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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgtaatagttttgtccattgtatttggtggctgtggttccaatctagaaaatcctaagtaacctcataagtgcatctatcaattggtgtagATTCCAGAAGAGGAAAAAAATATAGGCCCAAATGATCGGCTAATTCATGTTTATCACTTCAAGAAAGATATTAATCAGACTCAG

Basic information

species Zea mays
transcript GRMZM2G418232_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G418232_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os11g36470.1 (Oryza sativa), 3'ss of exon 23
--------------------------------------------gtgtgtaatagttttgtccattgtatttggtggctgtggttccaatctagaaaatcctaagtaacctcataagtgcatctatcaattggtgtagATTCCAGAAGAGGAAAAAAATATAGGCCCAAATGATCGGCTAATTCATGTTTATCACTTCAAGAAAGATATTAATCAGACTCAG
                                               |||||   |    || |||  ||||  ||  ||||  || ||    |    | |    || |||||||  ||| |||    ||||||  |||||||||| ||||| |||||| | || |||||||||||| ||||||||||||||||||||| ||||||   |  ||||| ||||
gtatgtaatgttctttttggttgcatttggtgctccatttcgtgaactgtaaagttgcaatctatttcatttcctgcttgtg--tcaaaatgtgcgccttcattctatcctcatatctgcttctgcttattggtacagATTCCAGAGGAGGAGAAAAATCTCGGTCCAAATGATCGGTTAATTCATGTTTATCACTTCATGAAAGACCCTCTTCAGAATCAG
















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|76936264|gb|DV174663.1|DV174663
EST:     AGAAGATAGAGAATATAAACGACCAATATTGGACACTACGTGCTGAGGAG                         ATTCCAGAAGAGGNNNNNNNTATAGGCCCAAATGATCGGCTAATTCATGTT
genomic: AGAAGATAGAGAATATAAACGACCAATATTGGACACTACGTGCTGAGGAGgtgtgtaata ... attggtgtagATTCCAGAAGAGGAAAAAAATATAGGCCCAAATGATCGGCTAATTCATGTT
EST: gi|78113609|gb|DV532000.1|DV532000
EST:     AGAAGATAGAGAATATAAACGACCCATATTGGACACTACGTGCTGAGGAG                         ATTCCAGAAGAGG
genomic: AGAAGATAGAGAATATAAACGACCAATATTGGACACTACGTGCTGAGGAGgtgtgtaata ... attggtgtagATTCCAGAAGAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttccaatctagaaaatcctaagtaacctcataagtgcatctatcaattggtgtagATTCCAGAAGAGGAAAAAAATATAGGCCCAAATGATCGGCTAATTCATGTTTATCACTTCAAGAAAGATATTAATCAGACTCAG
                   aagtaac  putative branch site (score: 2)
        tagaaaat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtgtaatagttttgtccattgtatttggtggctgtggttccaatctagaaaatcctaagtaacctcataagtgcatctatcaattggtgtagATTCCAGAAGAGGAAAAAAATATAGGCCCAAATGATCGGCTAATTCATGTTTATCACTTCAAGAAAGATATTAATCAGACTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA