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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ataggaaacttttggccgttaccttgacttgcatgagctttacaaacagttttaattatgttttctgatgaagtgatgatctggttctgcattttgatagGAAACTTTTGGCCGTTACCTTGACTTGCATGAGCTTTATAATGAGTTCATAAATTCCAAGTTCGGAACACTGATGGAATATTCAGCTTATGTTGGCTGTT

Basic information

species Zea mays
transcript GRMZM2G178227_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G178227_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g50850.1 (Oryza sativa), 3'ss of exon 3
atagGAAACTTTTGGCCGTTACCTTGACTTGCATGAGCTTTACAAACAGTTTTAATTA-TGTTTTCTGATGAAGTGATGATCTGGTTCTGCATTTTGATAGGAAACTTTTGGCCGTTACCTTGACTTGCATGAGCTTTATAATGAGTTCATAAATTCCAAGTTCGGAACACTGATGGAATATTCAGCTTATGTTGGCTGTT
|   | | |   || ||   ||  ||  |  |||  ||| |  |     || | |||  ||  |||   |    | ||| | |||||||||| ||| ||||||| |||||||||| ||||| ||||||||||||||||| ||||||||||||||||||||||| ||||| |  |||||||| ||||| |||||||||   |
agtcgcatcgcatgtccaccactgtggttgtcatt-gctatgtactattttatcattgctgaattcaagtatgctaatggtttggttctgcaatttaatagGAAGCTTTTGGCCGATACCTGGACTTGCATGAGCTTTACAATGAGTTCATAAATTCCAAGTTTGGAACTCCAATGGAATACTCAGCATATGTTGGCACCT

upper sequence: GRMZM2G178227_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g50850.1 (Oryza sativa), 3'ss of exon 3
atagGAAACTTTTGGCCGTTACCTTGACTTGCATGAGCTTTACAAACAGTTTTAATTA-TGTTTTCTGATGAAGTGATGATCTGGTTCTGCATTTTGATAGGAAACTTTTGGCCGTTACCTTGACTTGCATGAGCTTTATAATGAGTTCATAAATTCCAAGTTCGGAACACTGATGGAATATTCAGCTTATGTTGGCTGTT
|   | | |   || ||   ||  ||  |  |||  ||| |  |     || | |||  ||  |||   |    | ||| | |||||||||| ||| ||||||| |||||||||| ||||| ||||||||||||||||| ||||||||||||||||||||||| ||||| |  |||||||| ||||| |||||||||   |
agtcgcatcgcatgtccaccactgtggttgtcatt-gctatgtactattttatcattgctgaattcaagtatgctaatggtttggttctgcaatttaatagGAAGCTTTTGGCCGATACCTGGACTTGCATGAGCTTTACAATGAGTTCATAAATTCCAAGTTTGGAACTCCAATGGAATACTCAGCATATGTTGGCACCT
















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|60393978|gb|DN226848.1|DN226848
EST:     ACTATGAAGAGCTTCTAAAGGAGGAACCAGTTATTGAATTCACTGGCGAG                         GAAACTTTTGGCCGTTACCTTGACTTGCATGAGCTTTATAATGAGTTCATA
genomic: ACTATGAAGAGCTTCTAAAGGAGGAACCAGTTATTGAATTCACTGGCGAGgtattgtcac ... attttgatagGAAACTTTTGGCCGTTACCTTGACTTGCATGAGCTTTATAATGAGTTCATA
EST: gi|76290494|gb|DV030062.1|DV030062
EST:     ACTATGAAGAGCTTCTAAAGGAGGAACCAGTTATTGAATTCACTGGCGAG                         GAAACTTTTGGCCGTTACCTTGACTTGCATGAGCTTTATAATGAGTTCATA
genomic: ACTATGAAGAGCTTCTAAAGGAGGAACCAGTTATTGAATTCACTGGCGAGgtattgtcac ... attttgatagGAAACTTTTGGCCGTTACCTTGACTTGCATGAGCTTTATAATGAGTTCATA
EST: gi|31353537|gb|CD437894.1|CD437894
EST:     ACTATGAAGAGCTTCTAAAGGAGGAACCAGTTATTGAATTCACTGGCGAG                         GAAACTTTTGGCCGTTACCTTGACTTGCATGAGCTTTATAATGAGTTCATA
genomic: ACTATGAAGAGCTTCTAAAGGAGGAACCAGTTATTGAATTCACTGGCGAGgtattgtcac ... attttgatagGAAACTTTTGGCCGTTACCTTGACTTGCATGAGCTTTATAATGAGTTCATA
EST: gi|78087329|gb|DV515722.1|DV515722
EST:     ACTATGAAGAGCTTCTAAAGGAGGAACCAGTTATTGAATTCACTGGCGAG                         GAAACTTTTGGCCGTTACCTTGACTTGCATGAGCTTTATAATGAGTTCATA
genomic: ACTATGAAGAGCTTCTAAAGGAGGAACCAGTTATTGAATTCACTGGCGAGgtattgtcac ... attttgatagGAAACTTTTGGCCGTTACCTTGACTTGCATGAGCTTTATAATGAGTTCATA
EST: gi|211324079|gb|FL420998.1|FL420998
EST:     ACTATGAAGAGCTTCTAAAGGAGGAACCAGTTATTGAATTCACTGGCGAG                         GAAACTTTTGGCCGTT
genomic: ACTATGAAGAGCTTCTAAAGGAGGAACCAGTTATTGAATTCACTGGCGAGgtattgtcac ... attttgatagGAAACTTTTGGCCGTT
EST: gi|76285477|gb|DV025045.1|DV025045
EST:     ACTATGAAGAGCTTCTAAAGGAGGAACCAGTTATTGAATTCACTGGCGAG                         GAAACTTTTGGCCGTTACCTTGACTTGCATGAGCTTTATAATGAGTTCATA
genomic: ACTATGAAGAGCTTCTAAAGGAGGAACCAGTTATTGAATTCACTGGCGAGgtattgtcac ... attttgatagGAAACTTTTGGCCGTTACCTTGACTTGCATGAGCTTTATAATGAGTTCATA
EST: gi|211048309|gb|FL397306.1|FL397306
EST:     ACTATGAAGAGCTTCTAAAGGAGGAACCAGTTATTGAATTCACTGGCGAG                         GAAACTTTTGGCCGTTACCTTGACTTGCATGAGCTTTAT
genomic: ACTATGAAGAGCTTCTAAAGGAGGAACCAGTTATTGAATTCACTGGCGAGgtattgtcac ... attttgatagGAAACTTTTGGCCGTTACCTTGACTTGCATGAGCTTTAT
EST: gi|211186071|gb|FL219845.1|FL219845
EST:     ACTATGAAGAGCTTCTAAAGGAGGAACCAGTTATTGAATTCACTGGCGAG                         GAAACTTTTGGCCGTTACCTTGACTTGCATGAGCTTTATAATGAGTTCATA
genomic: ACTATGAAGAGCTTCTAAAGGAGGAACCAGTTATTGAATTCACTGGCGAGgtattgtcac ... attttgatagGAAACTTTTGGCCGTTACCTTGACTTGCATGAGCTTTATAATGAGTTCATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acagttttaattatgttttctgatgaagtgatgatctggttctgcattttgatagGAAACTTTTGGCCGTTACCTTGACTTGCATGAGCTTTATAATGAGTTCATAAATTCCAAGTTCGGAACACTGATGGAATATTCAGCTTATGTTGGCTGTT
                 ttctgat  putative branch site (score: 3)
     tttaattatgttttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ataggaaacttttggccgttaccttgacttgcatgagctttacaaacagttttaattatgttttctgatgaagtgatgatctggttctgcattttgatagGAAACTTTTGGCCGTTACCTTGACTTGCATGAGCTTTATAATGAGTTCATAAATTCCAAGTTCGGAACACTGATGGAATATTCAGCTTATGTTGGCTGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - -tgcatga
- - - - - - - - - - - - - - - - - - - - -acaaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatgat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gttctgc