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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactgttacttgacttctctcagtatcatactatcattgttttattcttctaaagtgtacaattagtaactgcaacctctgattggaattttaaaagGTCTGATAAATGCTCTAAAGCTTATCCAACCAATCAAGGACAAGTACCCTAGTATCACTTATGCAGATTTATTTCAGTTGGCAAGTGCTACAGCAATTGA

Basic information

species Zea mays
transcript GRMZM2G120517_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G120517_T03 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os04g35520.2 (Oryza sativa), 3'ss of exon 3
gtactgttacttgacttctctcagtatcatactatcattgttttattcttctaaagtgtacaattagtaactgcaacctctgattggaattttaaaagGTCTGATAAATGCTCTAAAGCTTATCCAACCAATCAAGGACAAGTACCCTAGTATCACTTATGCAGATTTATTTCAGTTGGCAAGTGCTACAGCAATTGA
     || || | || | |       |||   | || ||   || ||  |   ||||||||  | || ||||  ||   ||||||| | | || || || ||| ||||||||||||||||| ||||||| ||||||||||| ||||| | |||| | ||||| |||||||| ||| ||||||||||||||||||||||
-----gtaacattaccttt-------tcacgatttcgtttccttgttgcttgtaagtgtactttcagcaactaaaaatcctgattgaattattgaagGG-CTGGTAAATGCTCTAAAGCTTGTCCAACCTATCAAGGACAAATACCCAAATATCTCATATGCGGATTTATTCCAGCTGGCAAGTGCTACAGCAATTGA
















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|15177551|gb|BI398490.1|BI398490
EST:     TAATGGAAGTTTAAGATTTGATGTTGAGTTGAAACATGGAGCCAATGCTG                         GTCTGATAAATGCTCTAAAGCTTATCCAACCA-TCAAGGACAAGTACCCTA
genomic: TAATGGAAGTTTAAGATTTGATGTTGAGTTGAAACATGGAGCCAATGCTGgtactgttac ... attttaaaagGTCTGATAAATGCTCTAAAGCTTATCCAACCAATCAAGGACAAGTACCCTA
EST: gi|22489220|gb|BU049143.1|BU049143
EST:     TAATGGAAGTTTAAGATTTGATGTTGAGTTGAAACATGGAGCCAATGCTG                         GTCTGATAAATGCTCTAAAGCTTATCCAACCAATCAAGGACAAGTACCCTA
genomic: TAATGGAAGTTTAAGATTTGATGTTGAGTTGAAACATGGAGCCAATGCTGgtactgttac ... attttaaaagGTCTGATAAATGCTCTAAAGCTTATCCAACCAATCAAGGACAAGTACCCTA
EST: gi|15188187|gb|BI417164.1|BI417164
EST:     TAATGGAAGTTTAAGATTTGATGTTGAGTTGAAACATGGAGCCAATGCTG                         GTCTGATAAATGCTCTAAAGCTTATCCAACCAATCAAGGACCAGCACCCTA
genomic: TAATGGAAGTTTAAGATTTGATGTTGAGTTGAAACATGGAGCCAATGCTGgtactgttac ... attttaaaagGTCTGATAAATGCTCTAAAGCTTATCCAACCAATCAAGGACAAGTACCCTA
EST: gi|16137300|gb|BI894165.1|BI894165
EST:     TAATGGAAGTTTAAGATTTGATGTTGAGTTGAAACATGGAGCCAATGCTG                         GTCTGATAAATGCTCTAAAGCTTATCCA-CCAATCAAGGACAAGTACCCTA
genomic: TAATGGAAGTTTAAGATTTGATGTTGAGTTGAAACATGGAGCCAATGCTGgtactgttac ... attttaaaagGTCTGATAAATGCTCTAAAGCTTATCCAACCAATCAAGGACAAGTACCCTA
EST: gi|15323578|gb|BI478812.1|BI478812
EST:     TAATGGAAGTTTAAGATTTGATGTTGAGTTGAAACATGGAGCCAATGCTG                         GTCTGATAAATGCTCTAAAGCTTATCCAACCAATCAAGGACAAGTACCCTA
genomic: TAATGGAAGTTTAAGATTTGATGTTGAGTTGAAACATGGAGCCAATGCTGgtactgttac ... attttaaaagGTCTGATAAATGCTCTAAAGCTTATCCAACCAATCAAGGACAAGTACCCTA
EST: gi|15323577|gb|BI478811.1|BI478811
EST:     TAATGGAAGTTTAAGATTTGATGTTGAGTTGAAACATGGAGCCAATGCTG                         GTCTGATAA-TGCTCTAA-GCTTATCCAA
genomic: TAATGGAAGTTTAAGATTTGATGTTGAGTTGAAACATGGAGCCAATGCTGgtactgttac ... attttaaaagGTCTGATAAATGCTCTAAAGCTTATCCAA
EST: gi|18181579|gb|BM382789.1|BM382789
EST:     TAATGGAAGTTTAAGATTTGATGTTGAGTTGAAACATGGAGCCAATGCTG                         GTCTGATAAATGCTCTAAAGCTTATCCAACCAATCAAGGACAAGTACCCTA
genomic: TAATGGAAGTTTAAGATTTGATGTTGAGTTGAAACATGGAGCCAATGCTGgtactgttac ... attttaaaagGTCTGATAAATGCTCTAAAGCTTATCCAACCAATCAAGGACAAGTACCCTA
EST: gi|89106264|gb|DY576481.1|DY576481
EST:     TAATGGAAGTTTAAGATTTGATGTTGAGTTGAAACATGGAGCCAATGCTG                         GTCTGATAAATGCTCTAAAGCTTATCCAACCAATCAAGGACAAGTACCCTA
genomic: TAATGGAAGTTTAAGATTTGATGTTGAGTTGAAACATGGAGCCAATGCTGgtactgttac ... attttaaaagGTCTGATAAATGCTCTAAAGCTTATCCAACCAATCAAGGACAAGTACCCTA
EST: gi|7238058|gb|AW573325.1|AW573325
EST:     TAATGGAAGTTTAAGATTTGATGTTGAGTTGAAACATGGAGCCAATGCTG                         GTCTGATAAATGCTCTAAAGCTTATCCAACCAATCAAGGACAAGTACCCTA
genomic: TAATGGAAGTTTAAGATTTGATGTTGAGTTGAAACATGGAGCCAATGCTGgtactgttac ... attttaaaagGTCTGATAAATGCTCTAAAGCTTATCCAACCAATCAAGGACAAGTACCCTA
EST: gi|15177552|gb|BI398491.1|BI398491
EST:     TAATGGAAGTTTAAGATTTGATGTTGAGTTGAAACATGGAGCCAATGCTG                         GTCTGATAAATGCTCTAAAGCTTATCCA-CCAATCAAGGACAAGTACCCTA
genomic: TAATGGAAGTTTAAGATTTGATGTTGAGTTGAAACATGGAGCCAATGCTGgtactgttac ... attttaaaagGTCTGATAAATGCTCTAAAGCTTATCCAACCAATCAAGGACAAGTACCCTA
EST: gi|16137301|gb|BI894166.1|BI894166
EST:     TAATGGAAGTTTAAGATTTGATGTTGAGTTGAAACATGGAGCCAATGCTG                         GTCTGATAAATGCTCTAAAGCTTATCCAACCA-TCAAGGACA-GTACCCTA
genomic: TAATGGAAGTTTAAGATTTGATGTTGAGTTGAAACATGGAGCCAATGCTGgtactgttac ... attttaaaagGTCTGATAAATGCTCTAAAGCTTATCCAACCAATCAAGGACAAGTACCCTA
EST: gi|18383811|gb|BM417011.1|BM417011
EST:     TAAGATTTGATGTTGAGTTGAAACATGGAGCCAATGCTG                         GTCTGATAAATGCTCTAAAGCTTATCCAACCAATCAAGGACAAGTACCCTA
genomic: TAAGATTTGATGTTGAGTTGAAACATGGAGCCAATGCTGgtactgttac ... attttaaaagGTCTGATAAATGCTCTAAAGCTTATCCAACCAATCAAGGACAAGTACCCTA
EST: gi|18383818|gb|BM417018.1|BM417018
EST:     TAATGGAAGTTTAAGATTTGATGTTGAGTTGAAACATGGAGCCAATGCTG                         GTCTGATAAATGCTCTAAAGCTTATCCAACCAATCAAGGACAAGTACCCTA
genomic: TAATGGAAGTTTAAGATTTGATGTTGAGTTGAAACATGGAGCCAATGCTGgtactgttac ... attttaaaagGTCTGATAAATGCTCTAAAGCTTATCCAACCAATCAAGGACAAGTACCCTA
EST: gi|22489146|gb|BU049069.1|BU049069
EST:     TAATGGAAGTTTAAGATTTGATGTTGAGTTGAAACATGGAGCCAATGCTG                         GTCTGATAAATGCTCTAAAGCTTATCCAACCAATCAAGGACAAGTACCCTA
genomic: TAATGGAAGTTTAAGATTTGATGTTGAGTTGAAACATGGAGCCAATGCTGgtactgttac ... attttaaaagGTCTGATAAATGCTCTAAAGCTTATCCAACCAATCAAGGACAAGTACCCTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattcttctaaagtgtacaattagtaactgcaacctctgattggaattttaaaagGTCTGATAAATGCTCTAAAGCTTATCCAACCAATCAAGGACAAGTACCCTAGTATCACTTATGCAGATTTATTTCAGTTGGCAAGTGCTACAGCAATTGA
                                       attggaattttaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactgttacttgacttctctcagtatcatactatcattgttttattcttctaaagtgtacaattagtaactgcaacctctgattggaattttaaaagGTCTGATAAATGCTCTAAAGCTTATCCAACCAATCAAGGACAAGTACCCTAGTATCACTTATGCAGATTTATTTCAGTTGGCAAGTGCTACAGCAATTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT