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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtatttagcagtaaataacactacagtggtttactagtagaggactactggtcaaccatcatatcgcgcgcggtcccgttgcctggtgatgtgcttgtgtgctttgcgttattgcagGTTGATAGGGAAAGTGGCAGCCGACCACAGCCACAAGTGGGTGTTCCAGGAGGCCCAGGAGCACGAGATCAACCTCATCTCCTCCTGGAGCAACCCTGCC

Basic information

species Zea mays
transcript GRMZM2G116185_T03
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G116185_T03 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os02g50900.1 (Oryza sativa), 3'ss of exon 3
-------------------------------------gtacgt-atttagcagtaaataacactacagtgg-----tttactagtagaggactactggtc----aaccatcatatcgcgcgcggtcccgttgcctggtgatgtgc-------ttgtgtgctttgcgttattgcagGTTGATAGGGAAAGTGGCAGCCGACCACAGCCACAAGTGGGTGTTCCAGGAGGCCCAGGAGCACGAGATCAACCTCATCTCCTCCTGGAGCAACCCTGCC
                                       || | ||| |  | | | |  ||    | |||     |||  || |     |    || ||        | | ||       |  |   ||   |  |||| |  |       |  || | |   |  | ||| |||||| | |||||||| ||||| |||||  ||||||||||||||| |||||||||| | |||||||||||||||||  |  |||| |||| ||||||||||
gtatgtggtagtactaattaattagcagtttggcttgaaacatcattaattaattagtgtcatagtattggccgtctttcttaattagtaatctatgttctttgggaaaacctacgctaatcactttagtcagcacgtgaagcacgatctcatgatgcgatgatccatcttgaagGTTGGTTGGGAAAGTTGCAGCTGACCATGGCCACAAGTGGGTGTCCCAGGAGGCCAATGAGCACGAGATCAACCTGGTTACCTCATGGAACAACCCTGCC

upper sequence: GRMZM2G116185_T03 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA01G03940.1 (Glycine max), 3'ss of exon 3
gtacgtatttagcagtaaataacactacagtggtttactagtagaggactactggtcaaccatcatatcgcgcgcggtcccgttgcctggtgatgtgcttgtgtgctttgcgttattg--cagGTTGATAGGGAAAGTGGCAGCCGACCACAGCCACAAGTGGGTGTTCCAGGAGGCCCAGGAGCACGAGATCAACCTCATCTCCTCCTGGAGCAACCCTGCC
     |||  |  | |||  |||| || | |    || | ||     | | ||     ||  |  | | |   |  || |        |  | ||   |  |    | ||  | || |  |||||||||||| |||||||| || || ||||||||||||||| |   | | ||| |  | || || || |||||| || | ||  | |||  |||  | || 
--gtatatgcaatattaatcaacatta-atttacctatttgtgtcacatttct--cttactttgttcttgaaagatgttcaaagctaagaggttgatttaattaattatgtttaatggagcagGTTGATAGGAAAAGTGGCTGCAGATCACAGCCACAAGTGGATAAACAAAGAGCCTAATGATCAAGAAATCAACTTCTTGTCAGCATGGCACAATTCAGCA

upper sequence: GRMZM2G116185_T03 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA02G03740.1 (Glycine max), 3'ss of exon 3
gtacgtatttagcagtaaataacactacagtggtttactagtagaggactact---ggtcaaccatcatatcgcgcgcggtcccgttgcctggtgatgtgcttgtgtgctttgcgttattg--cagGTTGATAGGGAAAGTGGCAGCCGACCACAGCCACAAGTGGGTGTTCCAGGAGGCCCAGGAGCACGAGATCAACCTCATCTCCTCCTGGAGCAACCCTGCC
    ||||  |  | |||  |||| | || |   ||| | ||     | | ||   | |   |  |   |    |  |      |      ||| ||  |||  |      ||  | || |  |||||||||||| |||||||| || || ||||||||||||||| | | | | ||| |  | || || || |||||| || |  |  | |||  |||  | || 
----gtatgcaatattaatcaacatt-catttacttatttgtgtcacatttctcttgttttgctcttgaaagatgttcatcaaagcaaagaggttataggctaattaatcatgtctaatggagcagGTTGATAGGAAAAGTGGCTGCAGATCACAGCCACAAGTGGATATACAAAGAGCCTAATGATCAAGAAATCAACTTCTTGACAGCATGGCACAATTCAGCA

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|78086977|gb|DV515370.1|DV515370
EST:     CCTGAGCTCTTCTTCA-GATGTCCCACGACATCTACAACTACGGTGAAGG                         GGTGATAGGGGAAGTGGCAGCCGATCACAGCCACAA
genomic: CCTGAGCTCTTCTTCAAGATGTCCCACGACATCTACAACTACGGTGAAGGgtacgtattt ... gttattgcagGTTGATAGGGAAAGTGGCAGCCGACCACAGCCACAA
EST: gi|20803186|gb|BQ294236.1|BQ294236
EST:     CCTGAGCTCTTCTTCAAGATGTCCCACGACATCTACAACTACGGTGAAGG                         GTTGATAGGGAAAGTGGCAGCCGACCACAGCCACAAGTGGGTGTTCCAGGA
genomic: CCTGAGCTCTTCTTCAAGATGTCCCACGACATCTACAACTACGGTGAAGGgtacgtattt ... gttattgcagGTTGATAGGGAAAGTGGCAGCCGACCACAGCCACAAGTGGGTGTTCCAGGA
EST: gi|148953903|gb|EC899284.2|EC899284
EST:     CCTGAGCTCTTCTTCAAGATGTCCCACGACATCTACAACTACGGTGAAGG                         GTTGATAGGGAAAGTGGCAGCCGACCACAGTCACAAGTGGGTGTTCCAGGA
genomic: CCTGAGCTCTTCTTCAAGATGTCCCACGACATCTACAACTACGGTGAAGGgtacgtattt ... gttattgcagGTTGATAGGGAAAGTGGCAGCCGACCACAGCCACAAGTGGGTGTTCCAGGA
EST: gi|91049965|gb|EB160383.1|EB160383
EST:     CCTGAGCTCTTCTTCAAGATGTCCCACGACATCTACAACTACGGTGAAGG                         GTTGATAGGGAAAGTGGCAGC
genomic: CCTGAGCTCTTCTTCAAGATGTCCCACGACATCTACAACTACGGTGAAGGgtacgtattt ... gttattgcagGTTGATAGGGAAAGTGGCAGC
EST: gi|89250173|gb|DY621959.1|DY621959
EST:     CTGAGCTTTTCTTCAAGATGTCCCACGACATCTACAATTACGG-GAAGGG                         GTTGATAGGGAAAGTGGCACCCGACCACACCCACAAGTGGGTGTTCCAAG
genomic: CTGAGCTCTTCTTCAAGATGTCCCACGACATCTACAACTACGGTGAA-GGgtacgtattt ... gttattgcagGTTGATAGGGAAAGTGGCAGCCGACCACAGCCACAAGTGGGTGTTCC-AG
EST: gi|26456486|gb|CA828069.1|CA828069
EST:     CCTGAGCTCTTCTTCAAGATGTCCCACGACATCTACAACTACGGTGAAGG                         GTTGATAGGGAAAGTGGCAGCCGACCACAGCCACAAGTGGGTGTTCCAGGA
genomic: CCTGAGCTCTTCTTCAAGATGTCCCACGACATCTACAACTACGGTGAAGGgtacgtattt ... gttattgcagGTTGATAGGGAAAGTGGCAGCCGACCACAGCCACAAGTGGGTGTTCCAGGA
EST: gi|93012864|gb|EB638384.1|EB638384
EST:     CCTGAGCTCTTCTTCAAGATGTCCCACGACATCTACAACTACGGTGAAGG                         GGTGATAGGGA
genomic: CCTGAGCTCTTCTTCAAGATGTCCCACGACATCTACAACTACGGTGAAGGgtacgtattt ... gttattgcagGTTGATAGGGA
EST: gi|50336651|gb|CO531777.1|CO531777
EST:     CCTGAGCTCTTCTTCAAGATGTCCCACGACATCTACAACTACGGTGAAGG                         GTTGATAGGGAAAGTGGCAGCCGACCACAGCCACAAGTGGGTGTTCCAGGA
genomic: CCTGAGCTCTTCTTCAAGATGTCCCACGACATCTACAACTACGGTGAAGGgtacgtattt ... gttattgcagGTTGATAGGGAAAGTGGCAGCCGACCACAGCCACAAGTGGGTGTTCCAGGA
EST: gi|78112591|gb|DV530985.1|DV530985
EST:     CCTGAGCTCTTCTTCAAGATGTCCCACGACATCTACAACTACGGTGAAGG                         GTTGATAGGGAAAGTGGCAGCCGACCACAGCCACAAGTGGGTGTTCCAGGA
genomic: CCTGAGCTCTTCTTCAAGATGTCCCACGACATCTACAACTACGGTGAAGGgtacgtattt ... gttattgcagGTTGATAGGGAAAGTGGCAGCCGACCACAGCCACAAGTGGGTGTTCCAGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcgcgcgcggtcccgttgcctggtgatgtgcttgtgtgctttgcgttattgcagGTTGATAGGGAAAGTGGCAGCCGACCACAGCCACAAGTGGGTGTTCCAGGAGGCCCAGGAGCACGAGATCAACCTCATCTCCTCCTGGAGCAACCCTGCC
                                              ttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgtatttagcagtaaataacactacagtggtttactagtagaggactactggtcaaccatcatatcgcgcgcggtcccgttgcctggtgatgtgcttgtgtgctttgcgttattgcagGTTGATAGGGAAAGTGGCAGCCGACCACAGCCACAAGTGGGTGTTCCAGGAGGCCCAGGAGCACGAGATCAACCTCATCTCCTCCTGGAGCAACCCTGCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA