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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCCTAATGCATGTGGTTGGGCTTATGGAATGAACATGTTTGATCTGGAAGAATGGAAGAAGAAAGACATTACTGGAATCTACCACAAATGGCAGAACATGgtgaattggaagattttacattacttgcatcttgacaccttttcttttaatattgcatttaattttcctatacgtacacagccatcttgctgatttatat...

Basic information

species Zea mays
transcript GRMZM2G076276_T01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G076276_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os06g49810.1 (Oryza sativa), 5'ss of exon 8
TCCTAATGCATGTGGTTGGGCTTATGGAATGAACATGTTTGATCTGGAAGAATGGAAGAAGAAAGACATTACTGGAATCTACCACAAATGGCAGAACATGgtgaattgga--agattttacattacttgcatcttgacaccttttcttttaatattgcatt--taattttcctatacgtacacagccatcttgctgatttatat--
||||||||| ||||| ||||| ||||||||||| ||||||||| ||||||||||||||||||| ||||||||||| || || |||||||||||||||||||| | ||| |  |   |||| ||||||    | |  |    |||||| |  | ||| || |   || |||| |   |    |||  ||   |     ||| |    
TCCTAATGCTTGTGGCTGGGCGTATGGAATGAATATGTTTGATTTGGAAGAATGGAAGAAGAAGGACATTACTGGCATTTATCACAAATGGCAGAACATGgtaagttgaaataaggtttatattact---gtttccat---ttttctgtagaaatttcaatggcaaatttctttcgctataacatgcaatatttcagtttctgcaa

upper sequence: GRMZM2G076276_T01 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA18G45750.1 (Glycine max), 5'ss of exon 8
TCCTAATGCATGTGGTTGGGCTTATGGAATGAACATGTTTGATCTGGAAGAATGGAAGAAGAAAGACATTACTGGAATCTACCACAAATGGCAGAACATGgtgaattggaagattttacatta-cttgcatcttgacaccttttcttttaatattgcatttaattttcctatacgtacacagccatcttgctgatttatat------
 || ||||| ||||||||||| || || ||||||||||||||| || | |  ||||| ||||| ||||| ||||| || || ||||| ||||||||  ||||||   |    |  |||||||   || ||||   |   || |||||  |  ||        ||      | ||  |   | |     |   |   ||  |      
-CCAAATGCTTGTGGTTGGGCATACGGGATGAACATGTTTGATTTGAAGGTGTGGAAAAAGAAGGACATCACTGGCATATATCACAAGTGGCAGAATTTGGtgagaagttgaacattacattggtttacatca-aatgtctattcttacataataa-----gatgactacagacagatttaactgctctaaagggatagttaccctt

upper sequence: GRMZM2G076276_T01 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA07G08910.1 (Glycine max), 5'ss of exon 6
TCCTAATGCATGTGGTTGGGCTTATGGAATGAACATGTTTGATCTGGAAGAATGGAAGAAGAAAGACATTACTGGAATCTACCACAAATGGCAGAACATGgtgaattggaagattttacattacttgcatcttgacaccttttcttttaatattgcatttaattttcctatacgtacacagccatcttgctgatttatat
|||  |||| ||||||||||| || || |||||||||||||||||| | |  ||||| ||||| || || || || || || ||||| |||||||| ||||| |   |    |     ||||  ||            || ||||   |    |  |    ||||||    ||  ||       |  || |   || || 
TCCACATGCTTGTGGTTGGGCATACGGGATGAACATGTTTGATCTGAAGGTGTGGAAAAAGAAGGATATCACCGGCATATATCACAAGTGGCAGAATATGgtaagcagatgaacaaagcattggtttacataaattgtctattctcgcacagatagaagagattttc----actgacttgttttttctgtttgattctag

upper sequence: GRMZM2G076276_T01 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA03G02250.1 (Glycine max), 5'ss of exon 14
TCCTAATGCATGTGGTTGGGCTTATGGAATGAACATGTTTGATCTGGAAGAATGGAAGAAGAAAGACATTACTGGAATCTACCACAAATGGCAGAACATGgtgaattggaagattttacatta-cttgcatc--ttgacaccttttcttttaatat--tgca--tttaattttcctatacgtacacagccatcttgctgatttatat
||| ||||| ||||||||||| || || |||||||||||||||||| | |  ||||| ||||| || || || || || || ||||| |||||||| ||||| |        |     ||||   || ||||  ||| |   | |      ||||   ||||  | |     |  |  ||  ||       |  || |   || || 
TCCAAATGCTTGTGGTTGGGCATACGGGATGAACATGTTTGATCTGAAGGTGTGGAAAAAGAAGGATATCACCGGCATATATCACAAGTGGCAGAATATGgtaagcaaaggaacgaagcattggtttacatcaattgtctattctcacacaaatagaatgcaggtatggagatttttcactgacttgtttgttatgtttgattctag

upper sequence: GRMZM2G076276_T01 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA09G40260.1 (Glycine max), 5'ss of exon 9
TCCTAATGCATGTGGTTGGGCTTATGGAATGAACATGTTTGATCTGGAAGAATGGAAGAAGAAAGACATTACTGGAATCTACCACAAATGGCAGAACATGgtgaattggaagattttacatta-cttgcatcttgacaccttttcttttaatattgcatttaattttcctatacgtacacagccatcttgctgatttatat-
||| ||||| ||||||||||| || || ||||||||||||||| || | |  ||||| ||||| ||||| ||||| || || ||||| ||||||||  ||||||   |    |  | |||||   || ||||   |   || |||||  | || |    | | |      | |  ||      |     |  || |||    
TCCAAATGCTTGTGGTTGGGCATACGGGATGAACATGTTTGATTTGAAGGTGTGGAAAAAGAAGGACATCACTGGCATATATCACAAGTGGCAGAATTTGgtgagcagttgaacataacattggtttacatcac-atgtctgttcttaca-taataagatgactacagacagatttaactcctctaaagggagagttaccct

upper sequence: GRMZM2G076276_T01 (Zea mays), 5'ss of exon 7
lower sequence: AT2G46480.1 (Arabidopsis thaliana), 5'ss of exon 5
TCCTAATGCATGTGGTTGGGCTTATGGAATGAACATGTTTGATCTGGAAGAATGGAAGAAGAAAGACATTACTGGAATCTACCACAAATGGCAGAACATGgtgaattggaagattttacattacttgcatcttgacaccttttcttttaatattgcatttaattttcctatacgtacacagccatcttgctgatttatat
||| ||    || || ||||||||||| |||||||| || || ||| ||||||||||||||||  ||||||| | ||  || |||   ||||| ||| |||| |  |       ||  | |  |||  ||||  |    || |   || |  |||    | || |   ||| |           | |||| |        
TCCCAAGTTCTGCGGATGGGCTTATGGGATGAACATCTTCGACCTGAAAGAATGGAAGAAGAACAACATTACAGAAACTTATCACTTTTGGCAAAACCTGgtcagctcttcttcttggcttatctttaatctaaaactgttgtagatttaagttgagagtgatatgt-tattcccctgt-----ttttgcag--------

upper sequence: GRMZM2G076276_T01 (Zea mays), 5'ss of exon 7
lower sequence: Vv15s0048g01300.t01 (Vitis vinifera), 5'ss of exon 9
TCCTAATGCATGTGGTTGGGCTTATGGAATGAACATGTTTGATCTGGAAGAATGGAAGAAGAAAGACATTACTGGAATCTACCACAAATGGCAGAACATGgtgaat---tgga-agattttacattacttgcat-cttgacaccttttcttttaatattgcatttaattttcctatacgtacacagccatcttgctgatttatat
||| ||||| ||||| ||||| |||||||||||||| ||||||||  | || ||||  |  |  || |||||||| || || || || |||||||||||||||| |   || | | || |    ||| |||||| |||      ||||  ||| | |   || ||  ||||| |  | ||  |     || ||  |         
TCCAAATGCTTGTGGGTGGGCATATGGAATGAACATTTTTGATCTCAAGGAGTGGACAAGAAGGGATATTACTGGCATATATCATAAGTGGCAGAACATGgtgagtctttgaataaatctcgttttatttgcatgctttgtgtttttttcttttacaa-acaattttttttcatgcatgtgaatgtttatgttatttgacc----

upper sequence: GRMZM2G076276_T01 (Zea mays), 5'ss of exon 7
lower sequence: PP1S251_8V6.1 (Physcomitrella patens), 5'ss of exon 9
TCCTAATGCATGTGGTTGGGCTTATGGAATGAACATGTTTGATCTGGAAGAATGGAAGAAGAAAGACATTACTGGAATCTACCACAAATGGCAGAACATGgtgaattggaagattttacattacttgcatc-ttgacaccttttcttttaatattgcatttaattttcctatacgtacacagccatcttgctgatttatat--
  |  |||| ||||||||||| |||||||||||||| |||||| || |  ||||||| |   ||||||| || || || ||||| |||||||| | ||||||    ||  |   | |   || | |  ||| ||||        | |||   | || ||    | |   |    || || | |  |  ||||    ||||   
ATCAGATGCTTGTGGTTGGGCCTATGGAATGAACATTTTTGATTTGAAGCAATGGAAAATCCAAGACATCACGGGTATTTACCATAAATGGCAAAGCATGgta---tgtgaacctctgatttccatatatccttgagcaaacaccatttttaactggatcatctctaagttattgtgcatatcagttgtgcttcaatatactt

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|211198455|gb|FL128768.1|FL128768
EST:     AATGGAAGAAGAAAGACATTACTGGAATCTACCACAAATGGCAGAACATG                         AACGAGAACAGGCTGCTCTGGAAATTGGGGACATTGCCGCCAGGGCTTCTA
genomic: AATGGAAGAAGAAAGACATTACTGGAATCTACCACAAATGGCAGAACATGgtgaattgga ... ctttatacagAACGAGAACAGGCTGCTCTGGAAATTGGGGACATTGCCGCCAGGGCTTCTA
EST: gi|71429642|gb|DR810692.1|DR810692
EST:     AATGGAAGAAGAAAGACATTACTGGAATCTACCACAAATGGCAGAACATG                         AACGAGAACAGGCTGCTCTGGAAATTGGGGACATTGCCGCCAGGGCTTCTA
genomic: AATGGAAGAAGAAAGACATTACTGGAATCTACCACAAATGGCAGAACATGgtgaattgga ... ctttatacagAACGAGAACAGGCTGCTCTGGAAATTGGGGACATTGCCGCCAGGGCTTCTA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCCTAATGCATGTGGTTGGGCTTATGGAATGAACATGTTTGATCTGGAAGAATGGAAGAAGAAAGACATTACTGGAATCTACCACAAATGGCAGAACATGgtgaattggaagattttacattacttgcatcttgacaccttttcttttaatattgcatttaattttcctatacgtacacagccatcttgctgatttatat

- - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA