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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTTGTCCAAAGCAAAGAGAGGGCCAAAGAGCTTTACAAAGAACTGGCATTTGATGACATTAGAGTTGATGTAATTCATGCAGATCTCAGTGAGCAGCAGgtatagctttgcatattattgtcactgctatatttcagagacatctttcatgttttgttagagttgcgctacttgtgtatgaggtttacatgttgtcaacatatgtttcctttactgcag

Basic information

species Zea mays
transcript GRMZM2G083580_T01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G083580_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os07g45360.1 (Oryza sativa), 5'ss of exon 9
TTTTGTCCAAAGCAAAGAGAGGGCCAAAGAGCTTTACAAAGAACTGGCATTTGATGACATTAGAGTTGATGTAATTCATGCAGATCTCAGTGAGCAGCAGgtatagctttgcatattattgtca-ctgctatatttcagagacatctttcat-gttttgttagagttgcgctacttgtgtatgaggtttacatgttgtcaacatatgtttcctttactgcag
 ||||| ||||||||||||||||| ||||| ||||||||||||||||||||||||||| | |||| ||||||||||||||| || ||   |||| |||||||||  |||   |||| ||| | |  |||||      | | |  | | |  | ||||||||     |||   |||||  |      |||  || |  |||    |                 
CTTTGTTCAAAGCAAAGAGAGGGCAAAAGAACTTTACAAAGAACTGGCATTTGATGACGTAAGAGCTGATGTAATTCATGCGGACCTTGATGAGGAGCAGgtatcactta--atatcatttttagttgcta------ataaatgtttgtggtagttttgttttcactgctacacttggctc---aatttctatctcctcactgaag----------------

upper sequence: GRMZM2G083580_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA19G36300.2 (Glycine max), 5'ss of exon 10
TTTTGTCCAAAGCAAAGAGAGGGCCAAAGAGCTTTACAAAGAACTGGCATTTGATGACATTAGAGTTGATGTAATTCATGCAGATCTCAGTGAGCAGCAGgtatagctttgcatattattgt-cactgctatat-ttcagagacatctttcatgttttgttagagttgcgctacttgtgtatg-aggtttacatgttgtcaacatatgtttcctttactgcag
|||| |||||||||| ||| | ||||| ||||| ||||  ||||| ||||||||  |||||||||||||||| || ||| | ||| |  ||    |||||   ||| | |  |     |||  ||     | || || |  |  |  |   |   | ||  |   || | || |      |   |       |   ||  ||                     
TTTTCTCCAAAGCAAGGAGCGTGCCAAGGAGCTGTACAGTGAACTTGCATTTGACAACATTAGAGTTGATGTTATCCATTCTGATTT--GTCTCAAGCAGAGgtagttctcaacccctttgaacaacataagatatttattggaaaataagaaaatatgaaacgtttcccctccccaccaaaataaaaaagaaaactgataa---------------------

upper sequence: GRMZM2G083580_T01 (Zea mays), 5'ss of exon 9
lower sequence: Vv08s0040g02300.t01 (Vitis vinifera), 5'ss of exon 10
TTTTGTCCAAAGCAAAGAGAGGGCCAAAGAGCTTTACAAAGAACTGGCATTTGATGACATTAGAGTTGATGTAATTCATGCAGATCTCAGTGAGCAGCAGgta-tagctttgcatattattgt-cactgctatatttcagagacatctttcatgttttgttagagttgcgctacttgtgtatgaggt-ttacatgttgtcaacatatgtttcctttactgcag
 |||||||||||||| ||  | || || ||||| ||||  |||||||||||||||||||||||||||||||| || ||||| ||| |     |    |||||| |  |||  ||  ||  | |  ||| |||        |  | | || | | |   |  | ||        || | || | || | | | |  |||  |                      
CTTTGTCCAAAGCAAGGAACGTGCAAAGGAGCTCTACACGGAACTGGCATTTGATGACATTAGAGTTGATGTTATCCATGCTGATTTGTCCCAATCACAGgtaattacttgtcaatttggtatatacttctac-caatgtattctttttgcctatccagaaaaagagataaacctcgagtgttagctgtcagaacttgata----------------------

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|71766777|gb|DR964714.1|DR964714
EST:     TTGATGACATTAGAGTTGATGTAATTCATGCAGATCTCAGTGAGCAGCAG                         CGTCAAGATGCTGTTGACAATTTGAGAGCTGGAAAGACCTGGGTACTGATA
genomic: TTGATGACATTAGAGTTGATGTAATTCATGCAGATCTCAGTGAGCAGCAGgtatagcttt ... tttactgcagCGTCAAGATGCTGTTGACAATTTGAGAGCTGGAAAGACCTGGGTACTGATA
EST: gi|40302886|gb|CK347273.1|CK347273
EST:     TTGATGACATTAGAGTTGATGTAATTCATGCAGATCTCAGTGAGCAGCAG                         CGTCAAGATGCTGTTGACAATTTGAGAGCTGGAAAGACCTGGGTACTGATA
genomic: TTGATGACATTAGAGTTGATGTAATTCATGCAGATCTCAGTGAGCAGCAGgtatagcttt ... tttactgcagCGTCAAGATGCTGTTGACAATTTGAGAGCTGGAAAGACCTGGGTACTGATA
EST: gi|60356063|gb|DN223036.1|DN223036
EST:     TGTAATTCATGCAGATCTCAGTGAGCAGCAG                         CGTCAAGATGCTGTTGACAATTTGAGAGCTGGAAAGACCTGGGTACTGATA
genomic: TGTAATTCATGCAGATCTCAGTGAGCAGCAGgtatagcttt ... tttactgcagCGTCAAGATGCTGTTGACAATTTGAGAGCTGGAAAGACCTGGGTACTGATA
EST: gi|71766778|gb|DR964715.1|DR964715
EST:     TTGATGACATTAGAGTTGATGTAATTCATGCAGATCTCAGTGAGCAGCAG                         CGTCAAGATGCTGTTGACAATTTGAGAGCTGGAAAGACCTGGGTACTGATA
genomic: TTGATGACATTAGAGTTGATGTAATTCATGCAGATCTCAGTGAGCAGCAGgtatagcttt ... tttactgcagCGTCAAGATGCTGTTGACAATTTGAGAGCTGGAAAGACCTGGGTACTGATA
EST: gi|78115305|gb|DV533693.1|DV533693
EST:     TTGATGACATTAGAGTTGATGTAATTCATGCAGATCTCAGTGAGCAGCAG                         CGTCAAGATGCTGTTGACAATTTGAGAGCTGGAAAGACCTGGGTACTGATA
genomic: TTGATGACATTAGAGTTGATGTAATTCATGCAGATCTCAGTGAGCAGCAGgtatagcttt ... tttactgcagCGTCAAGATGCTGTTGACAATTTGAGAGCTGGAAAGACCTGGGTACTGATA
EST: gi|78115306|gb|DV533694.1|DV533694
EST:     TTGATGACATTAGAGTTGATGTAATTCATGCAGATCTCAGTGAGCAGCAG                         CGTCAAGATGCTGTTGACAATTTGAGAGCTGGNAAGACCTGGGTACTGATA
genomic: TTGATGACATTAGAGTTGATGTAATTCATGCAGATCTCAGTGAGCAGCAGgtatagcttt ... tttactgcagCGTCAAGATGCTGTTGACAATTTGAGAGCTGGAAAGACCTGGGTACTGATA
EST: gi|32944128|gb|CF048947.1|CF048947
EST:     TTGATGACATTAGAGTTGATGTAATTCATGCAGATCTCAGTGAGCAGCAG                         CGTCAAGATGCTGTTGACAATTTGAGAGCTGGAAAGACCTGGGT
genomic: TTGATGACATTAGAGTTGATGTAATTCATGCAGATCTCAGTGAGCAGCAGgtatagcttt ... tttactgcagCGTCAAGATGCTGTTGACAATTTGAGAGCTGGAAAGACCTGGGT
EST: gi|33098086|gb|CF058046.1|CF058046
EST:     TTGATGACATTAGAGTTGATGTAATTCATGCAGATCTCAGTGAGCAGCAG                         CGTCAAGATGC
genomic: TTGATGACATTAGAGTTGATGTAATTCATGCAGATCTCAGTGAGCAGCAGgtatagcttt ... tttactgcagCGTCAAGATGC
EST: gi|60397325|gb|DN230141.1|DN230141
EST:     ATTAGAGTTGATGTAATTCATGCAGATCTCAGTGAGCAGCAG                         CGTCAAGATGCTGTTGACAATTTGAGAGCTGGAAAGACCTGGGTACTGATA
genomic: ATTAGAGTTGATGTAATTCATGCAGATCTCAGTGAGCAGCAGgtatagcttt ... tttactgcagCGTCAAGATGCTGTTGACAATTTGAGAGCTGGAAAGACCTGGGTACTGATA
EST: gi|32930531|gb|CF035343.1|CF035343
EST:     TTGATGACATTAGAGTTGATGTAATTCATGCAGATCTCAGTGAGCAGCAG                         CGTCAAGATGCTGTTGACAATTTGAGAGCTGGAAAGACCTGGGTAC
genomic: TTGATGACATTAGAGTTGATGTAATTCATGCAGATCTCAGTGAGCAGCAGgtatagcttt ... tttactgcagCGTCAAGATGCTGTTGACAATTTGAGAGCTGGAAAGACCTGGGTAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTTGTCCAAAGCAAAGAGAGGGCCAAAGAGCTTTACAAAGAACTGGCATTTGATGACATTAGAGTTGATGTAATTCATGCAGATCTCAGTGAGCAGCAGgtatagctttgcatattattgtcactgctatatttcagagacatctttcatgttttgttagagttgcgctacttgtgtatgaggtttacatgttgtcaacatatgtttcctttactgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG