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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccaaatatgaataactctgtttgaacttgctgtacttacttcagctgccccaggccaaaacaactctgtattctttctgatcattaacacgtactttcagGTGTTTGAGATAAAAAATGATGCTAAAATGAAAAGGACAATGCGACGGCCCCTGCCATCTGGTCGCATTAGTCCTGCACATGCTGCGATGTGGGCTACAA

Basic information

species Zea mays
transcript GRMZM2G178859_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G178859_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g34390.1 (Oryza sativa), 3'ss of exon 2
-----ccaaatatgaataactctgtttgaacttgctgtacttacttcagctgccccaggccaaaacaactctgtattctttctgatcattaacacgtactttcagGTGTTTGAGATAAAAAATGATGCTAAAATGAAAAGGACAATGCGACGGCCCCTGCCATCTGGTCGCATTAGTCCTGCACATGCTGCGATGTGGGCTACAA
       || |||   |   |  |||   |     || |  | ||  |  |||   | ||      |  |||| || |  | |||  | ||||   |  ||| |||||||||||||||| ||||| |||||||||||||| || |||||||||||||| ||||| || ||||||||||||||||||||||| ||||||||||| |
cctcgttaattatagttgttttcgttcagagaaaatgaatgttctgtacttgctttaagcatctgta--tctgaatacagtttga--aataactt-tgtttttagGTGTTTGAGATAAAGAATGACGCTAAAATGAAAAGAACCATGCGACGGCCCCTACCATCAGGGCGCATTAGTCCTGCACATGCTGCCATGTGGGCTACTA

upper sequence: GRMZM2G178859_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA20G38710.1 (Glycine max), 3'ss of exon 2
ccaaatatgaataactctg---tttgaacttgctgtacttacttca-gctgcccc--aggccaaaacaactctgtattctttctgatcattaacacgtactttcagGTGTTTGAGATAAAAAATGATGCTAAAATGAAAAGGACAATGCGACGGCCCCTGCCATCTGGTCGCATTAGTCCTGCACATGCTGCGATGTGGGCTACAA
   |||| || |   ||||   | ||  |||  | | |   ||| | |||||     |          |   |    ||| |   ||   |    | |  ||| ||||||||||||| || ||||||||||||||||| || ||||  ||  |||| || || || || ||||| |      | ||||| |     |||||  |  
---aata-gatttgttctgaagtatgggctttttattcccccttaatgctgctgttaaatttttggtcaacataagatctattcaatggctgtttctt--ttttagGTGTTTGAGATCAATAATGATGCTAAAATGAAGAGAACAAGTCGCAGGCCACTACCCTCAGGACGCATCACAATACCTCATGCAGTTGGCTGGGCATCCT

upper sequence: GRMZM2G178859_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA10G43980.1 (Glycine max), 3'ss of exon 3
------------------------------------------------------------------------ccaaatatgaataactctg---tttgaacttgctgtacttacttca-gctgcccc---aggccaaaacaactctgtattctttctgatcattaacacgtactttcagGTGTTTGAGATAAAAAATGATGCTAAAATGAAAAGGACAATGCGACGGCCCCTGCCATCTGGTCGCATTAGTCCTGCACATGCTGCGATGTGGGCTACAA
                                                                          ||||| || |   ||||   | ||  |||  | | |   ||| | |||| | |              |   |    ||| |   ||  ||  | |    ||| ||||||||||||| || ||||||||||||||||| || ||||  ||| |||| || || || || ||||| |      | |||||||     | |||  |  
gtttttttccttctagctatgtaactgttattaatgtcaaatatattatttttattatggcttaaagaccttttaaata-gatttgttctgaagtatgtgctttttattcccccttaatgctgtctcttagatttttggtcaacgtaagatctattcaatggttgtctc---tttttagGTGTTTGAGATCAATAATGATGCTAAAATGAAGAGAACAAGTCGAAGGCCACTACCCTCAGGACGCATCACAATACCTCATGCTGTTGGCTCGGCATCCT

upper sequence: GRMZM2G178859_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv15s0021g00430.t01 (Vitis vinifera), 3'ss of exon 2
-------------------------------------------------------ccaaatatgaataac-tctgtttgaacttgc-tgtacttacttcagctgccccaggccaaaacaactctgtattctttctgatcatt--aacacgtactttcagGTGTTTGAGATAAAAAATGATGCTAAAATGAAAAGGACAATGCGACGGCCCCTGCCATCTGGTCGCATTAGTCCTGCACATGCTGCGATGTGGGCTACAA
                                                       |  | ||  | ||   ||| | ||    |||  |  | | |    ||   |    || |       |   | |||   || ||| ||  |    ||| | | |||||||||||||||| ||||||||||||||||| || |||||| || |||| || || ||||||||| |||||    | ||||| |  |  |||||| |  
gtttcttttgaactgcttattattattattattattttccaatcacaatcattttcatattacaagtactgtctatgtgtgtgtgcgcgcgcatgcgcatgcgtgcatgtgctaggctgcttgaattttcagactaatctttgcattttgtattgttagGTGTTTGAGATAAATAATGATGCTAAAATGAAGAGAACAATGAGAAGGCCACTACCTTCTGGTCGCCTTAGTATACCTCATGCAGTCACCTGGGCTTCTT

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|71329079|gb|DR801247.1|DR801247
EST:     CATGTGCCGGTACAATGATGGTTGCAGCATCTGCAAATACCCTCAACCAG                         GTGTTTGAGATAAAAAATGATGCTAAAATGAAAAGGACAATGCGACGCCCC
genomic: CATGTGCCGGTACAATGATGGTTGCAGCATCTGCAAATACCCTCAACCAGgtacatttct ... gtactttcagGTGTTTGAGATAAAAAATGATGCTAAAATGAAAAGGACAATGCGACGGCCC
EST: gi|31361673|gb|CD446030.1|CD446030
EST:     CATGTGCCGGTACAATGATGGTTGCAGCATCTGCAAATACCCTCAACCAG                         GTGTTTGAGATAAAAAATGATGCTAAAATGAAAAGGACAATGCGACGCCCC
genomic: CATGTGCCGGTACAATGATGGTTGCAGCATCTGCAAATACCCTCAACCAGgtacatttct ... gtactttcagGTGTTTGAGATAAAAAATGATGCTAAAATGAAAAGGACAATGCGACGGCCC
EST: gi|211400285|gb|FL144411.1|FL144411
EST:     CATGTGCCGGTACAATGATGGTTGCAGCATCTGCAAATACCCTCAACCAG                         GTGTTTGAGATAAAAAATGATGCTAAAATGAAAAGGACAATGCGACGGCCC
genomic: CATGTGCCGGTACAATGATGGTTGCAGCATCTGCAAATACCCTCAACCAGgtacatttct ... gtactttcagGTGTTTGAGATAAAAAATGATGCTAAAATGAAAAGGACAATGCGACGGCCC
EST: gi|71329076|gb|DR801246.1|DR801246
EST:     CATGTGCCGGTACAATGATGGTTGCAGCATCTGCAAATACCCTCAACCAG                         GTGTTTGAGATAAAAAATGATGCTAAAATGAAAAGGACAATGCGACGCCCC
genomic: CATGTGCCGGTACAATGATGGTTGCAGCATCTGCAAATACCCTCAACCAGgtacatttct ... gtactttcagGTGTTTGAGATAAAAAATGATGCTAAAATGAAAAGGACAATGCGACGGCCC
EST: gi|211400287|gb|FL144413.1|FL144413
EST:     CATGTGCCGGTACAATGATGGTTGCAGCATCTGCAAATACCCTCAACCAG                         GTGTTTGAGATAAAAAATGATGCTAAAATGAAAAGGACAATGCGACGGCCC
genomic: CATGTGCCGGTACAATGATGGTTGCAGCATCTGCAAATACCCTCAACCAGgtacatttct ... gtactttcagGTGTTTGAGATAAAAAATGATGCTAAAATGAAAAGGACAATGCGACGGCCC
EST: gi|71443478|gb|DR824528.1|DR824528
EST:     CATGTGCCGGTACAATGATGGTTGCAGCATCTGCAAATACCCTCAACCAG                         GTGTTTGAGATAAAAAATGATGCTAAAATGAAAAGGACAATGCGACGGCCC
genomic: CATGTGCCGGTACAATGATGGTTGCAGCATCTGCAAATACCCTCAACCAGgtacatttct ... gtactttcagGTGTTTGAGATAAAAAATGATGCTAAAATGAAAAGGACAATGCGACGGCCC
EST: gi|71320010|gb|DR796769.1|DR796769
EST:     CATGTGCCGGTACAATGATGGTTGCAGCATCTGCAAATACCCTCAACCAG                         GTGTTTGAGATAAAAAATGATGCTAAAATGAAAAGGACAATGCGACGGCCC
genomic: CATGTGCCGGTACAATGATGGTTGCAGCATCTGCAAATACCCTCAACCAGgtacatttct ... gtactttcagGTGTTTGAGATAAAAAATGATGCTAAAATGAAAAGGACAATGCGACGGCCC
EST: gi|71318333|gb|DR795929.1|DR795929
EST:     CATGTGCCGGTACAATGATGGTTGCAGCATCTGCAAATACCCTCAACCAG                         GTGTTTGAGATAAAAAATGATGCTAAAATGAAAAGGACAATGCGACGGCCC
genomic: CATGTGCCGGTACAATGATGGTTGCAGCATCTGCAAATACCCTCAACCAGgtacatttct ... gtactttcagGTGTTTGAGATAAAAAATGATGCTAAAATGAAAAGGACAATGCGACGGCCC
EST: gi|76921322|gb|DV168542.1|DV168542
EST:     CATGTGCCGGTACAATGATGGTTGCAGCATCTGCAAATACCCTCAACCAG                         GTGTTTGAGATAAAAAATGATGCTAAAATGAAAAGGACAATGCGACGGCCC
genomic: CATGTGCCGGTACAATGATGGTTGCAGCATCTGCAAATACCCTCAACCAGgtacatttct ... gtactttcagGTGTTTGAGATAAAAAATGATGCTAAAATGAAAAGGACAATGCGACGGCCC
EST: gi|78081008|gb|DV509420.1|DV509420
EST:     CATGTGCCGGTACAATGATGGTTGCAGCATCTGCAAATACCCTCAACCAG                         GTGTTTGAGATAAAAAATGATGCTAAAATGAAAAGGACAATGCGACGCCCC
genomic: CATGTGCCGGTACAATGATGGTTGCAGCATCTGCAAATACCCTCAACCAGgtacatttct ... gtactttcagGTGTTTGAGATAAAAAATGATGCTAAAATGAAAAGGACAATGCGACGGCCC
EST: gi|211426733|gb|FL188786.1|FL188786
EST:     CATGTGCCGGTACAATGATGGTTGCAGCATCTGCAAATACCCTCAACCAG                         GTGTTTGAGATAAAAAATGATGCTAAAATGAAAAGGACAA
genomic: CATGTGCCGGTACAATGATGGTTGCAGCATCTGCAAATACCCTCAACCAGgtacatttct ... gtactttcagGTGTTTGAGATAAAAAATGATGCTAAAATGAAAAGGACAA
EST: gi|211400284|gb|FL144410.1|FL144410
EST:     CATGTGCCGGTACAATGATGGTTGCAGCATCTGCAAATACCCTCAACCAG                         GTGTTTGAGATAAAAAATGATGCTAAAATGAAAAGGACAATGCGACGCCCC
genomic: CATGTGCCGGTACAATGATGGTTGCAGCATCTGCAAATACCCTCAACCAGgtacatttct ... gtactttcagGTGTTTGAGATAAAAAATGATGCTAAAATGAAAAGGACAATGCGACGGCCC
EST: gi|71434316|gb|DR815366.1|DR815366
EST:     CATGTGCCGGTACAATGATGGTTGCAGCATCTGCAAATACCCTCAACCAG                         GTGTTTGAGATAAAAAATGATGCTAAAATGAAAAGGACAATGGCGACGGGC
genomic: CATGTGCCGGTACAATGATGGTTGCAGCATCTGCAAATACCCTCAACCAGgtacatttct ... gtactttcagGTGTTTGAGATAAAAAATGATGCTAAAATGAAAAGGACAATG-CGACGG-C


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgccccaggccaaaacaactctgtattctttctgatcattaacacgtactttcagGTGTTTGAGATAAAAAATGATGCTAAAATGAAAAGGACAATGCGACGGCCCCTGCCATCTGGTCGCATTAGTCCTGCACATGCTGCGATGTGGGCTACAA
                                    cattaac  putative branch site (score: 2)
                                              tactttc  putative PPT
                       tattcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccaaatatgaataactctgtttgaacttgctgtacttacttcagctgccccaggccaaaacaactctgtattctttctgatcattaacacgtactttcagGTGTTTGAGATAAAAAATGATGCTAAAATGAAAAGGACAATGCGACGGCCCCTGCCATCTGGTCGCATTAGTCCTGCACATGCTGCGATGTGGGCTACAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - -tctgttt
- - - - - - - - - - - - -cttgctg
- - - - - - - - - - - - - - - - - - - - -cagctgc
- - - - - - - - - - - - - - - - - - - - - - - - -ccaggcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaacaa