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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtatctaatgcagttccaatttttttctttaaaatgttctcgtctggttttctcagtttcttaattgattcaatttgttcctttaacagTATGCCTGTTGAAATGGTGGCTTGCATTGCTATAGAAGCAATTTCCATACTGGAGAAGATGCACTCAAAAGG

Basic information

species Zea mays
transcript GRMZM2G116151_T03
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G116151_T03 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os05g11140.1 (Oryza sativa), 3'ss of exon 5
gtaagtatctaatgcagttccaatttttttctttaaaatgttctcgtctggttttctcagtttcttaattgattcaatttgttcctttaacagTATGCCTGTTGAAATGGTGGCTTGCATTGCTATAGAAGCAATTTCCATACTGGAGAAGATGCACTCAAAAGG
|||||| |   |     |    | | | |||||   |||||||  || |  ||  |||||||    |||    |   ||| || || | |||| ||| ||||||||||||| ||||| ||||||||||||||||| |||||| ||||||||||||| || |||||
gtaagttttctagttgttcgtcaatatattctt--gaatgttcatgtttaattagctcagtt----aatatgatatttttctttctattacagAATGTCTGTTGAAATGGTTGCTTGTATTGCTATAGAAGCAATCTCCATATTGGAGAAGATGCATTCGAAAGG

upper sequence: GRMZM2G116151_T03 (Zea mays), 3'ss of exon 5
lower sequence: Vv09s0002g03680.t01 (Vitis vinifera), 3'ss of exon 5
---------gtaagtatctaatgcagttccaatttttttctttaaaatgttctcgtctggttttctcagtttct-----taattg---attcaatttgttcctttaa---cagTATGCCTGTTGAAATGGTGGCTTGCATTGCTATAGAAGCAATTTCCATACTGGAGAAGATGCACTCAAAAGG
          | |  || | ||  | |     || | | ||  |||  |||||    || ||||  || ||| |     || |||   | | ||  | ||   ||||   ||||||| |  |||||||||| || ||||||||||| |||||||| |||||| |||||||||||||||| | |||
gtgagtgagatgaaaatatgatttattattttttatatgctacaaatggttct--gttgcttttaccattttgtgcttgtatttgcctaatgaagatatttgcttaattccagTATGTCCATTGAAATGGTTGCATGCATTGCTATTGAAGCAATATCCATATTGGAGAAGATGCACTCCAGAGG

upper sequence: GRMZM2G116151_T03 (Zea mays), 3'ss of exon 5
lower sequence: Vv04s0008g00160.t01 (Vitis vinifera), 3'ss of exon 5
-------------gtaagtatctaatgcagttccaatttttttct--ttaaaatgtt-ctcgtctggttttctcagtttcttaattga--ttcaatttgttcctttaacagTATGCCTGTTGAAATGGTGGCTTGCATTGCTATAGAAGCAATTTCCATACTGGAGAAGATGCACTCAAAAGG
               || ||| |   | |       || | || |  || | ||||  | | |    ||| |||   |      || |  |||| |||||   |||  ||| ||| |  |||||||||| || || |||||||| |||||||| || ||| | |||||||||||||| | |||
gtaagtttctttttcaaatatgtggcggaaagtgtgttatcttttagtttatatgtaacacatgcaatttactcttatctaatgtttactttcactttgtcaattt--cagGATGTCCATTGAAATGGTAGCATGTATTGCTATTGAAGCAATCTCTATATTAGAGAAGATGCACTCTAGAGG

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|101387539|gb|EB815784.1|EB815784
EST:     GACATGTTGGGGCCAAGCCTATGGGATGTTTGGAATAATAACTCTCACTC                         TATGCCTGTTGAAATGGTGGCTTGCATTGCTATAGAAGCAATTTCCATACT
genomic: GACATGTTGGGGCCAAGCCTATGGGATGTTTGGAATAATAACTCTCACTCgtaagtatct ... cctttaacagTATGCCTGTTGAAATGGTGGCTTGCATTGCTATAGAAGCAATTTCCATACT
EST: gi|211200248|gb|FK978072.1|FK978072
EST:     CATGTTGGGGCCAAGCCCTATGGGATGTTTGGGAATAATAACTCTCACTC                         TATGCCTGTTGAAATTGGTGGGCTTGCATGGCTATAGAAGCAATTTCCATA
genomic: CATGTTGGGGCCAAGCC-TATGGGATGTTTGG-AATAATAACTCTCACTCgtaagtatct ... cctttaacagTATGCCTGTTGAAAT-GGTGG-CTTGCATTGCTATAGAAGCAATTTCCATA
EST: gi|71767696|gb|DR965633.1|DR965633
EST:     GACATGTTGGGGCCAAGCCTATGGGATGTTTGGAATAATAACTCTCACTC                         TATGCCTGTTGAAATGGTGGCTTGCATTGCTATAGAAGCAATTTCCATACT
genomic: GACATGTTGGGGCCAAGCCTATGGGATGTTTGGAATAATAACTCTCACTCgtaagtatct ... cctttaacagTATGCCTGTTGAAATGGTGGCTTGCATTGCTATAGAAGCAATTTCCATACT
EST: gi|78112677|gb|DV531071.1|DV531071
EST:     GACATGTTGGGGCCAAGCCTATGGGATGTTTGGAATAATAACTCTCACTC                         TATGCCTGTTGAAATGGTGGCTTGCATTGCTATAGAAGCAATTTCCATACT
genomic: GACATGTTGGGGCCAAGCCTATGGGATGTTTGGAATAATAACTCTCACTCgtaagtatct ... cctttaacagTATGCCTGTTGAAATGGTGGCTTGCATTGCTATAGAAGCAATTTCCATACT
EST: gi|149078987|gb|EE167841.2|EE167841
EST:     ACATGTTGGGGCCAAGCCTATGGGATGTTTGGAATAATAACTCTCACCTC                         TATGCCTGTTGAAATGGTGGCTTGCATTGCTATAGAAG
genomic: ACATGTTGGGGCCAAGCCTATGGGATGTTTGGAATAATAACTCTCAC-TCgtaagtatct ... cctttaacagTATGCCTGTTGAAATGGTGGCTTGCATTGCTATAGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttctcgtctggttttctcagtttcttaattgattcaatttgttcctttaacagTATGCCTGTTGAAATGGTGGCTTGCATTGCTATAGAAGCAATTTCCATACTGGAGAAGATGCACTCAAAAGG
                                       tttgttccttt  CT-rich tract
                          ttaattgattcaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtatctaatgcagttccaatttttttctttaaaatgttctcgtctggttttctcagtttcttaattgattcaatttgttcctttaacagTATGCCTGTTGAAATGGTGGCTTGCATTGCTATAGAAGCAATTTCCATACTGGAGAAGATGCACTCAAAAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG