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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAATGATGCTGGACTGGCAGCAGCTGAATTAGCATTAGCAGTCGAGAAACATGTCCTGGAATCAGGATCAATTGATACGGTTGGCACCGTTGgtatgttttataaaccatatttagctttttacataaaatctatcattccatcctgtttgtgacatcataatatcatgtaatacatttggactaaatatgt...

Basic information

species Zea mays
transcript GRMZM2G130034_T01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G130034_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os12g40550.1 (Oryza sativa), 5'ss of exon 8
AAATGATGCTGGACTGGCAGCAGCTGAATTAGCATTAGCAGTCGAGAAACATGTCCTGGAATCAGGATCAATTGATACGGTTGGCACCGTTGgtatgttttataaaccatatttagctttttacataaaatctatcattccatcctgtttgtgacatcataatatcatgtaatacatttggac-taaatatgt-
|||||||||||||||||| |||||||| || ||||||||||| |||||||| ||  |||||||||||||||||||||| ||||| || ||||||||| || || ||    ||||   ||| |   |  ||| ||||||||  || ||  |||||  |  |||||     || || ||| |||| || || ||  
AAATGATGCTGGACTGGCGGCAGCTGAGTTGGCATTAGCAGTTGAGAAACACGTTTTGGAATCAGGATCAATTGATACTGTTGGGACAGTTGgtatgcttgatgaaattgattttattttctg--ttgaatatatcattctttcatgactgtgatgttttaatactccatagtaaattaggacatacatgtgcc

upper sequence: GRMZM2G130034_T01 (Zea mays), 5'ss of exon 8
lower sequence: Vv05s0020g04900.t01 (Vitis vinifera), 5'ss of exon 8
AAATGATGCTGGACTGGCAGCAGCTGAATTAGCATTAGCAGTCGAGAAACATGTCCTGGAATCAGGATCAATTGATACGGTTGGCACCGTTGgtatgttttataaaccatatttagctttttacataaaatctatcattccatcctgtttgtgacatcataatatcatgtaatacatttggac-taaatatgt----
||||||||| ||| ||||||| || || |||||| |||| || |||||||||||  | ||||| ||||| |||||||| ||||| || || |||  ||  | |   |   |||   | |  |    ||  |  |  | |  |   || || | ||||  | | ||  | | ||| || | ||  |  ||||||    
AAATGATGCAGGATTGGCAGCTGCAGAGTTAGCACTAGCTGTTGAGAAACATGTGTTAGAATCTGGATCTATTGATACTGTTGGTACTGTGGgtgagtcatgttttcttcatt---cctgatgtccaag-tgcaggaatatagtttggttattacatactga-attttattatatatattgatatttatatgtatct
















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|31362362|gb|CD446719.1|CD446719
EST:     GAATCAGGATCAATTGATACGGTTGGCACCGTTG                         GTATTCTGCAGTTACATCCAGGAGCAATCAATAGCATCCCAAGCAAATCAC
genomic: GAATCAGGATCAATTGATACGGTTGGCACCGTTGgtatgtttta ... tcctcttcagGTATTCTGCAGTTACATCCAGGAGCAATCAATAGCATCCCAAGCAAATCAC
EST: gi|33466598|gb|CF243647.1|CF243647
EST:     CGAGAAACATGTCCTGGAATCAGGATCAATTGATACGGTTGGCACCGTTG                         GTATTCTGCAGTTACATCCAGGAGCAATCAATAGCATCCCAAGCAAATCAC
genomic: CGAGAAACATGTCCTGGAATCAGGATCAATTGATACGGTTGGCACCGTTGgtatgtttta ... tcctcttcagGTATTCTGCAGTTACATCCAGGAGCAATCAATAGCATCCCAAGCAAATCAC
EST: gi|78022951|gb|DV491338.1|DV491338
EST:     CGAGAAACATGTCCTGGAATCAGGATCAATTGATACGGTTGGCACCGTTG                         GTATTCTGCAGTTACATCCAGGAGCAATCAATAGCATCCCAAGCAAATCAC
genomic: CGAGAAACATGTCCTGGAATCAGGATCAATTGATACGGTTGGCACCGTTGgtatgtttta ... tcctcttcagGTATTCTGCAGTTACATCCAGGAGCAATCAATAGCATCCCAAGCAAATCAC
EST: gi|50333648|gb|CO528774.1|CO528774
EST:     CGAGAAACATGTCCTGGAATCAGGATCAATTGATACGGTTGGCACCGTTG                         GTATTCTGCAGTTACATCCAGGAGCAATCAATAGCATCCCAAGCAAATCAC
genomic: CGAGAAACATGTCCTGGAATCAGGATCAATTGATACGGTTGGCACCGTTGgtatgtttta ... tcctcttcagGTATTCTGCAGTTACATCCAGGAGCAATCAATAGCATCCCAAGCAAATCAC
EST: gi|71775246|gb|DR973124.1|DR973124
EST:     CGAGAAACATGTCCTGGAATCAGGATCAATTGATACGGTTGGCACCGTTG                         GTATTCTGCAGTTACATCCAGGAGCAATCAATAGCATCCCAAGCAAATCAC
genomic: CGAGAAACATGTCCTGGAATCAGGATCAATTGATACGGTTGGCACCGTTGgtatgtttta ... tcctcttcagGTATTCTGCAGTTACATCCAGGAGCAATCAATAGCATCCCAAGCAAATCAC
EST: gi|211502325|gb|FL069734.1|FL069734
EST:     GATACGGTTGGCACCGTTG                         GTATTCTGCAGTTACATCCAGGAGCAATCAATAGCATCCCAAGCAAATCAC
genomic: GATACGGTTGGCACCGTTGgtatgtttta ... tcctcttcagGTATTCTGCAGTTACATCCAGGAGCAATCAATAGCATCCCAAGCAAATCAC
EST: gi|91874397|gb|EB404354.1|EB404354
EST:     CGAGAAACATGTCCTGGAATCAGGATCAATTGATACGGTTGGCACCGTGG                         GTATTCTGCAGTTACATCCAGGAGCAATCAATAGCATCCCAAGCAAATCAC
genomic: CGAGAAACATGTCCTGGAATCAGGATCAATTGATACGGTTGGCACCGTTGgtatgtttta ... tcctcttcagGTATTCTGCAGTTACATCCAGGAGCAATCAATAGCATCCCAAGCAAATCAC
EST: gi|71441172|gb|DR822222.1|DR822222
EST:     CAGGATCAATTGATACGGTTGGCACCGTTG                         GTATTCTGCAGTTACATCCAGGAGCAATCAATAGCATCCCAAGCAAATCAC
genomic: CAGGATCAATTGATACGGTTGGCACCGTTGgtatgtttta ... tcctcttcagGTATTCTGCAGTTACATCCAGGAGCAATCAATAGCATCCCAAGCAAATCAC
EST: gi|148944451|gb|EC889566.2|EC889566
EST:     CGAGAAACATGTCCTGGAATCAGGATCAATTGATACGGTTGGCACCGTTG                         GTATTCTGCAGTTACATCCAGGAGCAATCAATAGCATCCCAAGCAAATCAC
genomic: CGAGAAACATGTCCTGGAATCAGGATCAATTGATACGGTTGGCACCGTTGgtatgtttta ... tcctcttcagGTATTCTGCAGTTACATCCAGGAGCAATCAATAGCATCCCAAGCAAATCAC
EST: gi|78107617|gb|DV526035.1|DV526035
EST:     CGAGAAACATGTCCTGGAATCAGGATCAATTGATACGGTTGGCACCGTTG                         GTATTCTGCAGTTACATCCAGGAGCAATCAATAGCATCCCAAGCAAATCAC
genomic: CGAGAAACATGTCCTGGAATCAGGATCAATTGATACGGTTGGCACCGTTGgtatgtttta ... tcctcttcagGTATTCTGCAGTTACATCCAGGAGCAATCAATAGCATCCCAAGCAAATCAC
EST: gi|5714250|gb|AI944235.1|AI944235
EST:     CGAGAAACATGTCCTGGAATCAGGATCAATTGATACGGTTGGCACCGTTG                         GTATTCTGCAGTTACATCCAGGAGCAATCAATAGCATCCCAAGCAAATCAC
genomic: CGAGAAACATGTCCTGGAATCAGGATCAATTGATACGGTTGGCACCGTTGgtatgtttta ... tcctcttcagGTATTCTGCAGTTACATCCAGGAGCAATCAATAGCATCCCAAGCAAATCAC
EST: gi|148983477|gb|EE029495.2|EE029495
EST:     CGAGAAACATGTCCTGGAATCAGGATCAATTGATACGGTTGGCACCGTTG                         GTATTCTGCAGTTACATCCAGGAGCAATCAATAGCATCCCAAGCAAATCAC
genomic: CGAGAAACATGTCCTGGAATCAGGATCAATTGATACGGTTGGCACCGTTGgtatgtttta ... tcctcttcagGTATTCTGCAGTTACATCCAGGAGCAATCAATAGCATCCCAAGCAAATCAC
EST: gi|71427277|gb|DR808327.1|DR808327
EST:     CGAGAAACATGTCCTGGAATCAGGATCAATTGATACGGTTGGCACCGTTG                         GTATTCTGCAGTTACATCCAGGAGCAATCAATAGCATCCCAAGCAAATCAC
genomic: CGAGAAACATGTCCTGGAATCAGGATCAATTGATACGGTTGGCACCGTTGgtatgtttta ... tcctcttcagGTATTCTGCAGTTACATCCAGGAGCAATCAATAGCATCCCAAGCAAATCAC
EST: gi|149103752|gb|EE289158.2|EE289158
EST:     GAATCAGGATCAATTGATACGGTTGGCACCGTTG                         GTATTCTGCAGTTACATCCAGGAGCAATCAATAGCATCCCAAGCAAATCAC
genomic: GAATCAGGATCAATTGATACGGTTGGCACCGTTGgtatgtttta ... tcctcttcagGTATTCTGCAGTTACATCCAGGAGCAATCAATAGCATCCCAAGCAAATCAC

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: 46 (upstream exon), 48 (downstream exon)
Score: 108

AAATGATGCTGGACTGGCAGCAGCTGAATTAGCATTAGCAGTCGAGAAACATGTCCTGGAATCAGGATCAATTGATACGGTTGGCACCGTTGgtatgtttta ... tcctcttcagGTATTCTGCAGTTACATCCAGGAGCAATCAATAGCATCCCAAGCAAATCACACCTAGAAATTG


Block sizes: 46 (upstream exon), 45 (downstream exon)
Score: 66

AAATGATGCTGGACTGGCAGCAGCTGAATTAGCATTAGCAGTCGAGAAACATGTCCTGGAATCAGGATCAATTGATACGGTTGGCACCGTTGgtatgtttta ... tcctcttcagGTATTCTGCAGTTACATCCAGGAGCAATCAATAGCATCCCAAGCAAATCACACCTAGAAATTG


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 86

AAATGATGCTGGACTGGCAGCAGCTGAATTAGCATTAGCAGTCGAGAAACATGTCCTGGAATCAGGATCAATTGATACGGTTGGCACCGTTGgtatgtttta ... tcctcttcagGTATTCTGCAGTTACATCCAGGAGCAATCAATAGCATCCCAAGCAAATCACACCTAGAAATTG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 105

AAATGATGCTGGACTGGCAGCAGCTGAATTAGCATTAGCAGTCGAGAAACATGTCCTGGAATCAGGATCAATTGATACGGTTGGCACCGTTGgtatgtttta ... tcctcttcagGTATTCTGCAGTTACATCCAGGAGCAATCAATAGCATCCCAAGCAAATCACACCTAGAAATTG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAATGATGCTGGACTGGCAGCAGCTGAATTAGCATTAGCAGTCGAGAAACATGTCCTGGAATCAGGATCAATTGATACGGTTGGCACCGTTGgtatgttttataaaccatatttagctttttacataaaatctatcattccatcctgtttgtgacatcataatatcatgtaatacatttggactaaatatgt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acataaaa