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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGATTAGTTATAGTAAGAGAAGAAGCTCGGAATATGATGGGAGGTGGCCTGTTAGATGAGAGAAATGATCGTGGTTTGACTACCCTCCCTGAGGCAGAGgtacttttaaacttggaaatcttaatgtgacatgcatggtagatgtgtattccatgactaattgcaaaatatccttttataagggtcttcagtctctttg...

Basic information

species Zea mays
transcript GRMZM2G079452_T02
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G079452_T02 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os11g23790.2 (Oryza sativa), 5'ss of exon 5
AAGATTAGTTATAGTAAGAGAAGAAGCTCGGAATATGATGGGAGGTGGCCTGTTAGATGAGAGAAATGATCGTGGTTTGACTACCCTCCCTGAGGCAGAGgtacttttaaacttggaaatcttaatgtgacatgcatggtagatgtgtattccatgactaattgcaaaa-tatccttttataagggtcttcagtctctttg-----
 ||| ||||||| |||||||| || ||||| ||||||||||||||||||||||||||||| |||||||| |||||||| || || || ||||||||||||||| |     | ||| |  | ||   |       || ||   || |  ||||   || |   | |  |  ||    | || |  |    ||  | |   |      
TAGACTAGTTATCGTAAGAGAGGAGGCTCGAAATATGATGGGAGGTGGCCTGTTAGATGAAAGAAATGACCGTGGTTTCACAACGCTTCCTGAGGCAGAGgtatt-----atttgcacttgttggggcttgggacacggggaat-tacattcttagaatctctacccatctagttctatacatagaatatcttttttactaacatt

upper sequence: GRMZM2G079452_T02 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA03G22370.1 (Glycine max), 5'ss of exon 5
AAGATTAGTTATAGTAAGAGAAGAAGCTCGGAATATGATGGGAGGTGGCCTGTTAGATGAGAGAAATGATCGTGGTTTGACTACCCTCCCTGAGGCAGAGgtacttttaaacttggaaatcttaatgtgacat--gcatggtagatgtgtattccatgac-taattgcaaaatatccttttataag--ggtcttcagtctctttg-------------------------------------------------------------------------------------------
|||  | ||| |  | |||||||||||||| |||||||||||||| ||  |    || || |||||  | ||||| ||   ||| || ||| || | ||||||  || |    | |   || |  |||||  |  |||||||       | |  |   || | |    | | |||  | || | |   | | ||     |  |||                                                                                           
AAGGCTTGTTTTGATTAGAGAAGAAGCTCGTAATATGATGGGAGGGGGAATTACGGACGAAAGAAACCACCGTGGATTCTATACTCTTCCTCAGCCTGAGgtatgttgatctatagttttcatcttgtgatcttagcatggttctcacttctagcgaaacattacctaacagtattttgttttcatctgattttacccgttgttgctaaaagggcttggaaattaaaactacatagatattgtctttcattgtcagaaatactgtcttggcatctttaaaaccgttgacagtgcag

upper sequence: GRMZM2G079452_T02 (Zea mays), 5'ss of exon 5
lower sequence: Vv00s0333g00020.t01 (Vitis vinifera), 5'ss of exon 5
AAGATTAGTTATAGTAAGAGAAGAAGCTCGGAATATGATGGGAGGTGGCCTGTTAGATGAGAGAAATGATCGTGGTTTGACTACCCTCCCTGAGGCAGAGgt----acttttaaacttggaaatcttaatgtgacatgcatggtagatgtgtattccatgactaattgcaaaatatccttttataagggtcttcagtctctttg
|||| | ||| |  | ||||| ||||| ||||||||||||||||||||  |  ||||||| || ||||| |||||||||| ||||||||| ||  |||||||    | | ||||  | ||  ||||| |    |  |  | |   |     |  | | | | |      ||  |    |||  | |      | | |       
AAGACTGGTTTTGATCAGAGAGGAAGCCCGGAATATGATGGGAGGTGGAATACTAGATGAAAGGAATGACCGTGGTTTGAATACCCTCCCCGAATCAGAGgtttgtattcttaatttagggtatcttgaatctaattataggacggccagatgattc-tcattggcc-taactttgtttttagtgaaatatattaatgaaaa--

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|71311108|gb|DR791867.1|DR791867
EST:     TGTTAGATGAGAGAAATGATCGTGGTTTGACTACCCTCCCTGAGGCAGAG                         GTAAACTTTTTGAGCAAGCTCGTTGCTCTTAA
genomic: TGTTAGATGAGAGAAATGATCGTGGTTTGACTACCCTCCCTGAGGCAGAGgtacttttaa ... aaattgacagGTAAACTTTTTGAGCAAGCTCGTTGCTCTTAA
EST: gi|76012260|gb|DT939430.1|DT939430
EST:     TGTTAGATGAGAGAAATGATCGTGGTTTGACTACCCTCCCTGAGGCAGAG                         GTAAACTTTTTGAGCAAGCTCGTTGCTCTTAAACC
genomic: TGTTAGATGAGAGAAATGATCGTGGTTTGACTACCCTCCCTGAGGCAGAGgtacttttaa ... aaattgacagGTAAACTTTTTGAGCAAGCTCGTTGCTCTTAAACC
EST: gi|71429968|gb|DR811018.1|DR811018
EST:     TGTTAGATGAGAGAAATGATCGTGGTTTGACTACCCTCCCTGAGGCAGAA                         GTAAACTTTTTGAGCAAGCTCGTTGC
genomic: TGTTAGATGAGAGAAATGATCGTGGTTTGACTACCCTCCCTGAGGCAGAGgtacttttaa ... aaattgacagGTAAACTTTTTGAGCAAGCTCGTTGC
EST: gi|78090608|gb|DV518982.1|DV518982
EST:     TGTTAGATGAGAGAAATGATCGTGGTTTGACTACCCTCTCTGAGGCAGAG                         GTAAACTTTTTGAGCAAGCTCGTTGCTCTTAAACCTGGGAAGGCATTGGAA
genomic: TGTTAGATGAGAGAAATGATCGTGGTTTGACTACCCTCCCTGAGGCAGAGgtacttttaa ... aaattgacagGTAAACTTTTTGAGCAAGCTCGTTGCTCTTAAACCTGGGAAGGCATTGGAA
EST: gi|149096864|gb|EE182658.2|EE182658
EST:     TGTTAGATGAGAGAAATGATCGTGGTTTGACTACCCTCCCTGAGGCAGAG                         GTAAACTTTTTGAAGCA-GCTCGTTGCTCTTAAAACTGG
genomic: TGTTAGATGAGAGAAATGATCGTGGTTTGACTACCCTCCCTGAGGCAGAGgtacttttaa ... aaattgacagGTAAACTTTTTGA-GCAAGCTCGTTGCTCTTAAACCTGG
EST: gi|71444932|gb|DR825982.1|DR825982
EST:     TGTTAGATGAGAGAAATGATCGTGGTTTGACTACCCTCCCTGAGGCAGAG                         GTAAACTTTTTGAGCAAGCTCGTTGC
genomic: TGTTAGATGAGAGAAATGATCGTGGTTTGACTACCCTCCCTGAGGCAGAGgtacttttaa ... aaattgacagGTAAACTTTTTGAGCAAGCTCGTTGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAGATTAGTTATAGTAAGAGAAGAAGCTCGGAATATGATGGGAGGTGGCCTGTTAGATGAGAGAAATGATCGTGGTTTGACTACCCTCCCTGAGGCAGAGgtacttttaaacttggaaatcttaatgtgacatgcatggtagatgtgtattccatgactaattgcaaaatatccttttataagggtcttcagtctctttg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcaaaata