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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTATGGTGTTAGTGCGTACAAGGTCAGATCTCACCCTGATGACATTATGGCAGAAGTTTACAAAAATGGACCTGTTGAGGTTGCCTTCACTGTTTACGAGgtaaatactaggttctagagtgatcaaagatatgattatattatggaactccacatgttcatgtatctttctgttcttctacag

Basic information

species Arabidopsis thaliana
transcript AT1G02305.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G02305.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: GRMZM2G108849_T01 (Zea mays), 5'ss of exon 7
TTATGGTGTTAGTGCGTACAAGGTCAGATCTCACCCTGATGACATTATGGCAGAAGTTTACAAAAATGGACCTGTTGAGGTTGCCTTCACTGTTTACGAGgtaaatactaggt------tctagagtgatcaaag-atatgatta-----tattatggaactcc-acatgttcatgtatctttctgttcttctacag----------------------------------------------------------------
||   |  ||  ||||||||   | |  ||  | ||  ||||||| |||||||| || ||||||||||| ||||| || ||||| ||||| |||||||||||||   | || |      |||  |||  || | | || |  | |     | || || | ||   || |  | | | |   |   || |   ||| |                                                                
TTTCAGCATTGATGCGTACAGAATAAATTCAGATCCACATGACATAATGGCAGAGGTCTACAAAAATGGTCCTGTAGAAGTTGCTTTCACAGTTTACGAGgtaatgtccagctgctttgtctcaagttctccatgcattttgtcaacagattttgtgtagctgagacgttatgaaggactatggggtgcagatactgctagtacttttagaggacaaacattccatacaaaaacttacaaagactattatctaaataaaag

upper sequence: AT1G02305.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: GRMZM2G108849_T04 (Zea mays), 5'ss of exon 8
TTATGGTGTTAGTGCGTACAAGGTCAGATCTCACCCTGATGACATTATGGCAGAAGTTTACAAAAATGGACCTGTTGAGGTTGCCTTCACTGTTTACGAGgtaaatactaggt------tctagagtgatcaaag-atatgatta-----tattatggaactcc-acatgttcatgtatctttctgttcttctacag---
||   |  ||  ||||||||   | |  ||  | ||  ||||||| |||||||| || ||||||||||| ||||| || ||||| ||||| |||||||||||||   | || |      |||  |||  || | | || |  | |     | || || | ||   || |  | | | |   |   || |   ||| |   
TTTCAGCATTGATGCGTACAGAATAAATTCAGATCCACATGACATAATGGCAGAGGTCTACAAAAATGGTCCTGTAGAAGTTGCTTTCACAGTTTACGAGgtaatgtccagctgctttgtctcaagttctccatgcattttgtcaacagattttgtgtagctgagacgttatgaaggactatggggtgcagatactgcta

upper sequence: AT1G02305.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: GLYMA19G41120.1 (Glycine max), 5'ss of exon 8
TTATGGTGTTAGTGCGTACAAGGTCAGATCTCACCCTGATGACATTATGGCAGAAGTTTACAAAAATGGACCTGTTGAGGTTGCCTTCACTGTTTACGAGgtaaat---act-----aggttctagagtgatcaaag---atatgattatattatggaactccacatgttcatgtatctttctgttc---ttctacag--
 ||| |||| | ||| ||||  || || ||| | ||  |||| || ||| | ||||||||||| ||||| || ||||| ||||| ||||||||||| |||||||||   |||     |   |||   | ||| ||      |   | |   ||    || | |  |    |    | | | || ||     | || |   
CTATAGTGTCAATGCATACAGAGTGAGCTCTGATCCCCATGATATCATGACGGAAGTTTACAAGAATGGGCCAGTTGAAGTTGCATTCACTGTTTATGAGgtaaatgaaactcttacacactcttttgcgattaatttttctgcaacttcctttgtcaatttctgaaaacccaaaaccatcctatttaaaatttataatt

upper sequence: AT1G02305.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: Vv07s0005g02820.t01 (Vitis vinifera), 5'ss of exon 7
TTATGGTGTTAGTGCGTACAAGGTCAGATCTCACCCTGATGACATTATGGCAGAAGTTTACAAAAATGGACCTGTTGAGGTTGCCTTCACTGTTTACGAGgtaaatactaggttctagagtg-atcaaagatatgattatattatgg---aactccacatgttc--atgtat---ctttctgttcttctacag-------
|||||||   ||||| || |   |||| ||| | ||  |  | |||||||||||||| ||||| |||||||||||||||||||||||||||||||| ||||||||    ||   ||    ||  | |  | ||||| | |  |   |   |    || || |||  | | ||   |  | ||    ||||          
TTATGGTCAAAGTGCATATAGAATCAGTTCTGATCCCTACCAAATTATGGCAGAAGTGTACAAGAATGGACCTGTTGAGGTTGCCTTCACTGTTTATGAGgtaaaagaaagcacctgttctgcgttattgttatgaatttgatgcagctaatgagcatatcttctgacgcatgaccaatttggcactctaagaccatggt

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|164152362|gb|ES206952.1|ES206952
EST:     GAAGTTTACAAAAAATGGACCTGTTGAGGTTGCCTTCACTGTTTACGAG                         GACTTTGCGCATTACAAATCTGGAGTGTACAAGCACATAACAGGTACTAAC
genomic: GAAGTTTAC-AAAAATGGACCTGTTGAGGTTGCCTTCACTGTTTACGAGgtaaatacta ... tcttctacagGACTTTGCGCATTACAAATCTGGAGTGTACAAGCACATAACAGGTACTAAC
EST: gi|125090924|gb|EL148747.1|EL148747
EST:     CAGAAGTTTACAAAAATGGACCTGTTGAGGTTGCCTTCACTGTTTACGAG                         GACTTTGCGCATTACAAATCTGGAGTGTACAAGCACATAA
genomic: CAGAAGTTTACAAAAATGGACCTGTTGAGGTTGCCTTCACTGTTTACGAGgtaaatacta ... tcttctacagGACTTTGCGCATTACAAATCTGGAGTGTACAAGCACATAA
EST: gi|86079522|gb|DR375279.1|DR375279
EST:     CAGAAGTTTACAAAAATGGACCTGTTGAGGTTGCCTTCACTGTTTACGAG                         GACTTTGCGCATTACAAATCTGGAGTGTACAAGCACATAACAGGTACTAAC
genomic: CAGAAGTTTACAAAAATGGACCTGTTGAGGTTGCCTTCACTGTTTACGAGgtaaatacta ... tcttctacagGACTTTGCGCATTACAAATCTGGAGTGTACAAGCACATAACAGGTACTAAC
EST: gi|163983069|gb|ES208749.1|ES208749
EST:     CAGAAGTTTACAAAAATGGACCTGTTGAGGTTGCCTTCACTGTTTACGAG                         GACTTTGCGCATTACAAATCTGGAGTGTACAAGCACATAACAGGTAC
genomic: CAGAAGTTTACAAAAATGGACCTGTTGAGGTTGCCTTCACTGTTTACGAGgtaaatacta ... tcttctacagGACTTTGCGCATTACAAATCTGGAGTGTACAAGCACATAACAGGTAC
EST: gi|124746389|gb|EH836723.1|EH836723
EST:     CAGAAGTTTACAAAAATGGACCTGTTGAGGTTGCCTTCACTGTTTACGAG                         GACTTTGCGCATTACAAATCTGGAGTGTACAAGCACATAACAGGTACTAAC
genomic: CAGAAGTTTACAAAAATGGACCTGTTGAGGTTGCCTTCACTGTTTACGAGgtaaatacta ... tcttctacagGACTTTGCGCATTACAAATCTGGAGTGTACAAGCACATAACAGGTACTAAC
EST: gi|125027178|gb|EL099447.1|EL099447
EST:     CAGAAGTTTACAAAAATGGACCTGTTGAGGTTGCCTTCACTGTTTACGAG                         GACTTTGCGCATTACAAATCTGGAGTGTACAAGCACATAACAGGTACTAAC
genomic: CAGAAGTTTACAAAAATGGACCTGTTGAGGTTGCCTTCACTGTTTACGAGgtaaatacta ... tcttctacagGACTTTGCGCATTACAAATCTGGAGTGTACAAGCACATAACAGGTACTAAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTATGGTGTTAGTGCGTACAAGGTCAGATCTCACCCTGATGACATTATGGCAGAAGTTTACAAAAATGGACCTGTTGAGGTTGCCTTCACTGTTTACGAGgtaaatactaggttctagagtgatcaaagatatgattatattatggaactccacatgttcatgtatctttctgttcttctacag

- - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT