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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagaaacaaagaaagaaagaaaaaaacccttaaaactcttaattaatcaacatcaacgactgcccgttcccttgtgttgcagAGGCAAACCTTCTGTTCCTCGAGTCGCCCGCGGGAGTCGGCTTCTCCTACGCCAACACCACCTCGGACCTCAAGACGTCGGGCGACGAGAGGACCG

Basic information

species Zea mays
transcript GRMZM5G879749_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G879749_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g55130.5 (Oryza sativa), 3'ss of exon 2
gtgagaaacaaagaaagaaagaaaaaaacccttaaaactcttaat-taatcaacatcaacgactgcccgttcccttgt-gttgcagAGGCAAACCTTCTGTTCCTCGAGTCGCCCGCGGGAGTCGGCTTCTCCTACGCCAACACCACCTCGGACCTCAAGACGTCGGGCGACGAGAGGACCG
       || ||||   |    | |||  | | |   ||  | ||  |||     |||  |||||       | ||||   ||||||||||||||| |||||||| || || || || ||||| ||||| || ||| ||||||||||||| || |||||||| || || || |||||||| |
-----gtactaagactaagctcagaaactcatcatgcctaatgatgcaatgcctgtcactgactgatgaacactttgttactgcagAGGCAAACCTCCTGTTCCTGGAATCACCTGCCGGAGTTGGCTTTTCATACTCCAACACCACCTCTGATCTCAAGACATCTGGTGATGAGAGGACAG
















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|94479697|gb|EB708655.1|EB708655
EST:     CAAACCAAACGGGACAGGCCTGTTCCTCAACAAGTACTCATGGAACAGAG                         AGGCAAACCTTCTGTTCCTCGAGTCGCCCGCGGGAGTCGGCTTCTCCTACG
genomic: CAAACCAAACGGGACAGGCCTGTTCCTCAACAAGTACTCATGGAACAGAGgtgagaaaca ... tgtgttgcagAGGCAAACCTTCTGTTCCTCGAGTCGCCCGCGGGAGTCGGCTTCTCCTACG
EST: gi|91050418|gb|EB160836.1|EB160836
EST:     CAAACCAAACGGGACAGGCCTGTTCCTCAACAAGTACTCATGGAACAGAG                         AGGCAAACCTTCTGTTCCTCGAGTCGCCCGCGGGAGTCGGCTTCTCCTACG
genomic: CAAACCAAACGGGACAGGCCTGTTCCTCAACAAGTACTCATGGAACAGAGgtgagaaaca ... tgtgttgcagAGGCAAACCTTCTGTTCCTCGAGTCGCCCGCGGGAGTCGGCTTCTCCTACG
EST: gi|29946821|gb|CB816342.1|CB816342
EST:     CAAACCAAACGGGACAGGCCTGTTCCTCAACAAGTACTCATGGAACAGAG                         AGGCAAACCTTCTGTTCCTCGAGTCGCCCGCGGGAGTCGGCTTCTCCTACG
genomic: CAAACCAAACGGGACAGGCCTGTTCCTCAACAAGTACTCATGGAACAGAGgtgagaaaca ... tgtgttgcagAGGCAAACCTTCTGTTCCTCGAGTCGCCCGCGGGAGTCGGCTTCTCCTACG
EST: gi|101395266|gb|EB819563.1|EB819563
EST:     CAAACCAAACGGGACAGGCCTGTTCCTCAACAAGTACTCATGGAACAGAG                         AGGCAAACCTTCTGTTCCTCGAGTCGCCCGCGGGAGTCGGCTTCTCCTACG
genomic: CAAACCAAACGGGACAGGCCTGTTCCTCAACAAGTACTCATGGAACAGAGgtgagaaaca ... tgtgttgcagAGGCAAACCTTCTGTTCCTCGAGTCGCCCGCGGGAGTCGGCTTCTCCTACG
EST: gi|71775053|gb|DR972931.1|DR972931
EST:     CAAACCAAACGGGACAGGCCTGTTCCTCAACAAGTACTCATGGAACAGAG                         AGGCAAACCTTCTGTTCCTCGAGTCGCCCGCGGGAGTCGGCTTCTCCTACG
genomic: CAAACCAAACGGGACAGGCCTGTTCCTCAACAAGTACTCATGGAACAGAGgtgagaaaca ... tgtgttgcagAGGCAAACCTTCTGTTCCTCGAGTCGCCCGCGGGAGTCGGCTTCTCCTACG
EST: gi|32164980|gb|CD670298.1|CD670298
EST:     CAAACCAAACGGGACAGGCCTGTTCCTCAACAAGTACTCATGGAACAGAG                         AGGCAAACCTTCTGTTCCTCGAGTCGCCCGCGGGAG
genomic: CAAACCAAACGGGACAGGCCTGTTCCTCAACAAGTACTCATGGAACAGAGgtgagaaaca ... tgtgttgcagAGGCAAACCTTCTGTTCCTCGAGTCGCCCGCGGGAG
EST: gi|76020009|gb|DT947179.1|DT947179
EST:     CAAACCAAACGGGACAGGCCTGTTCCTCAACAAGTACTCATGGAACAGAG                         AGGCAAACCTTCTGTTCCTCGAGTCGCCCGCGGGAGTCGGCTTCTCCTACG
genomic: CAAACCAAACGGGACAGGCCTGTTCCTCAACAAGTACTCATGGAACAGAGgtgagaaaca ... tgtgttgcagAGGCAAACCTTCTGTTCCTCGAGTCGCCCGCGGGAGTCGGCTTCTCCTACG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccttaaaactcttaattaatcaacatcaacgactgcccgttcccttgtgttgcagAGGCAAACCTTCTGTTCCTCGAGTCGCCCGCGGGAGTCGGCTTCTCCTACGCCAACACCACCTCGGACCTCAAGACGTCGGGCGACGAGAGGACCG
             aattaat  putative branch site (score: 3)
                                ctgcccgttccctt  putative PPT
     aaactcttaattaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagaaacaaagaaagaaagaaaaaaacccttaaaactcttaattaatcaacatcaacgactgcccgttcccttgtgttgcagAGGCAAACCTTCTGTTCCTCGAGTCGCCCGCGGGAGTCGGCTTCTCCTACGCCAACACCACCTCGGACCTCAAGACGTCGGGCGACGAGAGGACCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA