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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcgagtggatacagaagacattgctgttctcatagtttttttaacaaaatattataaaggcatgctttgtcctttttctcacataaccaagctgttgtcttttacttgcagAGCATTTTACTTTCAGTCAATGACCTACTGGCATGCTGCGGTTTTATGTGCGGCGATGGGTGTGATGGAGGCTATCCTATAGAGGCATGGCGCTACTTTG

Basic information

species Zea mays
transcript GRMZM2G108849_T04
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G108849_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os05g24550.4 (Oryza sativa), 3'ss of exon 7
gcgagtggatacagaagacattgctgttctcatagtttttttaacaaaatattataaaggcatgctttgtcctttttctcacataaccaagctgttgtctttta---cttgcagAGCATTTTACTTTCAGTCAATGACCTACTGGCATGCTGCGGTTTTATGTGCGGCGATGGGTGTGATGGAGGCTATCCTATAGAGGCATGGCGCTACTTTG
|  |||| |||   | ||||   | |||||||| |           ||   || |||    ||   |||| | ||| |||||||| |||||||  ||| |||||   |||| ||| |||||  || || |||||||||||| |||||||||||||||| |||||||||||||| ||||||||||||||||||||   |||||||||||||||||
gtcagtgaatatgaatgacaagtccgttctcatggcc---------aaggcttctaacttaatttattgttcctttgctcacatagccaagctactgttttttattccttgtagAACATTTCGCTATCTGTCAATGACCTAGTGGCATGCTGCGGTTTCATGTGCGGCGATGGTTGTGATGGAGGCTATCCTATCATGGCATGGCGCTACTTTG
















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|14191382|gb|BG833612.1|BG833612
EST:     TTGGTGCTGTGGAGTGCCTCCAGGACCGTTTTTGCATTCACCTCAACATG                         AGCATTTTACTTTCAGTCAATGACCTACTGGCATGCTGCGGTTTTATGTGC
genomic: TTGGTGCTGTGGAGTGCCTCCAGGACCGTTTTTGCATTCACCTCAACATGgcgagtggat ... ttacttgcagAGCATTTTACTTTCAGTCAATGACCTACTGGCATGCTGCGGTTTTATGTGC
EST: gi|211436684|gb|FL284632.1|FL284632
EST:     TTGGTGCTGTGGAGTGCCTCCAGGACCGTTTTTGCATTCACCTCAACATG                         AGCATTTTACTTTCAGTCAATGACCTACTGGCATG
genomic: TTGGTGCTGTGGAGTGCCTCCAGGACCGTTTTTGCATTCACCTCAACATGgcgagtggat ... ttacttgcagAGCATTTTACTTTCAGTCAATGACCTACTGGCATG
EST: gi|26557852|gb|CA830087.1|CA830087
EST:     TTGGTGCTGTGGAGTGCCTCCAGGACCGTTTTTGCATTCACCTCAACATG                         AGCATTTTACTTTCAGTCAATGACCTACT
genomic: TTGGTGCTGTGGAGTGCCTCCAGGACCGTTTTTGCATTCACCTCAACATGgcgagtggat ... ttacttgcagAGCATTTTACTTTCAGTCAATGACCTACT
EST: gi|211436683|gb|FL284631.1|FL284631
EST:     TTGGTGCTGTGGAGTGCCTCCAGGACCGTTTTTGCATTCACCTCAACATG                         AGCATTTTACTTTCAGTCAATGACCTACTGGCATGCTGCGGTTTTATGTGC
genomic: TTGGTGCTGTGGAGTGCCTCCAGGACCGTTTTTGCATTCACCTCAACATGgcgagtggat ... ttacttgcagAGCATTTTACTTTCAGTCAATGACCTACTGGCATGCTGCGGTTTTATGTGC
EST: gi|76282755|gb|DV022323.1|DV022323
EST:     TTGGTGCTGTGGAGTGCCTCCAGGACCGTTTTTGCATTCACCTCAACATG                         AGCATTTTACTTTCAGTCAATGACCTACTGGCATGCTGCGGTTTTATGTGC
genomic: TTGGTGCTGTGGAGTGCCTCCAGGACCGTTTTTGCATTCACCTCAACATGgcgagtggat ... ttacttgcagAGCATTTTACTTTCAGTCAATGACCTACTGGCATGCTGCGGTTTTATGTGC
EST: gi|33104176|gb|CF064136.1|CF064136
EST:     TTGGTGCTGTGGAGTGCCTCCAGGACCGTTTTTGCATTCACCTCAACATG                         AGCATTTTACTTTCAGTCAATGACCTACTGGCATGCTGCGGTTTTATGTGC
genomic: TTGGTGCTGTGGAGTGCCTCCAGGACCGTTTTTGCATTCACCTCAACATGgcgagtggat ... ttacttgcagAGCATTTTACTTTCAGTCAATGACCTACTGGCATGCTGCGGTTTTATGTGC
EST: gi|31354590|gb|CD438947.1|CD438947
EST:     TTGGTGCTGTGGAGTGCCTCCAGGACCGTTTTTGCATTCACCTCAACATG                         AGCATTTTACTTTCAGTCAATGACCTACTGGCATGCTGCGGTTTTATGTGC
genomic: TTGGTGCTGTGGAGTGCCTCCAGGACCGTTTTTGCATTCACCTCAACATGgcgagtggat ... ttacttgcagAGCATTTTACTTTCAGTCAATGACCTACTGGCATGCTGCGGTTTTATGTGC
EST: gi|211491805|gb|FL092420.1|FL092420
EST:     TTGGTGCTGTGGAGTGCCTCCASSACCGTTTTTGCATTCACCTCAACATG                         AGCATTTTACTTTCAGTCAATGACCTACTGGCATGCTGCGGTTTTATGTGC
genomic: TTGGTGCTGTGGAGTGCCTCCAGGACCGTTTTTGCATTCACCTCAACATGgcgagtggat ... ttacttgcagAGCATTTTACTTTCAGTCAATGACCTACTGGCATGCTGCGGTTTTATGTGC
EST: gi|211436676|gb|FL284624.1|FL284624
EST:     TTGGTGCTGTGGAGTGCCTCCAGGACCGTTTTTGCATTCACCTCAACATG                         AGCATTTTACTTTCAGTCAATGACCTACTGGCATGCTGCNGTTTTATGTGC
genomic: TTGGTGCTGTGGAGTGCCTCCAGGACCGTTTTTGCATTCACCTCAACATGgcgagtggat ... ttacttgcagAGCATTTTACTTTCAGTCAATGACCTACTGGCATGCTGCGGTTTTATGTGC
EST: gi|213184041|gb|FM183748.1|FM183748
EST:     TTGGTGCTGTGGAGTGCCTCCAGGACCGTTTTTGCATTCACCTCAACATG                         AGCATTTTACTTTCAGTCAATGACCTACTGGCATGCTGCGGTTTTATGTGC
genomic: TTGGTGCTGTGGAGTGCCTCCAGGACCGTTTTTGCATTCACCTCAACATGgcgagtggat ... ttacttgcagAGCATTTTACTTTCAGTCAATGACCTACTGGCATGCTGCGGTTTTATGTGC
EST: gi|211491804|gb|FL092419.1|FL092419
EST:     TTGGTGCTGTGGAGTGCCTCCAGGACCGTTTTTGCATTCACCTCAACATG                         AGCATTTTACTTTCAGTCAATGACCTACTGGCATGCTGCGGTTTTATGTGC
genomic: TTGGTGCTGTGGAGTGCCTCCAGGACCGTTTTTGCATTCACCTCAACATGgcgagtggat ... ttacttgcagAGCATTTTACTTTCAGTCAATGACCTACTGGCATGCTGCGGTTTTATGTGC
EST: gi|31355458|gb|CD439815.1|CD439815
EST:     TTGGTGCTGTGGAGTGCCTCCAGGACCGTTTTTGCATTCACCTCAACATG                         AGCATTTTACTTTCAGTCAATGACCTACTGGCATGCTGCGGTTTTATGTGC
genomic: TTGGTGCTGTGGAGTGCCTCCAGGACCGTTTTTGCATTCACCTCAACATGgcgagtggat ... ttacttgcagAGCATTTTACTTTCAGTCAATGACCTACTGGCATGCTGCGGTTTTATGTGC
EST: gi|33100519|gb|CF060479.1|CF060479
EST:     TTGGTGCTGTGGAGTGCCTCCAGGACCGTTTTTGCATTCACCTCAACATG                         AGCATTTTACTTTCAGTCAATGACCTACTGGCATGCTGCGGTTTTATGTGC
genomic: TTGGTGCTGTGGAGTGCCTCCAGGACCGTTTTTGCATTCACCTCAACATGgcgagtggat ... ttacttgcagAGCATTTTACTTTCAGTCAATGACCTACTGGCATGCTGCGGTTTTATGTGC
EST: gi|33092955|gb|CF052949.1|CF052949
EST:     TTGGTGCTGTGGAGTGCCTCCAGGACCGTTTTTGCATTCACCTCAACATG                         AGCATTTTACTTTCAGTCAATGACCTACTGGCATGCTGCGGTTTTATGTGC
genomic: TTGGTGCTGTGGAGTGCCTCCAGGACCGTTTTTGCATTCACCTCAACATGgcgagtggat ... ttacttgcagAGCATTTTACTTTCAGTCAATGACCTACTGGCATGCTGCGGTTTTATGTGC
EST: gi|211488929|gb|FL092414.1|FL092414
EST:     TTGGTGCTGTGGAGTGCCTCCAGGACCGTTTTTGCATTCACCTCAACATG                         AGCATTTTACTTTCAGTCAATGACCTACTGGCATGCTGCGGTTTTATGTGC
genomic: TTGGTGCTGTGGAGTGCCTCCAGGACCGTTTTTGCATTCACCTCAACATGgcgagtggat ... ttacttgcagAGCATTTTACTTTCAGTCAATGACCTACTGGCATGCTGCGGTTTTATGTGC
EST: gi|60345830|gb|DN212803.1|DN212803
EST:     TTGGTGCTGTGGAGTGCCTCCAGGACCGTTTTTGCATTCACCTCAACATG                         AGCATTTTACTTTCAGTCAATGACCTACTGGCATGCTGCGGTTTTATGTGC
genomic: TTGGTGCTGTGGAGTGCCTCCAGGACCGTTTTTGCATTCACCTCAACATGgcgagtggat ... ttacttgcagAGCATTTTACTTTCAGTCAATGACCTACTGGCATGCTGCGGTTTTATGTGC
EST: gi|211491801|gb|FL092416.1|FL092416
EST:     TTGGTGCTGTGGAGTGCCTCCAGGACCGTTTTTGCATTCACCTCAACATG                         AGCATTTTACTTTCAGTCAATGACCTACTGGCATGCTGCGGTTCTATGTGC
genomic: TTGGTGCTGTGGAGTGCCTCCAGGACCGTTTTTGCATTCACCTCAACATGgcgagtggat ... ttacttgcagAGCATTTTACTTTCAGTCAATGACCTACTGGCATGCTGCGGTTTTATGTGC
EST: gi|14191380|gb|BG833610.1|BG833610
EST:     TTGGTGCTGTGGAGTGCCTCCAGGACCGTTTTTGCATTCACCTCAACATG                         AGCATTTTACTTTCAGTCAATGACCTACTGGCATGCTGCGGTTTTATGTGC
genomic: TTGGTGCTGTGGAGTGCCTCCAGGACCGTTTTTGCATTCACCTCAACATGgcgagtggat ... ttacttgcagAGCATTTTACTTTCAGTCAATGACCTACTGGCATGCTGCGGTTTTATGTGC
EST: gi|14203538|gb|BG837215.1|BG837215
EST:     TTGGTGCTGT-GAGT-SCTCCAGGACCG-TTTTGCATTCACCTCAACATG                         AGCATTTTACTTTCAGTCAATGACCTACTGGCATGCTGCGGTTTTATGTGC
genomic: TTGGTGCTGTGGAGTGCCTCCAGGACCGTTTTTGCATTCACCTCAACATGgcgagtggat ... ttacttgcagAGCATTTTACTTTCAGTCAATGACCTACTGGCATGCTGCGGTTTTATGTGC
EST: gi|211042386|gb|FL284653.1|FL284653
EST:     TGGNTGCTGTGGAGTGC-TCCANGACCGTTTTTGCATTCAC-TCAACATG                         AGCATTTTACTTTCAGTCA-TGAC
genomic: TGG-TGCTGTGGAGTGCCTCCAGGACCGTTTTTGCATTCACCTCAACATGgcgagtggat ... ttacttgcagAGCATTTTACTTTCAGTCAATGAC
EST: gi|14191381|gb|BG833611.1|BG833611
EST:     TTGGTGCTGTGGAGTGCCTCCAGGACCGTTTTTGCATTCACCTCAACATG                         AGCATTTTACTTTCAGTCAATGACCTACTGGCATGCTGCGGTTTTATGTGC
genomic: TTGGTGCTGTGGAGTGCCTCCAGGACCGTTTTTGCATTCACCTCAACATGgcgagtggat ... ttacttgcagAGCATTTTACTTTCAGTCAATGACCTACTGGCATGCTGCGGTTTTATGTGC
EST: gi|93281375|gb|EB673639.1|EB673639
EST:     TTGGTGCTGTGGAGTGCCTCCAGGACCGTTTTTGCATTCACCTCAACATG                         AGCATTTTACTTTCAGTCAATGACCTACTGGCATGCTGCGGTTTTATGTGC
genomic: TTGGTGCTGTGGAGTGCCTCCAGGACCGTTTTTGCATTCACCTCAACATGgcgagtggat ... ttacttgcagAGCATTTTACTTTCAGTCAATGACCTACTGGCATGCTGCGGTTTTATGTGC
EST: gi|33101185|gb|CF061145.1|CF061145
EST:     TTGGTGCTGTGGAGTGCCTCCAGGACCGTTTTTGCATTCACCTCAACATG                         AGCATTTTACTTTCAGTCAATGACCTACTGGCATGCTGCGGTTTTATGTGC
genomic: TTGGTGCTGTGGAGTGCCTCCAGGACCGTTTTTGCATTCACCTCAACATGgcgagtggat ... ttacttgcagAGCATTTTACTTTCAGTCAATGACCTACTGGCATGCTGCGGTTTTATGTGC
EST: gi|211439270|gb|FL284637.1|FL284637
EST:     TTGGTGCTGTGGAGTGCCTCCAGGACCGTTTTTGCATTCACCTCAACATG                         AGCATTTTACTTTCAGTCAATGACCTACTGGCATGCTGCGGTTTTATGTGC
genomic: TTGGTGCTGTGGAGTGCCTCCAGGACCGTTTTTGCATTCACCTCAACATGgcgagtggat ... ttacttgcagAGCATTTTACTTTCAGTCAATGACCTACTGGCATGCTGCGGTTTTATGTGC
EST: gi|211439278|gb|FL284645.1|FL284645
EST:     TTGGTGCTGTGGAGTGCCTCCAGGACCGTTTTTGCATTCACCTCAACATG                         AGCATTTTACTTTCAGTCAATGACCTACTGGCATGCTGCGGTTTTATG
genomic: TTGGTGCTGTGGAGTGCCTCCAGGACCGTTTTTGCATTCACCTCAACATGgcgagtggat ... ttacttgcagAGCATTTTACTTTCAGTCAATGACCTACTGGCATGCTGCGGTTTTATG
EST: gi|211042388|gb|FL284655.1|FL284655
EST:     TTGGTGCTGTGGAGTGCCTCCAGGACCGTTTTTGCATTCACCTCAACATG                         AGCATTTTACTTTCAGTCAATGACCTACTGGCATGCTGCGGTTTTATGTGC
genomic: TTGGTGCTGTGGAGTGCCTCCAGGACCGTTTTTGCATTCACCTCAACATGgcgagtggat ... ttacttgcagAGCATTTTACTTTCAGTCAATGACCTACTGGCATGCTGCGGTTTTATGTGC
EST: gi|14203094|gb|BG836771.1|BG836771
EST:     CCAGGACCG-TTTTGAATTCACCTCAACATG                         AGCATTTTA-YTTCAGTCAATGACCTACTGGCATGCTGCGGTTTTATGTGC
genomic: CCAGGACCGTTTTTGCATTCACCTCAACATGgcgagtggat ... ttacttgcagAGCATTTTACTTTCAGTCAATGACCTACTGGCATGCTGCGGTTTTATGTGC
EST: gi|211436680|gb|FL284628.1|FL284628
EST:     TTGGTGCTGTGGAGTGCCTCCAGGACCGTTTTTGCATTCACCTCANCATG                         AGCATTTTACTTTCAGTCAATGACCTACTG
genomic: TTGGTGCTGTGGAGTGCCTCCAGGACCGTTTTTGCATTCACCTCAACATGgcgagtggat ... ttacttgcagAGCATTTTACTTTCAGTCAATGACCTACTG
EST: gi|33093900|gb|CF053894.1|CF053894
EST:     TTGGTGCTGTGGAGTGCCTCCAGGACCGTTTTTGCATTCACCTCAACATG                         AGCATTTTACTTTCAGTCAATGACCTACTGGCATGCTGCGGTTTTATGTGC
genomic: TTGGTGCTGTGGAGTGCCTCCAGGACCGTTTTTGCATTCACCTCAACATGgcgagtggat ... ttacttgcagAGCATTTTACTTTCAGTCAATGACCTACTGGCATGCTGCGGTTTTATGTGC
EST: gi|6012616|gb|AW062053.1|AW062053
EST:     TTGGTGCTGTGGAGTGCCTCCAGGTCCGTTTTTGCATTCACCTCAACATG                         AGCATTTTACTTTCAGTCAATGACCTACTGGCATGCTGCGGTTTTATGTGC
genomic: TTGGTGCTGTGGAGTGCCTCCAGGACCGTTTTTGCATTCACCTCAACATGgcgagtggat ... ttacttgcagAGCATTTTACTTTCAGTCAATGACCTACTGGCATGCTGCGGTTTTATGTGC
EST: gi|211488924|gb|FL092409.1|FL092409
EST:     TTGGTGCTGTGGAGTGCCTCCAGGACCGTTTTTGCATTCACCTCAACATG                         AGCATTTTACTTTCAGTCAATGACCTACTGGCATGCTGCGGTTTTATGTGC
genomic: TTGGTGCTGTGGAGTGCCTCCAGGACCGTTTTTGCATTCACCTCAACATGgcgagtggat ... ttacttgcagAGCATTTTACTTTCAGTCAATGACCTACTGGCATGCTGCGGTTTTATGTGC
EST: gi|211439279|gb|FL284646.1|FL284646
EST:     TTGGTGCTGTGGAGTGCCTCCAGGACCGTTTTTGCATTCACCTCAACATG                         AGCATTTTACTTTCAG
genomic: TTGGTGCTGTGGAGTGCCTCCAGGACCGTTTTTGCATTCACCTCAACATGgcgagtggat ... ttacttgcagAGCATTTTACTTTCAG
EST: gi|211436673|gb|FL284621.1|FL284621
EST:     GGTGCTGTGGAGTGCCTCCAGGACCGTTTTTTGCATTCACCTTCAACATG                         AGCATTTTACTTTCAGTCAATGA
genomic: GGTGCTGTGGAGTGCCTCCAGGACCGTTTTT-GCATTCACCT-CAACATGgcgagtggat ... ttacttgcagAGCATTTTACTTTCAGTCAATGA
EST: gi|211042384|gb|FL284651.1|FL284651
EST:     TTGGTGCTGTGGAGTGCCTCCAGGACCGTTTTTGCATTCACCTCAACATG                         AGCATTTTACTTTCAGTCAATGACCTACTGGCATGCTG
genomic: TTGGTGCTGTGGAGTGCCTCCAGGACCGTTTTTGCATTCACCTCAACATGgcgagtggat ... ttacttgcagAGCATTTTACTTTCAGTCAATGACCTACTGGCATGCTG
EST: gi|18963341|gb|BM660381.1|BM660381
EST:     TTGGTGCTGTGGAGTGCCTCCAGGACCGTTTTTGCATTCACCTCAACATG                         AGCATTTTACTTTCAGTCAATGACCTACTGGCATGCTGCGGTTTTATGTGC
genomic: TTGGTGCTGTGGAGTGCCTCCAGGACCGTTTTTGCATTCACCTCAACATGgcgagtggat ... ttacttgcagAGCATTTTACTTTCAGTCAATGACCTACTGGCATGCTGCGGTTTTATGTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaggcatgctttgtcctttttctcacataaccaagctgttgtcttttacttgcagAGCATTTTACTTTCAGTCAATGACCTACTGGCATGCTGCGGTTTTATGTGCGGCGATGGGTGTGATGGAGGCTATCCTATAGAGGCATGGCGCTACTTTG
                                         tcttttactt  CT-rich tract
                                           ttttactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcgagtggatacagaagacattgctgttctcatagtttttttaacaaaatattataaaggcatgctttgtcctttttctcacataaccaagctgttgtcttttacttgcagAGCATTTTACTTTCAGTCAATGACCTACTGGCATGCTGCGGTTTTATGTGCGGCGATGGGTGTGATGGAGGCTATCCTATAGAGGCATGGCGCTACTTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG