTGATGTACCTCGATGCGGgtaatc--tctttaacttctgtccctgtctaacattttgcaatcgatctcttaacgggatcattcagtatttgccttttctttcaacaagtaaaaacgtaaa
| || || || |||||| |||| ||||||||||||||||||||  | ||||| || ||||| || ||||||||||| || ||  ||||||| || ||| |||      |  | ||||| ||  |     |  ||| ||  |     ||| | ||    | |||  |    ||    ||| | | |||   |  |        
GGGCGTCTGGTGGTTGTCTTCTCTGCAAGAAAATGTGGTATCTCCTTCAACTTCATGCTCGAGCTTGCAAGGAATCTGAATGCCATGTACCACGTTGCAGgtttgtagttgtcaacttgtggtc---aatgccatcttaaatattgtctatgaatatca-catataaatcttatactttatcttaactcattcag-------

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|86063327|gb|DR359084.1|DR359084
EST:     CTCCACGCTCGGGCCTGCAAGGAATCCGAGTGTGATGTACCTCGATGCGG                         GGACCTAAAGGAACATCTGAGAAGGTTACAACAG-AATCAGATTCTAAGCG
genomic: CTCCACGCTCGGGCCTGCAAGGAATCCGAGTGTGATGTACCTCGATGCGGgtaatctctt ... ctcaattcagGGACCTAAAGGAACATCTGAGAAGGTTACAACAGCAATCAGATTCTAGGCG
EST: gi|124976757|gb|EL050149.1|EL050149
EST:     CTCCACGCTCGGGCCTGCAAGGAATCCGAGTGTGATGTACCTCGATGCGG                         G-ACCTAAAGGAACATCTGAGAAGGTTACAACAGCAA
genomic: CTCCACGCTCGGGCCTGCAAGGAATCCGAGTGTGATGTACCTCGATGCGGgtaatctctt ... ctcaattcagGGACCTAAAGGAACATCTGAGAAGGTTACAACAGCAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGCTTCAGGAGGTTGTGTTCTATGCAAGAAAATGTGGTATCTGTTGCAACTCCACGCTCGGGCCTGCAAGGAATCCGAGTGTGATGTACCTCGATGCGGgtaatctctttaacttctgtccctgtctaacattttgcaatcgatctcttaacgggatcattcagtatttgccttttctttcaacaagtaaaaacgtaaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA