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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttctttgttgcttttctctgctgatttgactactaccgcaggtaaagtataagggatggatgtactgagtgatataattcgtccagATCTTAAAAAGACCACAGATTGGACCAGGAAACAGAATCTTAGATATGATTATAGGACCATACAAGCTGTCTCGGCGGTGTGAAGTGACTGCAATCCTTA

Basic information

species Zea mays
transcript GRMZM2G099328_T02
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G099328_T04 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os12g40490.1 (Oryza sativa), 3'ss of exon 11
gtgagttctttgttgcttt-tctctgc--tgatttgactactaccgcaggtaaagtataagggatggatgtactgagtgatataattcgtccagATCTTAAAAAGACCACAGATTGGACCAGGAAACAGAATCTTAGATATGATTATAGGACCATACAAGCTGTCTCGGCGGTGTGAAGTGACTGCAATCCTTA
|||||||   |   || || |  ||||    ||||||  |||  |  |   |||  |||     || ||||  ||| | || |||| | |||||||||||| |||||||   |||||||| |||||||||||  |||||||||| | || |||||| ||||||    | || |||||||||||||||||||| |
gtgagttaaataccgccttgttactgcataaatttgataactggcagacacaaaaaata-----tgcatgtgatgaataatgtaatgcatccagATCTTAAGAAGACCAATAATTGGACCGGGAAACAGAATTATAGATATGATCACAGCACCATATAAGCTGGAAAGACGATGTGAAGTGACTGCAATCCTGA
















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|6020787|gb|AW065715.1|AW065715
EST:     TACCGGAAACCAGAGGTCTATGCCTTTCTGAGGAGCAAGTTGTTAGAACG                         ATCTTAAAAAGACCACAGATTGGACCAGGANACAGAATCTTAGATATGATT
genomic: TACCGGAAACCAGAGGTCTATGCCTTTCTGAGGAGCAAGTTGTTAGAACGgtgagttctt ... attcgtccagATCTTAAAAAGACCACAGATTGGACCAGGAAACAGAATCTTAGATATGATT
EST: gi|14203375|gb|BG837052.1|BG837052
EST:     GCAA-TTGTTAGAACG                         ATCTT-AAAAGACCACRGATTGGACCAGGAAACAGAATCTTAGATATGATT
genomic: GCAAGTTGTTAGAACGgtgagttctt ... attcgtccagATCTTAAAAAGACCACAGATTGGACCAGGAAACAGAATCTTAGATATGATT
EST: gi|32867973|gb|CF007655.1|CF007655
EST:     TACCGGAAACCAGAGGTCTATGCCTTTCTGAGGAGCAAGTTGTTAGAACG                         ATCTTAAAAAGACCACAGATTGGACCAGGAAACAGAATCTTAGATATGATT
genomic: TACCGGAAACCAGAGGTCTATGCCTTTCTGAGGAGCAAGTTGTTAGAACGgtgagttctt ... attcgtccagATCTTAAAAAGACCACAGATTGGACCAGGAAACAGAATCTTAGATATGATT
EST: gi|31362847|gb|CD447204.1|CD447204
EST:     TACCGGAAACCAGAGGTCTATGCCTTTCTGAGGAGCAAGTTGTTAGAACG                         ATCTTAAAAAGACCACAGATTGGACCAGGAAACAGAATCTTAGATATGATT
genomic: TACCGGAAACCAGAGGTCTATGCCTTTCTGAGGAGCAAGTTGTTAGAACGgtgagttctt ... attcgtccagATCTTAAAAAGACCACAGATTGGACCAGGAAACAGAATCTTAGATATGATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actaccgcaggtaaagtataagggatggatgtactgagtgatataattcgtccagATCTTAAAAAGACCACAGATTGGACCAGGAAACAGAATCTTAGATATGATTATAGGACCATACAAGCTGTCTCGGCGGTGTGAAGTGACTGCAATCCTTA
                                              ttcgtcc  CT-rich tract
           taaagtataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagttctttgttgcttttctctgctgatttgactactaccgcaggtaaagtataagggatggatgtactgagtgatataattcgtccagATCTTAAAAAGACCACAGATTGGACCAGGAAACAGAATCTTAGATATGATTATAGGACCATACAAGCTGTCTCGGCGGTGTGAAGTGACTGCAATCCTTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG