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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGTAAAGGGAGGAGCGGAGCGGCGAATTCTTGTGGTTTCCCAAGATGTCTTCTCCAAGCAAGCGCCGGGAGATGGACCTCATGAAGCTGTGAGGATTCTGgtggcgtgattcggtgattttttctataggatttcgatgcggattccttgatctgcgtttctactgcatgttgatgcctgcag

Basic information

species Zea mays
transcript GRMZM2G150867_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G150867_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os10g31000.1 (Oryza sativa), 5'ss of exon 1
---CGTAAAGGGAGGAGCGGAGCGGCGAATTCTTGTGGTTTCC---------CAAGATGTCTTCTCCAAGCAAGCGCCGGGAGATGGACCTCATGAAGCTGTGAGGATTCTGgtggcgtgattcggtgattttttctataggatttcgatgcgga---------ttccttgatctgcgtttctactgcatgttgatg-cctgcag------------------------------------------------------------------------------
    | |   |||| |   ||    | |  | ||    ||| |         |||||||||||| || ||||||||||| ||||||||| | ||||||||||||||||  ||    | | |||   | ||||||| |   ||     |  | |||         || |  | | ||  | | | ||   | ||| ||  || ||                                                                               
AGGAGGAGGAGGAGAAAAAGAAATCCAATCTTTTTCTTTTTTCTTCTTGTGTCAAGATGTCTTCCCCGAGCAAGCGCCGCGAGATGGACTTGATGAAGCTgtgaggatcttgtc--ctttatttatttattttttttggggggggggggggtggaattgtgtttttgcccggtttgattcttttctttctattggtggtctccatcgtctaatctgatgtgttgttgtttgttgttttgggggtggggggattggggattttcttggtttcttgttgttgcag

upper sequence: GRMZM2G150867_T01 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA09G39370.4 (Glycine max), 5'ss of exon 1
---------CGTAAAGGGAGGAGCGGAGCGGCGAATTCTTGTGGTTTCCCAAGA---TGTCTTCTCCAAGCAAGCGCCGGGAGATGGACCTCATGAAGCTGTGAGGATTCTGgtggcgtgattcggtgattttttctataggatttcgatgcgga---ttccttgatctgcgtttctactgcatgttgatgcctgcag
          | ||| ||   |   ||    |  |  |         | ||  |   ||||||| |||||||||||||| ||||||||| | ||||| |||| |    | |  |  |   ||||    |  |||         ||   ||| ||    |||||   |||| ||      ||  | ||| |  | | ||
CTTGCCAAAGGAAAAAGGCTAAAGAGAAACCCACACACACACACACACACAGAAATATGTCTTCCCCAAGCAAGCGCCGAGAGATGGACTTGATGAAACTgttaatcctttc-tctctcaattcatcaaagtttcaatcttttttctaatggggtctcttcctgattctgggtcctctttgtcttttgttttccgtag

upper sequence: GRMZM2G150867_T01 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA07G07540.1 (Glycine max), 5'ss of exon 1
-------CGTAAAGGGAGGAGCGGAGCG-GCGAATTCTTGTGGTTTCCCAAGA----TGTCTTCTCCAAGCAAGCGCCGGGAGATGGACCTCATGAAGCTGTGAGGATTCTGgtggcgtgattcggtgattttttctataggatttcgatgcggattccttgatctgcgtttctactgcatgttgatgcctgcag-------------------------------------------
            |      | |  | |   |  |     |      |  || |    ||||||||||||||||||| || ||||||||| | ||||| |||| |  || |      | |  |  | |    |||||  |   ||||| ||     ||      | |   ||   | ||  |||  | |  ||                                              
AAGTAACTAAGGAAAAGAAAACACAACACACACACAAAGGAAAAAACAGAAAAACCATGTCTTCTCCAAGCAAGCGGCGAGAGATGGACTTGATGAAACTgtta--atcc--accacttcttctgttttccttttcccttctatttccattaaagttataattttttttttctaattgggtgtctaagtttgactcttgattctgattttgatgttagtttttttttttaattaatag

upper sequence: GRMZM2G150867_T01 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA07G07540.2 (Glycine max), 5'ss of exon 1
CGTAAAGGGAGGAGCGGAGCGGCGAATTCTTGTGGTTTCCCAAGATGTCTTCTCCAAGCAAGCGCCGGGAGATGGACCTCATGAAGCTGTGAGGATTCTGgtggcgtgattcggtgattttttctataggatttcgatgcggattccttgatctgcgtttctactgcatgttgatgcctgcag-------------------------------------------
    |    |    |  |     |||            ||    |||||||||||||||||||| || ||||||||| | ||||| |||| |  || |      | |  |  | |    |||||  |   ||||| ||     ||      | |   ||   | ||  |||  | |  ||                                              
----ACACAACACACACACAAAGGAAAAAACAGAAAAACC----ATGTCTTCTCCAAGCAAGCGGCGAGAGATGGACTTGATGAAACTGTTA--ATCC--ACCACTTCTTCTgttttccttttcccttctatttccattaaagttataattttttttttctaattgggtgtctaagtttgactcttgattctgattttgatgttagtttttttttttaattaatag

upper sequence: GRMZM2G150867_T01 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA18G46940.1 (Glycine max), 5'ss of exon 1
----CGTAAAGGGAGGAGCGGAGCGGCGAATTCTTGTGGTTTCCCA-------AGATGTCTTCTCCAAGCAAGCGCCGGGAGATGGACCTCATGAAGCTGTGAGGATTCTGgtggcgt--------------gattcggtgattttttctataggat---ttcgatgcggattccttgatctgcgtttctactgcatgttgatgcctgcag-
       | | | |   ||  |||   | |            | ||       | |||||||| |||||||||||||| ||||||||| | ||||| |||| |    | |       |              | |||  |  |||| |  || || |   |||  |     |||||   |||| ||      ||  | ||     | | || 
GCTAAAGAGAAGAAAAGGCAAAGCAAGGGACCAACCAAAACACACACAGAGAAACATGTCTTCCCCAAGCAAGCGCCGAGAGATGGACTTGATGAAACTGttaatcctttctctctctctcaattcatcaaagtttcaatctttttgttaatggggtctcttccctttctgttcctgattctgggtcctctttgtcttttctcttccgtagg

upper sequence: GRMZM2G150867_T01 (Zea mays), 5'ss of exon 1
lower sequence: PP1S161_122V6.1 (Physcomitrella patens), 5'ss of exon 1
CGTAAAGGGAGGAGCGGAGCGGCGAATTCTTGTGGTTTCCCAAGATGTCTTCTCCAAGCAAGCGCCGGGAGATGGACCTCATGAAGCTGTGAGGATTCTGgtggcgtgattcggtgattttttctataggatttcgatgcggattccttgatctgcgtttctactgcatg----ttgatgcctgcag-----
                                            ||||| || ||||||||||| |||||||||||| | |||||||||| ||    |||||    |  || | |  |||| |    |   ||| | ||  | ||   ||   ||   ||  | ||| |     ||| |    | ||     
--------------------------------------------ATGTCATCCCCAAGCAAGCGGCGGGAGATGGACGTGATGAAGCTgtaagtcccctggtttaattgtttgct--ttttgttggaattgttttggtg--gttttggtgcggtgtagtttcagtgcttagtttttggtattggtaggattg

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|211541018|gb|FL000893.1|FL000893
EST:     TCTCCAAGCAAGCGCCGGGAGATGGACCTCATG-A------A-G---CT-                         GATGATGAGCGACTACAAGGTGGATATGGTGAACGATGGGATGCAGGAGTT
genomic: TCTCCAAGCAAGCGCCGGGAGATGGACCTCATGAAGCTGTGAGGATTCTGgtggcgtgat ... atgcctgcagGATGATGAGCGACTACAAGGTGGATATGGTGAACGATGGGATGCAGGAGTT
EST: gi|211427763|gb|FL233521.1|FL233521
EST:     TCTCCAAGCAAGCGCCGGGAGATGGACCTCATGAAGCTGTGAGGATTCTG                         GATGATGAGCGACTACAAGGTGGATATGGTGAACGATGGGATGCAGGAGTT
genomic: TCTCCAAGCAAGCGCCGGGAGATGGACCTCATGAAGCTGTGAGGATTCTGgtggcgtgat ... atgcctgcagGATGATGAGCGACTACAAGGTGGATATGGTGAACGATGGGATGCAGGAGTT
EST: gi|37394410|gb|CF634479.1|CF634479
EST:     TCTCCAAGCAAGCGCCGGGAGATGGACCTCATG-A------A-G---CT-                         GATGATGAGCGACTACAAGGTGGATATGGTGAACGATGGGATGCAGGAGTT
genomic: TCTCCAAGCAAGCGCCGGGAGATGGACCTCATGAAGCTGTGAGGATTCTGgtggcgtgat ... atgcctgcagGATGATGAGCGACTACAAGGTGGATATGGTGAACGATGGGATGCAGGAGTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGTAAAGGGAGGAGCGGAGCGGCGAATTCTTGTGGTTTCCCAAGATGTCTTCTCCAAGCAAGCGCCGGGAGATGGACCTCATGAAGCTGTGAGGATTCTGgtggcgtgattcggtgattttttctataggatttcgatgcggattccttgatctgcgtttctactgcatgttgatgcctgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT