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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcatgaggtatttgtatgcataaccataacacttacctcaatgaaattcaaggttcttttctgtctatctaagttaacttgtaaatttttttgagtttagTCAATTTGTAGGAGAGGGGACGCCATACATCAAAGATGACTAAAGAAGAGGAAGATGAAGAATACCTCGAAGAGGAAGAAGATGCCCTTGCTGGTGCAGG

Basic information

species Zea mays
transcript GRMZM5G897073_T04
intron # 3
splice site 3'
intron type U2

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|88752874|gb|DY537015.1|DY537015
EST:     GTTGAGCCTGTACTTCGAGGAGTGCCTGCATCCGGGATTATCACACACAG                         TCAATTTGTAGGAGAGGGGACGCCATACATCAAAGATGACTAAAGAAGAGG
genomic: GTTGAGCCTGTACT-CGAGGAGTGCCTGCATCCGGGATTATCACACACAGgtagcctgca ... ttgagtttagTCAATTTGTAGGAGAGGGGACGCCATACATCAAAGATGACTAAAGAAGAGG
EST: gi|32837950|gb|CD977628.1|CD977628
EST:     ACTCGAGGAGTGCCTGCATCCGGGATTATCACACACAG                         TCAATTTGTAGGAGAGGGGACGCCATACATCAAAGATGACTAAAGAAGAGG
genomic: ACTCGAGGAGTGCCTGCATCCGGGATTATCACACACAGgtagcctgca ... ttgagtttagTCAATTTGTAGGAGAGGGGACGCCATACATCAAAGATGACTAAAGAAGAGG
EST: gi|60345564|gb|DN212537.1|DN212537
EST:     TGTTGAGCCTGTACTCGAGGAGTGCCTGCATCCGGGATTATCACACACAG                         TCAATTTGTAGGAGAGGGGACGCCATACATCAAAGATGACTAAAGAAGAGG
genomic: TGTTGAGCCTGTACTCGAGGAGTGCCTGCATCCGGGATTATCACACACAGgtagcctgca ... ttgagtttagTCAATTTGTAGGAGAGGGGACGCCATACATCAAAGATGACTAAAGAAGAGG
EST: gi|91050400|gb|EB160818.1|EB160818
EST:     TGTTGAGCCTGTACTCGAGGAGTGCCTGCATCCGGGATTATCACACACAG                         TCAATTTGTAGGAGAGGGGACGCCATACATCAAAGATGACTAAAGAAGAGG
genomic: TGTTGAGCCTGTACTCGAGGAGTGCCTGCATCCGGGATTATCACACACAGgtagcctgca ... ttgagtttagTCAATTTGTAGGAGAGGGGACGCCATACATCAAAGATGACTAAAGAAGAGG
EST: gi|32838909|gb|CD978590.1|CD978590
EST:     ACTCGAGGAGTGCCTGCATCCGGGATTATCACACACAG                         TCAATTTGTAGGAGAGGGGACGCCATACATCAAAGATGACTAAAGAAGAGG
genomic: ACTCGAGGAGTGCCTGCATCCGGGATTATCACACACAGgtagcctgca ... ttgagtttagTCAATTTGTAGGAGAGGGGACGCCATACATCAAAGATGACTAAAGAAGAGG
EST: gi|211423204|gb|FL142523.1|FL142523
EST:     TGTTGAGCCTGTACTCGAGGAGTGCCTGCATCCGGGATTATCACACACAG                         TCAATTTGTAGGARAGGGGACCGCCATACATCAAAGATGACTAAAGAAGAG
genomic: TGTTGAGCCTGTACTCGAGGAGTGCCTGCATCCGGGATTATCACACACAGgtagcctgca ... ttgagtttagTCAATTTGTAGGAGAGGGGAC-GCCATACATCAAAGATGACTAAAGAAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attcaaggttcttttctgtctatctaagttaacttgtaaatttttttgagtttagTCAATTTGTAGGAGAGGGGACGCCATACATCAAAGATGACTAAAGAAGAGGAAGATGAAGAATACCTCGAAGAGGAAGAAGATGCCCTTGCTGGTGCAGG
                          agttaac  putative branch site (score: 3)
                                        ttttttt  putative PPT
                    tatctaagttaacttg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcatgaggtatttgtatgcataaccataacacttacctcaatgaaattcaaggttcttttctgtctatctaagttaacttgtaaatttttttgagtttagTCAATTTGTAGGAGAGGGGACGCCATACATCAAAGATGACTAAAGAAGAGGAAGATGAAGAATACCTCGAAGAGGAAGAAGATGCCCTTGCTGGTGCAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG