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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcagacagaaacttcgatattctataagtatatcggaattaaacttgtatactgacgctgtctgtcttgcctttttcagATCGCAAAGCTGTGTATCATTCCAGTCTTATGCATTCTGGAAATCATGTTCGACAAAGTCCGTTACTCTAGAGATACAAAGCTCAGTATAGTGCTTGTCC

Basic information

species Zea mays
transcript GRMZM2G089630_T04
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G089630_T04 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os02g40090.4 (Oryza sativa), 3'ss of exon 3
gtgcagacagaaacttcga--tattctataagta-tatcggaattaaacttgtatactgacgctgtctgtcttgcctttttcagATCGCAAAGCTGTGTATCATTCCAGTCTTATGCATTCTGGAAATCATGTTCGACAAAGTCCGTTACTCTAGAGATACAAAGCTCAGTATAGTGCTTGTCC
|||   | || || ||  |    |||||||   | | |  ||||  |      ||||| |   |   | || ||||| || ||||| || ||| ||||||| ||||||||||| ||||||||||||||| |||| ||||||||||||||||| ||  ||||||| |||||||||||||||||  
gtgggaagagtaattttaaatccttctatattcaatgttagaatggagggcacatactaattttcgtt-tcatgcctctt-cagATTGCCAAGTTGTGTATTATTCCAGTCTTGTGCATTCTGGAAATCCTGTTTGACAAAGTCCGTTACTCAAGGAATACAAAACTCAGTATAGTGCTTGTTT

upper sequence: GRMZM2G089630_T04 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os05g12490.1 (Oryza sativa), 3'ss of exon 3
gtgcagacagaaacttcgatattctataagta-tatcggaattaaacttgtatactgacgctgtctgtcttgcctttttcagATCGCAAAGCTGTGTATCATTCCAGTCTTATGCATTCTGGAAATCATGTTCGACAAAGTCCGTTACTCTAGAGATACAAAGCTCAGTATAGTGCTTGTCC
||| ||| || ||||  |   ||  ||    | | |  |||||  |    |||||| |   ||    || |||||||||||||| || ||| | || ||||||||||| || ||| ||||||||||| |||| || |||||||| ||||| |||||||||||| |||||||| || |||| |
gtgaagaaagtaactaagtcctttaatgttcacttttagaattggatgcatatactaat-ttgctcctcatgcctttttcagATTGCCAAGTTATGCATCATTCCAGTTTTGTGCTTTCTGGAAATCCTGTTTGATAAAGTCCGATACTCAAGAGATACAAAGTTCAGTATAATGGTTGTTC
















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|149080981|gb|EE170080.2|EE170080
EST:     TTGTTGGGATGAATGTAAGCTTGATGTGGAACTCTGTTGGATTCTATCAG                         ATCGCAAAGCTGTGTATCATTCCAGTCTTATGCATTCTGGAAATCATGTTC
genomic: TTGTTGGGATGAATGTAAGCTTGATGTGGAACTCTGTTGGATTCTATCAGgtgcagacag ... cctttttcagATCGCAAAGCTGTGTATCATTCCAGTCTTATGCATTCTGGAAATCATGTTC
EST: gi|149079572|gb|EE168560.2|EE168560
EST:     TTGTTGGGATGAATGTAAGCTTGATGTGGAACTCTGTTGGATTCTATCAG                         ATCGCAAAGCTGTGTATCATTCCAGTCTTATGCATTCTGGAAATCATGTTC
genomic: TTGTTGGGATGAATGTAAGCTTGATGTGGAACTCTGTTGGATTCTATCAGgtgcagacag ... cctttttcagATCGCAAAGCTGTGTATCATTCCAGTCTTATGCATTCTGGAAATCATGTTC
EST: gi|149096862|gb|EE182656.2|EE182656
EST:     TTGTTGGGATGAATGTAAGCTTGATGTGGAACTCTGTTGGATTCTATCAG                         ATCGCAAAGCTGTGTATCATTCCAGTCTTATGCATTCTGGAAATCATGTTC
genomic: TTGTTGGGATGAATGTAAGCTTGATGTGGAACTCTGTTGGATTCTATCAGgtgcagacag ... cctttttcagATCGCAAAGCTGTGTATCATTCCAGTCTTATGCATTCTGGAAATCATGTTC
EST: gi|93012953|gb|EB638473.1|EB638473
EST:     TTGTTGGGATGAATGTAAGCTTGATGTGGAACTCTGTTGGATTCTATCAG                         ATCGCAAAGCTGTGTATCATTCCAGTCTTATGCATTCTGGAAATCATGTTC
genomic: TTGTTGGGATGAATGTAAGCTTGATGTGGAACTCTGTTGGATTCTATCAGgtgcagacag ... cctttttcagATCGCAAAGCTGTGTATCATTCCAGTCTTATGCATTCTGGAAATCATGTTC
EST: gi|74239699|gb|DT647613.1|DT647613
EST:     TTGTTGGGATGAATGTAAGCTTGATGTGGAACTCTGTTGGATTCTATCAG                         ATCGCAAAGCTGTGTATCATTCCAGTCTTATGCATTCTGGAAATCATGTTC
genomic: TTGTTGGGATGAATGTAAGCTTGATGTGGAACTCTGTTGGATTCTATCAGgtgcagacag ... cctttttcagATCGCAAAGCTGTGTATCATTCCAGTCTTATGCATTCTGGAAATCATGTTC
EST: gi|149080644|gb|EE169696.2|EE169696
EST:     TTGTTGGGATGAATGTAAGCTTGATGTGGAACTCTGTTGGATTCTATCAG                         ATCGCAAAGCTGTGTATCATTCCAGTCTTATGCATTCTGGAAATCATGTTC
genomic: TTGTTGGGATGAATGTAAGCTTGATGTGGAACTCTGTTGGATTCTATCAGgtgcagacag ... cctttttcagATCGCAAAGCTGTGTATCATTCCAGTCTTATGCATTCTGGAAATCATGTTC
EST: gi|149088966|gb|EE178110.2|EE178110
EST:     TTGTTGGGATGAATGTAAGCTTGATGTGGAACTCTGTTGGATTCTATCAG                         ATCGCAAAGCTGTGTATCATTCCAGTCTTATGCATTCTGGAAATCATGTTC
genomic: TTGTTGGGATGAATGTAAGCTTGATGTGGAACTCTGTTGGATTCTATCAGgtgcagacag ... cctttttcagATCGCAAAGCTGTGTATCATTCCAGTCTTATGCATTCTGGAAATCATGTTC
EST: gi|32919453|gb|CF024265.1|CF024265
EST:     TTGTTGGGATGAATGTAAGCTTGATGTGGAACTCTGTTGGATTCTATCAG                         ATCGCAAAGCTGTGTATCATTCCAGTCTTATGCATTCTGGAAATCATGTTC
genomic: TTGTTGGGATGAATGTAAGCTTGATGTGGAACTCTGTTGGATTCTATCAGgtgcagacag ... cctttttcagATCGCAAAGCTGTGTATCATTCCAGTCTTATGCATTCTGGAAATCATGTTC
EST: gi|50326262|gb|CO521388.1|CO521388
EST:     TTGTTGGGATGAATGTAAGCTTGATGTGGAACTCTGTTGGATTCTATCAG                         ATCGCAAAGCTGTGTATCATTCCAGTCTTATGCATTCTGGAAATCATGTTC
genomic: TTGTTGGGATGAATGTAAGCTTGATGTGGAACTCTGTTGGATTCTATCAGgtgcagacag ... cctttttcagATCGCAAAGCTGTGTATCATTCCAGTCTTATGCATTCTGGAAATCATGTTC
EST: gi|37421524|gb|CF648462.1|CF648462
EST:     TTGTTGGGATGAATGTAAGCTTGATGTGGAACTCTGTTGGATTCTATCAG                         ATCGCAAAGCTGTGTATCATTCCAGTCTTATGCATTCTGGAAATCATGTTC
genomic: TTGTTGGGATGAATGTAAGCTTGATGTGGAACTCTGTTGGATTCTATCAGgtgcagacag ... cctttttcagATCGCAAAGCTGTGTATCATTCCAGTCTTATGCATTCTGGAAATCATGTTC
EST: gi|110223714|gb|EC905612.1|EC905612
EST:     TTGTTGGGATGAATGTAAGCTTGATGTGGAACTCTGTTGGATTCTATCAG                         ATCGCAAAGCTGTGTATCATTCCCAGTCTTATGCATTCTGGAAATC
genomic: TTGTTGGGATGAATGTAAGCTTGATGTGGAACTCTGTTGGATTCTATCAGgtgcagacag ... cctttttcagATCGCAAAGCTGTGTATCATTCC-AGTCTTATGCATTCTGGAAATC
EST: gi|71436369|gb|DR817419.1|DR817419
EST:     TTGTTGGGATGAATGTAAGCTTGATGTGGAACTCTGTTGGATTCTATCAG                         ATCGCAAAGCTGTGTATCATTCCAGTCTTATGCATTCTGGAAATCATGTTC
genomic: TTGTTGGGATGAATGTAAGCTTGATGTGGAACTCTGTTGGATTCTATCAGgtgcagacag ... cctttttcagATCGCAAAGCTGTGTATCATTCCAGTCTTATGCATTCTGGAAATCATGTTC
EST: gi|148945696|gb|EC890969.2|EC890969
EST:     TTGTTGGGATGAATGTAAGCTTGATGTGGAACTCTGTTGGATTCTATCAG                         ATCGCAAAGCTGTGTATCATTCCAGTCTTATGCATTCTGGAAATCATGTTC
genomic: TTGTTGGGATGAATGTAAGCTTGATGTGGAACTCTGTTGGATTCTATCAGgtgcagacag ... cctttttcagATCGCAAAGCTGTGTATCATTCCAGTCTTATGCATTCTGGAAATCATGTTC
EST: gi|149090129|gb|EE179428.2|EE179428
EST:     TTGTTGGGATGAATGTAAGCTTGATGTGGAACTCTGTTGGATTCTATCAG                         ATCGCAAAGCTGTGTATCATTCCAGTCTTATGCATTCTGGAAATCATGTTC
genomic: TTGTTGGGATGAATGTAAGCTTGATGTGGAACTCTGTTGGATTCTATCAGgtgcagacag ... cctttttcagATCGCAAAGCTGTGTATCATTCCAGTCTTATGCATTCTGGAAATCATGTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taagtatatcggaattaaacttgtatactgacgctgtctgtcttgcctttttcagATCGCAAAGCTGTGTATCATTCCAGTCTTATGCATTCTGGAAATCATGTTCGACAAAGTCCGTTACTCTAGAGATACAAAGCTCAGTATAGTGCTTGTCC
                         tactgac  putative branch site (score: 1)
                                    tctgtcttgccttttt  putative PPT
            aattaaacttgtata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcagacagaaacttcgatattctataagtatatcggaattaaacttgtatactgacgctgtctgtcttgcctttttcagATCGCAAAGCTGTGTATCATTCCAGTCTTATGCATTCTGGAAATCATGTTCGACAAAGTCCGTTACTCTAGAGATACAAAGCTCAGTATAGTGCTTGTCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA