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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggttcccagtaaattaacatgtttgcggtttcaagttgatggtatacaagtcttctcttacaatagGTATCCCTATTGGCATTGTTACTGCAATTGCTGCTCCTGCAAGTCTTAAGGTGGACTTTGAAGGGAATGGCGGTCATGCTGGAGCAGTGCTGATGCCTGC

Basic information

species Zea mays
transcript GRMZM2G130034_T02
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G130034_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os12g40550.1 (Oryza sativa), 3'ss of exon 6
-gtaggttcccagtaaattaacatgtttgcggtttcaagttgatggtatac--aagtcttctcttacaatagGTATCCCTATTGGCATTGTTACTGCAATTGCTGCTCCTGCAAGTCTTAAGGTGGACTTTGAAGGGAATGGCGGTCATGCTGGAGCAGTGCTGATGCCTGC
  | | ||   ||| |||||| | ||||  ||      |||  |  |||||  | || |  |||||||| |||||||   |||||| |||| ||||| |||||||||||||||||| |||||||||| |||||||||||||| || ||||||||||||||||| ||||||||
gttggattgtgagttaattaataagtttatggaaaattgttcttcttatactcatgtgtgttcttacaacagGTATCAAAATTGGCGTTGTCACTGCTATTGCTGCTCCTGCAAGTATTAAGGTGGAGTTTGAAGGGAATGGGGGCCATGCTGGAGCAGTGCTCATGCCTGC

upper sequence: GRMZM2G130034_T02 (Zea mays), 3'ss of exon 6
lower sequence: AT5G43600.1 (Arabidopsis thaliana), 3'ss of exon 6
------------------gtaggttcccagtaaattaacatgtttgcggtttcaagttgatggtatacaagtcttctcttacaatagGTATCCCTATTGGCATTGTTACTGCAATTGCTGCTCCTGCAAGTCTTAAGGTGGACTTTGAAGGGAATGGCGGTCATGCTGGAGCAGTGCTGATGCCTGC
                   |  |     |  || ||    | ||| |  | |    ||   | ||   |  || | | | || | |||| |   ||| ||  |||| || || ||||||||||| |||||| | |||||||| |||||||| ||||| ||||||||||| || || || |||||   
gtccggttaacttaccttttctgcgtggaagaattttgtgttttttctctctttcattatagttaataagatcatttttgaccacagGTTTAGATATCGGTGTTGTAACCGCCATTGCTGCTCCAGCAAGTTTGAAGGTGGAATTTGAAGGCAATGGAGGTCATGCTGGTGCTGTACTTATGCCATA

upper sequence: GRMZM2G130034_T02 (Zea mays), 3'ss of exon 6
lower sequence: Vv05s0020g04900.t01 (Vitis vinifera), 3'ss of exon 6
----------gtaggttcccagtaaattaa---catgtttgcgg-tttcaagttgatggtatacaagtct-tctcttacaatagGTATCCCTATTGGCATTGTTACTGCAATTGCTGCTCCTGCAAGTCTTAAGGTGGACTTTGAAGGGAATGGCGGTCATGCTGGAGCAGTGCTGATGCCTGC
           |  |||| || |  |||     ||      |   ||||||  |     | ||   |||| | | ||    |||| ||  ||||||||||||| ||||| |||||||| ||||||||| | || ||||| |||||||| ||||| || ||||| || || ||  |||||||   
gtaggcctctttctgttctcattttattcttttcacagccacaactttcaaaattcccatttattggtctatattttgatgtagGAATATCTATTGGCATTGTAACTGCCATTGCTGCCCCTGCAAGTATCAAAGTGGATTTTGAAGGCAATGGAGGCCATGCGGGTGCTGTCTTGATGCCAAA

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|148941174|gb|EC886056.2|EC886056
EST:     TGCTTTTATAGAACTGCACATTGAGCAGGGTCCCATCTTAGAAAAGGAGG                         GTATCCCTATTGGCATTGTTACTGCAATTGCTGCTCCTGCAAGTCTTAAGG
genomic: TGCTTTTATAGAACTGCACATTGAGCAGGGTCCCATCTTAGAAAAGGAGGgtaggttccc ... cttacaatagGTATCCCTATTGGCATTGTTACTGCAATTGCTGCTCCTGCAAGTCTTAAGG
EST: gi|31359313|gb|CD443670.1|CD443670
EST:     TGCTTTTATAGAACTGCACATTGAGCAGGGTCCCATCTTAGAAAAGGAGG                         GTATCCCTATTGGCATTGTTACTGCAATTGCTGCTCCTGCAAGTCTTAAGG
genomic: TGCTTTTATAGAACTGCACATTGAGCAGGGTCCCATCTTAGAAAAGGAGGgtaggttccc ... cttacaatagGTATCCCTATTGGCATTGTTACTGCAATTGCTGCTCCTGCAAGTCTTAAGG
EST: gi|148983478|gb|EE029496.2|EE029496
EST:     TGCTTTTATAGAACTGCACATTGAGCAGGGTCCCATCTTAGAAA-GGAGG                         GTATCCCTATTGGCAT
genomic: TGCTTTTATAGAACTGCACATTGAGCAGGGTCCCATCTTAGAAAAGGAGGgtaggttccc ... cttacaatagGTATCCCTATTGGCAT
EST: gi|149103753|gb|EE289159.2|EE289159
EST:     TGCTTTTATAGAACTGCACATTGAGCAGGGTCCCATCTTAGAAAAGGAGG                         GTATCCCTATTGGCATTGTTACTGCAATTGC
genomic: TGCTTTTATAGAACTGCACATTGAGCAGGGTCCCATCTTAGAAAAGGAGGgtaggttccc ... cttacaatagGTATCCCTATTGGCATTGTTACTGCAATTGC
EST: gi|148940595|gb|EC885401.2|EC885401
EST:     TGCTTTTATAGAACTGCACATTGAGCAGGGTCCCATCTTAGAAAAGGAGG                         GTATCCCTATTGGCATTGTTACTGGCA-TTGCTGCTCCTGCAAGTCTTAAG
genomic: TGCTTTTATAGAACTGCACATTGAGCAGGGTCCCATCTTAGAAAAGGAGGgtaggttccc ... cttacaatagGTATCCCTATTGGCATTGTTACTG-CAATTGCTGCTCCTGCAAGTCTTAAG
EST: gi|148944452|gb|EC889567.2|EC889567
EST:     GCTTTTATAGAACTGCACATTGAGCAGGGTCCCATCTTTAGAAAAG-AGG                         GGATCCCTATTGGC
genomic: GCTTTTATAGAACTGCACATTGAGCAGGGTCCCATCTT-AGAAAAGGAGGgtaggttccc ... cttacaatagGTATCCCTATTGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattaacatgtttgcggtttcaagttgatggtatacaagtcttctcttacaatagGTATCCCTATTGGCATTGTTACTGCAATTGCTGCTCCTGCAAGTCTTAAGGTGGACTTTGAAGGGAATGGCGGTCATGCTGGAGCAGTGCTGATGCCTGC
                                       tcttctcttac  CT-rich tract
                                              ttacaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggttcccagtaaattaacatgtttgcggtttcaagttgatggtatacaagtcttctcttacaatagGTATCCCTATTGGCATTGTTACTGCAATTGCTGCTCCTGCAAGTCTTAAGGTGGACTTTGAAGGGAATGGCGGTCATGCTGGAGCAGTGCTGATGCCTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT