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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTTATCTTTTCAATGATTACTGGGAAGATATTGGAACTATTAAGTCCTTCTTTGAGGCAAACCTTGCTCTTGCTGAACAGgtacgtgtttaatgattactggctttctgcaaactcttcgagtaactctttgtactgctttgctttacgttttttatatttctctagaaaagtactgaag...

Basic information

species Zea mays
transcript GRMZM2G391936_T04
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G391936_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os03g52460.1 (Oryza sativa), 5'ss of exon 10
GCTTATCTTTTCAATGATTACTGGGAAGATATTGGAACTATTAAGTCCTTCTTTGAGGCAAACCTTGCTCTTGCTGAACAGgtacgtgtttaatgattactggctttctgcaaactcttcgagtaactctttgtactgctttgctttacgtttt-ttatat-ttctctagaaaagtactgaag
|| |||||||||||||||||||||||||| || |||||||| || || |||||||| || || ||| ||||||||||||||||| |  |||| | ||       |  |     |  | |       |  ||| ||   || |  |  |  | |   | ||    ||  | |    ||||  | 
GCATATCTTTTCAATGATTACTGGGAAGACATAGGAACTATAAAATCATTCTTTGAAGCCAATCTTTCTCTTGCTGAACAGgtatgc-tttactaatacaaaattgccattttatccgtattcctgcagtttatatccctctaataaatatgtaactgtacacactgcaaattgatacttta-

upper sequence: GRMZM2G391936_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA07G38820.2 (Glycine max), 5'ss of exon 10
GCTTATCTTTTCAATGATTACTGGGAAGATATTGGAACTATTAAGTCCTTCTTTGAGGCAAACCTTGCTCTTGCTGAACAGgtacgtgtttaatga--ttactggctttctgcaaactcttcgagtaactctttgtactgctttgctttacgttttttatatttctctagaaaagtactgaag
|||||||| |||||||||||||||||||| || || ||||| |  || |||||||||||||| ||||| ||  |||| || ||  ||||  ||| |  ||  ||   |||    |  |    | ||     |   || |  || | |  | | || |  ||    |  | | ||| | |||| 
GCTTATCTATTCAATGATTACTGGGAAGACATAGGTACTATCAGATCATTCTTTGAGGCAAATCTTGCCCTCACTGAGCATgtgagtgtcaaatcaccttgttgagcttcgatgatttgaatgtgttgagttcattagtaattag-tggaaggttgtgctagaggtaaacataagaaatgaa-

upper sequence: GRMZM2G391936_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA17G01900.1 (Glycine max), 5'ss of exon 10
GCTTATCTTTTCAATGATTACTGGGAAGATATTGGAACTATTAAGTCCTTCTTTGAGGCAAACCTTGCTCTTGCTGAACAGgtacgtgtttaatga--ttactggctttctgcaaa------ctcttcgagtaactctttgtactgctttgctttacgttttttatatttctctagaaaagtactgaag---------------------------------------------------------------------------
|||||||| |||||||||||||||||||| || || ||||| |  |||||||| |||||||| ||||| ||  |||| || ||  ||||  ||| |  | | | |   |  | | |        ||    ||||   |  | | ||  ||   |||     || | |    |    ||   ||   | |                                                                           
GCTTATCTCTTCAATGATTACTGGGAAGACATAGGGACTATCAGATCCTTCTTCGAGGCAAATCTTGCCCTCACTGAGCATgtgagtgtcaaatcacctcattagtaattagtagaaggtcgtgctagaggtaaacataagaaatgaatttaattattaagttcaaaaacttagtcaactataagcatgtatcatttcatctttttcattttaagatctaaagtcttattttcccagaaaagcttacttctttaattttttcag

upper sequence: GRMZM2G391936_T01 (Zea mays), 5'ss of exon 6
lower sequence: PP1S347_12V6.1 (Physcomitrella patens), 5'ss of exon 8
GCTTATCTTTTCAATGATTACTGGGAAGATATTGGAACTATTAAGTCCTTCTTTGAGGCAAACCTTGCTCTTGCTGAACAGgta---cgtgtttaatgattactggctttctgcaaactcttcgagtaactctttgtact------gctttgctttacgttttttatatttctctagaaaagtactgaag---------------------------------------------------------------------------------
|| ||| | |||||||| |||||||| ||||||||||| || ||||| |||||||| || ||  | |||||| ||   ||||||   | |   |   | | |  |   || |  |        |   |||| | |||| |        | ||      ||   ||  ||| |  ||| |   || | ||                                                                                  
GCATATTTGTTCAATGACTACTGGGAGGATATTGGAACCATCAAGTCTTTCTTTGATGCTAATTTAGCTCTTACTTCTCAGgtattgccttcctctcgctcatagatgtttttta---ctgaaggaaaactgtgtgtagtcaatcaattatgtaacctgtgaattgaattacattaggatcatattaaacttgaatataggtttgtctctctacatttttcacttctcaatcgattcttacacagtgttgtgtgtgttcgtctttccacag

upper sequence: GRMZM2G391936_T01 (Zea mays), 5'ss of exon 6
lower sequence: PP1S389_5V6.1 (Physcomitrella patens), 5'ss of exon 9
GCTTATCTTTTCAATGATTACTGGGAAGATATTGGAACTATTAAGTCCTTCTTTGAGGCAAACCTTGCTCTTGCTGAACAGgtacgtgtttaatgattactggctttctgcaaactcttcgagt-aactctttgtactgctttgctttacgtttt---ttatatttctcta-gaaaagtactgaag----------------------------
|| ||  | || ||||| || ||||||||||||||||| ||||||||||||||||| || ||  | |||||  |||  |||||| |       || ||  |     | |||    ||   || |  | |  | |  ||||||||    || |      ||||  ||||| | |   ||| || ||                             
GCGTACTTGTTTAATGACTATTGGGAAGATATTGGAACCATTAAGTCCTTCTTTGATGCCAATTTAGCTCTCACTGCTCAGgtatggcacctttgttttataaaaatatgcttggtcagtgatttgagtactgggtctgctttgtaggacatgaaggattattattctccatgtggagttctaaaatgttttcttctctgttgtcttcctgcag

upper sequence: GRMZM2G391936_T01 (Zea mays), 5'ss of exon 6
lower sequence: EFJ23417 (Selaginella moellendorffii), 5'ss of exon 11
GCTTATCTTTTCAATGATTACTGGGAAGATATTGGAACTATTAAGTCCTTCTTTGAGGCAAACCTTGCTCTTGCTGAACAGgtacgtgtttaatgattactggctttctgcaaactcttcgagtaactctttgtactgctttgctttacgttttttatatttctctagaaaagtactgaag
|| ||||| |||||||| ||||||||||| ||||||||||||||||| || ||||| || || || |||||  |||  ||||||  ||  |   || |  |||   |  |||      |  |  |  |  |  |||          |   |||                            
GCGTATCTCTTCAATGACTACTGGGAAGACATTGGAACTATTAAGTCGTTTTTTGACGCTAATCTCGCTCTCACTGCTCAGgta-atgcctttggagt--tggaacttcgcag-----ttaaacacttactcatacaaaaaaaaaatctctttgcag------------------------

upper sequence: GRMZM2G391936_T01 (Zea mays), 5'ss of exon 6
lower sequence: EFJ25399 (Selaginella moellendorffii), 5'ss of exon 10
GCTTATCTTTTCAATGATTACTGGGAAGATATTGGAACTATTAAGTCCTTCTTTGAGGCAAACCTTGCTCTTGCTGAACAGgtacgtgtttaatgattactggctttctgcaaactcttcgagtaactctttgtactgctttgctttacgttttttatatttctctagaaaagtactgaag
|| ||||| |||||||| ||||||||||| ||||||||||||||||| || ||||| || || || |||||  | |  ||||||  ||  |   || |  |||   |  |||      |  |  |  |  |  |||           |  | ||||  |                      
GCGTATCTCTTCAATGACTACTGGGAAGACATTGGAACTATTAAGTCGTTTTTTGACGCTAATCTCGCTCTCACCGCTCAGgta-atgcctttggagt--tggaacttcgcag-----ttaaacacttactcatacaaaaaga---aaactcttttgcag---------------------

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|32934983|gb|CF039795.1|CF039795
EST:     TTGGAACTATTAAGTCCTTCTTTGAGGCAAACCTTGCTCTTGCTGAACAG                         CCTCCAAGGTTCAGTTTCTACGATGCTGACAAACCAATGTATACATCACGG
genomic: TTGGAACTATTAAGTCCTTCTTTGAGGCAAACCTTGCTCTTGCTGAACAGgtacgtgttt ... aactatgcagCCTCCAAGGTTCAGTTTCTACGATGCTGACAAACCAATGTATACATCACGG
EST: gi|13126505|gb|BG317075.1|BG317075
EST:     TTGGAACTATTAAGTCCTTCTTTGAGGCAAACCTTGCTCTTGCTGAACAG                         CCTCCAAGGTTCAGTTTCTACGATGCTGACAAACCAATGTA
genomic: TTGGAACTATTAAGTCCTTCTTTGAGGCAAACCTTGCTCTTGCTGAACAGgtacgtgttt ... aactatgcagCCTCCAAGGTTCAGTTTCTACGATGCTGACAAACCAATGTA
EST: gi|32934981|gb|CF039793.1|CF039793
EST:     TTGGAACTATTAAGTCCTTCTTTGAGGCAAACCTTGCTCTTGCTGAACAG                         CCTCCAAGGTTCAGTTTCTACGATGCTGACAAACCAATGTATACATCACGG
genomic: TTGGAACTATTAAGTCCTTCTTTGAGGCAAACCTTGCTCTTGCTGAACAGgtacgtgttt ... aactatgcagCCTCCAAGGTTCAGTTTCTACGATGCTGACAAACCAATGTATACATCACGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTTATCTTTTCAATGATTACTGGGAAGATATTGGAACTATTAAGTCCTTCTTTGAGGCAAACCTTGCTCTTGCTGAACAGgtacgtgtttaatgattactggctttctgcaaactcttcgagtaactctttgtactgctttgctttacgttttttatatttctctagaaaagtactgaag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaaaagta