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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTTTATCCCACTGCAATTGGATCCGAACCCCAGGATTGTAACCTGGATTCCCGTGAACATTGGAAGCGGGTTATGCAAGGCCATGCTGGTGCCAACTTGgtactgtttgttgtattgtacaagttcatgatgcgctatgaccttcattgaggaacaacaaagatgtttctttgttgttcctctaagtgatactggtgaagcatccacttctctggtcgcgttatgatttcagcttgaattatccag

Basic information

species Zea mays
transcript GRMZM2G073950_T01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G073950_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os02g33080.2 (Oryza sativa), 5'ss of exon 6
GTTTTATCCCACTGCAATTGGATCCGAACCCCAGGATTGTAACCTGGATTCCCGTGAACATTGGAAGCGGGTTATGCAAGGCCATGCTGGTGCCAACTTGgtactgtttgttgtattgtacaagttcatg----atgcgcta-tgaccttcattgaggaacaacaaagatgtttctttgttgttcctctaagtgatactggtgaagcatccacttctctggtcgcgttatgatttcagcttgaattatccag
||| ||||| ||||||||||| || || |||||||||  |||||| |||||||| ||||| |||||||| || |||||||| ||||||||||| ||| |||||||| |  |||| ||||   |  | |||    ||  |||| | | ||| |||||| ||  | | | ||   | ||| || ||         ||| ||   | ||        | |||| ||   || ||  | ||     ||| || |||
GTTCTATCCAACTGCAATTGGTTCTGAGCCCCAGGATAATAACCTAGATTCCCGAGAACACTGGAAGCGCGTCATGCAAGGACATGCTGGTGCTAACCTGgtactgctatttgttttgttataccttatgttttatcagctactcagctttattgagaaatcaaatatatacctattt-ttattt------acgatccttcggtag--------tttctgatca--ttctggatccatacc-aatcatgcag
















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|211141687|gb|FL053515.1|FL053515
EST:     CCCGTGAACATTGGAAGCGGGTTATGCAAGGCCATGCTGGTGCCAACTTG                         GTCCCTCTTGTTGCTTCCAACCGGATTGGCAGAGAAACTGTTGACACTGAG
genomic: CCCGTGAACATTGGAAGCGGGTTATGCAAGGCCATGCTGGTGCCAACTTGgtactgtttg ... aattatccagGTCCCTCTTGTTGCTTCCAACCGGATTGGCAGAGAAACTGTTGACACTGAG
EST: gi|78077685|gb|DV506119.1|DV506119
EST:     CCCGTGAACATTGGAAGCGGGTTATGCAAGGCCATGCTGGTGCCAACTTG                         GTCCCTCTTGTTGCTTCCAACCGGATTGGCAGAGAAACTGTTGACACTGAG
genomic: CCCGTGAACATTGGAAGCGGGTTATGCAAGGCCATGCTGGTGCCAACTTGgtactgtttg ... aattatccagGTCCCTCTTGTTGCTTCCAACCGGATTGGCAGAGAAACTGTTGACACTGAG
EST: gi|211141683|gb|FL053511.1|FL053511
EST:     CCCGTGAACATTGGAAGCGGGTTATGCAAGGCCATGCTGGTGCCAACTTG                         GTCCCTCTTGTTGCTTCCAACCGGATTGGCAGAGAAACTGTTGACACTGAG
genomic: CCCGTGAACATTGGAAGCGGGTTATGCAAGGCCATGCTGGTGCCAACTTGgtactgtttg ... aattatccagGTCCCTCTTGTTGCTTCCAACCGGATTGGCAGAGAAACTGTTGACACTGAG
EST: gi|32790714|gb|CD942950.1|CD942950
EST:     CCCGTGAACATTGGAAGCGGGTTATGCAAGGCCATGCTGGTGCCAACTTG                         GTCCCTCTTGGTGCTTCCAACCGGATTGGCAGAGAAACTGTTGACACTGAG
genomic: CCCGTGAACATTGGAAGCGGGTTATGCAAGGCCATGCTGGTGCCAACTTGgtactgtttg ... aattatccagGTCCCTCTTGTTGCTTCCAACCGGATTGGCAGAGAAACTGTTGACACTGAG
EST: gi|113702021|gb|EE679525.1|EE679525
EST:     CCCGTGAACATTGGAAGCGGGTTATGCAAGGCCATGCTGGTGCCAACTTG                         GTCCCTCTTGTTGCTTCCAACCGGATTGGCAGAGAAACTGTTGACACTGAG
genomic: CCCGTGAACATTGGAAGCGGGTTATGCAAGGCCATGCTGGTGCCAACTTGgtactgtttg ... aattatccagGTCCCTCTTGTTGCTTCCAACCGGATTGGCAGAGAAACTGTTGACACTGAG
EST: gi|50324198|gb|CO519324.1|CO519324
EST:     CCCGTGAACATTGGAAGCGGGTTATGCAAGGCCATGCTGGTGCCAACTTG                         GTCCCTCTTGTTGCTTCCAACCGGATTGGCAGAGAAACTGTTGACACTGAG
genomic: CCCGTGAACATTGGAAGCGGGTTATGCAAGGCCATGCTGGTGCCAACTTGgtactgtttg ... aattatccagGTCCCTCTTGTTGCTTCCAACCGGATTGGCAGAGAAACTGTTGACACTGAG
EST: gi|29130437|gb|CB381141.1|CB381141
EST:     CCCGTGAACATTGGAAGCGGGTTATGCAAGGCCATGCTGGTGCCAACTTG                         GTCCCTCTTGTTGCTTCCAACCGGATTGGCAGAGAAACTGTTGACACTGAG
genomic: CCCGTGAACATTGGAAGCGGGTTATGCAAGGCCATGCTGGTGCCAACTTGgtactgtttg ... aattatccagGTCCCTCTTGTTGCTTCCAACCGGATTGGCAGAGAAACTGTTGACACTGAG
EST: gi|101394654|gb|EB819259.1|EB819259
EST:     CCCGTGAACATTGGAAGCGGGTTATGCAAGGCCATGCTGGTGCCAACTTG                         GTCCCTCTTGTTGCTTCCAACCGGATTGGCAGAGAAACTGTTGACACTGAG
genomic: CCCGTGAACATTGGAAGCGGGTTATGCAAGGCCATGCTGGTGCCAACTTGgtactgtttg ... aattatccagGTCCCTCTTGTTGCTTCCAACCGGATTGGCAGAGAAACTGTTGACACTGAG
EST: gi|91056600|gb|EB167018.1|EB167018
EST:     CCCGTGAACATTGGAAGCGGGTTATGCAAGGCCATGCTGGTGCCAACTTG                         GTCCCTCTTGTTGCTTCCAACCGGATTGGC
genomic: CCCGTGAACATTGGAAGCGGGTTATGCAAGGCCATGCTGGTGCCAACTTGgtactgtttg ... aattatccagGTCCCTCTTGTTGCTTCCAACCGGATTGGC
EST: gi|148953399|gb|EE152896.2|EE152896
EST:     CCCGTGAACATTGGAAGCGGGTTATGCAAGGCCATGCTGGTGCCAACTTG                         GTCCCTCTTGTTGCTTCCAACCGGATTGGCAGAGAAACTGTTGACACTGAG
genomic: CCCGTGAACATTGGAAGCGGGTTATGCAAGGCCATGCTGGTGCCAACTTGgtactgtttg ... aattatccagGTCCCTCTTGTTGCTTCCAACCGGATTGGCAGAGAAACTGTTGACACTGAG
EST: gi|78081735|gb|DV510147.1|DV510147
EST:     CCCGTGAACATTGGAAGCGGGTTATGCAAGGCCATGCTGGTGCCAACTTG                         GTCCCTCTTGTTGCTTCCAACCGGATTGGCAGAGAAACTGTTGACACTGAG
genomic: CCCGTGAACATTGGAAGCGGGTTATGCAAGGCCATGCTGGTGCCAACTTGgtactgtttg ... aattatccagGTCCCTCTTGTTGCTTCCAACCGGATTGGCAGAGAAACTGTTGACACTGAG
EST: gi|88758160|gb|DY542301.1|DY542301
EST:     CCCGTGAACATTGGAAGCGGGTTATGCAAGGCCATGCTGGTGCCAACTTG                         GTCCCTCTTGTTGCTTCCAACCGGATTGGCAGAGAAACTGTTGACACTGAG
genomic: CCCGTGAACATTGGAAGCGGGTTATGCAAGGCCATGCTGGTGCCAACTTGgtactgtttg ... aattatccagGTCCCTCTTGTTGCTTCCAACCGGATTGGCAGAGAAACTGTTGACACTGAG
EST: gi|32802461|gb|CD954697.1|CD954697
EST:     CACGTGAACATTGGAAGCGGGTTATGCAAGGCCATGCTGGTGCCAACTTG                         GTCCCTCTTGTTGCTTCCAACCGGATTGGCAGAGAAACTGTTGACACTGAG
genomic: CCCGTGAACATTGGAAGCGGGTTATGCAAGGCCATGCTGGTGCCAACTTGgtactgtttg ... aattatccagGTCCCTCTTGTTGCTTCCAACCGGATTGGCAGAGAAACTGTTGACACTGAG
EST: gi|50324199|gb|CO519325.1|CO519325
EST:     CCCGTGAACATTGGAAGCGGGTTATGCAAGGCCATGCTGGTGCCAACTTG                         GTCCCTCTTGTTGCTTCCAACCGGATTGGCAGAGAAACTGTTGACACTGAG
genomic: CCCGTGAACATTGGAAGCGGGTTATGCAAGGCCATGCTGGTGCCAACTTGgtactgtttg ... aattatccagGTCCCTCTTGTTGCTTCCAACCGGATTGGCAGAGAAACTGTTGACACTGAG
EST: gi|84908437|gb|DW404315.1|DW404315
EST:     CCCGTGAACATTGGAAGCGGGTTATGCAAGGCCATGCTGGTGCCAACTTG                         GTCCCTCTTGTTGCTTCCAACCGGATTGGCAGAGAAACTGTTGACACTGAG
genomic: CCCGTGAACATTGGAAGCGGGTTATGCAAGGCCATGCTGGTGCCAACTTGgtactgtttg ... aattatccagGTCCCTCTTGTTGCTTCCAACCGGATTGGCAGAGAAACTGTTGACACTGAG
EST: gi|60346678|gb|DN213651.1|DN213651
EST:     CACGTGAACATTGGAAGCGGGTTATGCAAGGCCATGCTGGTGCCAACTTG                         GTCCCTCTTGTTGCTTCCAACCGGATTGGCAGAGAAACTGTTGACACTGAG
genomic: CCCGTGAACATTGGAAGCGGGTTATGCAAGGCCATGCTGGTGCCAACTTGgtactgtttg ... aattatccagGTCCCTCTTGTTGCTTCCAACCGGATTGGCAGAGAAACTGTTGACACTGAG
EST: gi|148939361|gb|EC883888.2|EC883888
EST:     CCCGTGAACATTGGAAGCGGGTTATGCAAGGCCATGCTGGTGCCAACTTG                         GTCCCTCTTGTTGCTTCCAACCGGATTGGCAGAGAA
genomic: CCCGTGAACATTGGAAGCGGGTTATGCAAGGCCATGCTGGTGCCAACTTGgtactgtttg ... aattatccagGTCCCTCTTGTTGCTTCCAACCGGATTGGCAGAGAA
EST: gi|78078908|gb|DV507320.1|DV507320
EST:     CCCGTGAACATTGGAAGCGGGTTATGCAAGGCCATGCTGGTGCCAACTTG                         GTCCCTCTTGTTGCTTCCAACCGGATTGGCAGAGAAACTGTTGACACTGAG
genomic: CCCGTGAACATTGGAAGCGGGTTATGCAAGGCCATGCTGGTGCCAACTTGgtactgtttg ... aattatccagGTCCCTCTTGTTGCTTCCAACCGGATTGGCAGAGAAACTGTTGACACTGAG
EST: gi|32804827|gb|CD957063.1|CD957063
EST:     CACGTGAACATTGGAAGCGGGTTATGCAAGGCCATGCTGGTGCCAACTTG                         GTCCCTCTTGTTGCTTCCAACCGGATTGGCAGAGAAACTGTTGACACTGAG
genomic: CCCGTGAACATTGGAAGCGGGTTATGCAAGGCCATGCTGGTGCCAACTTGgtactgtttg ... aattatccagGTCCCTCTTGTTGCTTCCAACCGGATTGGCAGAGAAACTGTTGACACTGAG
EST: gi|71417126|gb|DR803932.1|DR803932
EST:     CCCGTGAACATTGGAAGCGGGTTATGCAAGGCCATGCTGGTGCCAACTTG                         GTCCCTCTTGTTGCTTCCAACCGGATTGGCAGAGAAACTGTTGACACTGAG
genomic: CCCGTGAACATTGGAAGCGGGTTATGCAAGGCCATGCTGGTGCCAACTTGgtactgtttg ... aattatccagGTCCCTCTTGTTGCTTCCAACCGGATTGGCAGAGAAACTGTTGACACTGAG
EST: gi|71417127|gb|DR803933.1|DR803933
EST:     CCCGTGAACATTGGAAGCGGGTTATGCTAGGCCATGCTGGTGCCAACTTG                         GTCCCTCTTTGT-GCTTCCAACCGGATTGGCAGAGAAACTGTTGACACTGA
genomic: CCCGTGAACATTGGAAGCGGGTTATGCAAGGCCATGCTGGTGCCAACTTGgtactgtttg ... aattatccagGTCCCTCTT-GTTGCTTCCAACCGGATTGGCAGAGAAACTGTTGACACTGA
EST: gi|29544724|gb|CB605104.1|CB605104
EST:     CCCGTGAACATTGGAAGCGGGTTATGCAAGGCCATGCTGGTGCCAACTTG                         GTCCCTCTTGTTGCTTCCAACCGGATTGGCAGAGAAACTGTTGACACTGAG
genomic: CCCGTGAACATTGGAAGCGGGTTATGCAAGGCCATGCTGGTGCCAACTTGgtactgtttg ... aattatccagGTCCCTCTTGTTGCTTCCAACCGGATTGGCAGAGAAACTGTTGACACTGAG
EST: gi|78077686|gb|DV506120.1|DV506120
EST:     CCCGTGAACATTGGAAGCGGGTTATGCAAGGCCATGCTGGTGCCAACTTG                         GTCCCTCTTGTTGCTTCCCACCGGATTGGCAGAGAAACTGTTGACACTGAG
genomic: CCCGTGAACATTGGAAGCGGGTTATGCAAGGCCATGCTGGTGCCAACTTGgtactgtttg ... aattatccagGTCCCTCTTGTTGCTTCCAACCGGATTGGCAGAGAAACTGTTGACACTGAG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 145

GTTTTATCCCACTGCAATTGGATCCGAACCCCAGGATTGTAACCTGGATTCCCGTGAACATTGGAAGCGGGTTATGCAAGGCCATGCTGGTGCCAACTTGgtactgtttg ... aattatccagGTCCCTCTTGTTGCTTCCAACCGGATTGGCAGAGAAACTGTTGACACTGAGCATGGCAAGAGCTCGATAACCTTCTATGGGAATTCCTTCATTGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 180

GTTTTATCCCACTGCAATTGGATCCGAACCCCAGGATTGTAACCTGGATTCCCGTGAACATTGGAAGCGGGTTATGCAAGGCCATGCTGGTGCCAACTTGgtactgtttg ... aattatccagGTCCCTCTTGTTGCTTCCAACCGGATTGGCAGAGAAACTGTTGACACTGAGCATGGCAAGAGCTCGATAACCTTCTATGGGAATTCCTTCATTGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 244

GTTTTATCCCACTGCAATTGGATCCGAACCCCAGGATTGTAACCTGGATTCCCGTGAACATTGGAAGCGGGTTATGCAAGGCCATGCTGGTGCCAACTTGgtactgtttg ... aattatccagGTCCCTCTTGTTGCTTCCAACCGGATTGGCAGAGAAACTGTTGACACTGAGCATGGCAAGAGCTCGATAACCTTCTATGGGAATTCCTTCATTGCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 148

GTTTTATCCCACTGCAATTGGATCCGAACCCCAGGATTGTAACCTGGATTCCCGTGAACATTGGAAGCGGGTTATGCAAGGCCATGCTGGTGCCAACTTGgtactgtttg ... aattatccagGTCCCTCTTGTTGCTTCCAACCGGATTGGCAGAGAAACTGTTGACACTGAGCATGGCAAGAGCTCGATAACCTTCTATGGGAATTCCTTCATTGCAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTTTATCCCACTGCAATTGGATCCGAACCCCAGGATTGTAACCTGGATTCCCGTGAACATTGGAAGCGGGTTATGCAAGGCCATGCTGGTGCCAACTTGgtactgtttgttgtattgtacaagttcatgatgcgctatgaccttcattgaggaacaacaaagatgtttctttgttgttcctctaagtgatactggtgaagcatccacttctctggtcgcgttatgatttcagcttgaattatccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG