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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttggaactcactcgcatgctatctatttttctgcatgcttatttttggtcactacaataattaacaactgtttgtttgtcatgaagGGTATTTTGGCAGATGTGCTGAAGTGTCTTGGTGACAATAAGAAGCACATGCGAGAATGCACATTGACTGCTCTAGATTCGTGGGTTGCTGCAGCCCAAC

Basic information

species Zea mays
transcript GRMZM2G009849_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G009849_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os01g60040.2 (Oryza sativa), 3'ss of exon 27
gtttggaactcactcgcatgctatctatttttctgcatgcttatttttggtcactacaataattaacaactgtttgtttgtcatgaagGGTATTTTGGCAGATGTGCTGAAGTGTCTTGGTGACAATAAGAAGCACATGCGAGAATGCACATTGACTGCTCTAGATTCGTGGGTTGCTGCAGCCCAAC
||||||||          |||  | || |||     ||  | ||||   || |  |  | |   |   | | | | ||||| ||||||||||||||||||||||| || || |||||||| |||||||||||||||||| | ||||||||||||||||||||||| |  |||||||||||||| ||||
gtttggaatgtctagttttgcattatactttatattat--tcatttgcagttataatgaca--cagatattttctatttgttatgaagGGTATTTTGGCAGATGTCCTAAAATGTCTTGGCGACAATAAGAAGCACATGAGGGAATGCACATTGACTGCTCTAGACTTATGGGTTGCTGCAGCTCAAC

upper sequence: GRMZM2G009849_T01 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA10G35140.1 (Glycine max), 3'ss of exon 29
--gtttggaactcactcgcatgctatctattttt---ctgcatgcttatttttggtcactacaataattaacaactgtttgtttg---tcatgaagGGTATTTTGGCAGATGTGCTGAAGTGTCTTGGTGACAATAAGAAGCACATGCGAGAATGCACATTGACTGCTCTAGATTCGTGGGTTGCTGCAGCCCAAC
     ||||      ||   |  | | | |||||   |    || |  | ||| |    |       | ||||  | ||    ||   |  || |||||||| || | ||| |  |||| |||||||||||||| |||||||||||| |||||||   | ||| | |  ||||| | ||| | ||||| | ||| |
gtaagtggattctgttctgtttttgtattttttttccccatttggtactattttgctgttttctgtttgaacatttcttgaaatggtttgttgcagGGTATTCTGTCTGATATATTGAAATGTCTTGGTGACAACAAGAAGCACATGAGAGAATGTGTACTGAATACCTTAGATGCTTGGCTGGCTGCTGTCCATC

upper sequence: GRMZM2G009849_T01 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA20G32430.1 (Glycine max), 3'ss of exon 27
--gtttggaactcactcgcatgctatctatttttct-gcatgcttatttttggtcactacaataattaacaactgtttgtttg---tcatgaagGGTATTTTGGCAGATGTGCTGAAGTGTCTTGGTGACAATAAGAAGCACATGCGAGAATGCACATTGACTGCTCTAGATTCGTGGGTTGCTGCAGCCCAAC
      |||      ||   |  | | | ||||||     || |  | ||| | |  |       | || |  | ||    ||   |  || |||||||| || | |||||  |||| |||||||||||||| |||||||||||| |||||||     ||| | |  ||||  | ||| | ||||| |  || |
gtaagaggattctgttctgtttttgtatttttttcccatttggtactgttttgccgttttctatttgaatatttcttgaaatggtttgttgcagGGTATTCTGTCTGATGTATTGAAATGTCTTGGTGACAACAAGAAGCACATGAGAGAATGTGTGCTGAATACATTAGACGCTTGGCTGGCTGCTGTTCATC

upper sequence: GRMZM2G009849_T01 (Zea mays), 3'ss of exon 9
lower sequence: Vv10s0116g00460.t01 (Vitis vinifera), 3'ss of exon 18
gtttg--gaactcactcgcatgctatctatttttctgcatgcttatttttggtcactacaat-----aattaacaactgtttgtttgtcatgaagGGTATTTTGGCAGATGTGCTGAAGTGTCTTGGTGACAATAAGAAGCACATGCGAGAATGCACATTGACTGCTCTAGATTCGTGGGTTGCTGCAGCCCAAC
|||||  |   || |  |     ||| || |  | ||     || |  ||   |  || ||      | || |  |  |  |  || |  || |||| ||| |  | ||| | ||||| || |||||||||||||| ||||| ||| ||||||||||||||||| |||||||| | ||| ||||||| |  || |
gtttgttggcttctcatgatatttatttaatcctttgttgtgttttcattatcctttagaaacttgaagtttatcatggcattgtttttttgcagGGCATTCTTTCTGATATTCTGAAATGCCTTGGTGACAATAAAAAGCATATGAGAGAATGCACATTGACTACTCTAGATGCTTGGCTTGCTGCTGTTCATC

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|87153866|gb|DY398655.1|DY398655
EST:     TTGGTGGTCTTGCATCTGCTATGGGACTTTCTGTTGAAAAGTCAAGCAAG                         GGTATTTTGGCAGATGTGCTGAAGTGTCTTGGTGACAATAAGAAGCACATG
genomic: TTGGTGGTCTTGCATCTGCTATGGGACCTTCTGTTGAAAAGTCAAGCAAGgtttggaact ... tgtcatgaagGGTATTTTGGCAGATGTGCTGAAGTGTCTTGGTGACAATAAGAAGCACATG
EST: gi|87153811|gb|DY398600.1|DY398600
EST:     TGGTGGTC-TGNCATCTGCTATGGGACCTTCTG-TGAAAAGTCAAGCAAG                         GGTATTTTGGCAGATGTGCTGAAGTGTCTTGGTGACAATAAGAAGCACATG
genomic: TGGTGGTCTTG-CATCTGCTATGGGACCTTCTGTTGAAAAGTCAAGCAAGgtttggaact ... tgtcatgaagGGTATTTTGGCAGATGTGCTGAAGTGTCTTGGTGACAATAAGAAGCACATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcatgcttatttttggtcactacaataattaacaactgtttgtttgtcatgaagGGTATTTTGGCAGATGTGCTGAAGTGTCTTGGTGACAATAAGAAGCACATGCGAGAATGCACATTGACTGCTCTAGATTCGTGGGTTGCTGCAGCCCAAC
                           aattaac  putative branch site (score: 2)
                                       tttgttt  putative PPT
                     tacaataattaacaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttggaactcactcgcatgctatctatttttctgcatgcttatttttggtcactacaataattaacaactgtttgtttgtcatgaagGGTATTTTGGCAGATGTGCTGAAGTGTCTTGGTGACAATAAGAAGCACATGCGAGAATGCACATTGACTGCTCTAGATTCGTGGGTTGCTGCAGCCCAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG