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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATATCAAGGAGAACCCAGTCTTGATCTACATGAAGGGTTTTCCTGAGTCTCCAATGTGTGGCTTCAGTGCACTGGCTGTTAAGGTCTTCCAGCAATATGgtaagttggctctaattagtagatcgcaggatgatttgtttcgaatgcaggtaatagtaaatgacactttttaaattttaagctctatgttattgatttcag

Basic information

species Zea mays
transcript GRMZM5G880300_T02
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G880300_T02 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os01g07950.1 (Oryza sativa), 5'ss of exon 4
GATATCAAGGAGAACCCAGTCTTGATCTACATGAAGGGTTTTCCTGAGTCTCCAATGTGTGGCTTCAGTGCACTGGCTGTTAAGGTCTTCCAGCAATATGgtaagttggctctaattagtagatcgcaggatgatttgtttcgaatgcaggtaatagtaaatga-cactttttaaatt-ttaagctctatgttattg---atttcag
|||||||| |||||||||||||||||||||||||||||||||||||||||||| |||||||| ||||||||| |||| ||||| ||| || ||| ||||||||||||  | || | |      ||      ||||||||||  ||| ||| | ||  ||  ||    |    |||||| |||| |  ||| | ||     ||| |||
GATATCAAAGAGAACCCAGTCTTGATCTACATGAAGGGTTTTCCTGAGTCTCCTATGTGTGGATTCAGTGCATTGGCAGTTAAAGTCCTCAAGCTATATGgtaagttaacactgagt------tc------tgatttgtttgaaatacagttgatgatacgtgggtgcgccataaattcttaaaccatatatcataatctattgcag

upper sequence: GRMZM5G880300_T02 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os01g34620.5 (Oryza sativa), 5'ss of exon 4
GATATCAAGGAGAACCCAGTCTTGATCTACATGAAGGGTTTTCCTGAGTCTCCAATGTGTGGCTTCAGTGCACTGGCTGTTAAGGTCTTCCAGCAATATGgtaagttggctctaattagtagatcgcaggatgatttgtttcgaatgcaggtaatagtaaatgacactttttaaatt-ttaagctctat-gttattgatttcag
||||||||||||||||||||| |||||||||||||||||| ||||||  |||| | |||||| ||||||||  |||| ||||  ||| || ||||||||||||| ||  | || | |      ||      ||||||||||  |||   | | ||| ||     ||||    | ||| |||| || |||  | ||  ||| |||
GATATCAAGGAGAACCCAGTCCTGATCTACATGAAGGGTTATCCTGATGCTCCTAGGTGTGGGTTCAGTGCGTTGGCAGTTAGAGTCCTCAAGCAATATGgtaaattatcactgagt------tc------tgatttgtttgaaatatggttgataata-----cactccaaagattcttaaactatatcataatctattgcag
















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|211071256|gb|FL399022.1|FL399022
EST:     TCCAATGTGTGGCTTCAGTGCACTGGCTGTTAAGGTCTTCCAGCAATATG                         GCGTCCCTGTCTGTGGTAGA-ACATTCTTGGGGATCTTAAGCTC
genomic: TCCAATGTGTGGCTTCAGTGCACTGGCTGTTAAGGTCTTCCAGCAATATGgtaagttggc ... ttgatttcagGCGTCCCTGTCTGTGGTAGAGACATTCTTGGGGATCTTAAGCTC
EST: gi|74236784|gb|DT644698.1|DT644698
EST:     TCCAATGTGTGGCTTCAGTGCACTGGCTGTTAAGGTCTTCCAGCAATATG                         GCGTCCCTGTCTGTGGTAGAGACATTCTTGGGGATCTTAAGCTCAAAGAGT
genomic: TCCAATGTGTGGCTTCAGTGCACTGGCTGTTAAGGTCTTCCAGCAATATGgtaagttggc ... ttgatttcagGCGTCCCTGTCTGTGGTAGAGACATTCTTGGGGATCTTAAGCTCAAAGAGT
EST: gi|211479938|gb|FL425914.1|FL425914
EST:     TCCAATGTGTGGCTTCAGTGCACTGGCTGTTAAGGTCTTCCAGCAATATG                         GCGTCCCTGTCTGTGGTAGAGACATTCTTGGGGATCTTAAGCTCAAAGAGT
genomic: TCCAATGTGTGGCTTCAGTGCACTGGCTGTTAAGGTCTTCCAGCAATATGgtaagttggc ... ttgatttcagGCGTCCCTGTCTGTGGTAGAGACATTCTTGGGGATCTTAAGCTCAAAGAGT
EST: gi|91877551|gb|EB407508.1|EB407508
EST:     TCCAATGTGTGGCTTCAGTGCACTGGCTGTTAAGGTCTTCCAGCAATATG                         GCGTCCCTGTCTGTGGTAGAGACATTCTTGGGGATCTTAAGCTCAAAGAGT
genomic: TCCAATGTGTGGCTTCAGTGCACTGGCTGTTAAGGTCTTCCAGCAATATGgtaagttggc ... ttgatttcagGCGTCCCTGTCTGTGGTAGAGACATTCTTGGGGATCTTAAGCTCAAAGAGT
EST: gi|93017644|gb|EB643164.1|EB643164
EST:     TCCAATGTGTGGCTTCAGTGCACTGGCTGTTAAGGTCTTCCAGCAATATG                         GCGTCCCTGTCTGTGGTAGAGACATTCTTGGGGATCTTAAGCTCAAAGAGT
genomic: TCCAATGTGTGGCTTCAGTGCACTGGCTGTTAAGGTCTTCCAGCAATATGgtaagttggc ... ttgatttcagGCGTCCCTGTCTGTGGTAGAGACATTCTTGGGGATCTTAAGCTCAAAGAGT
EST: gi|76281315|gb|DV020883.1|DV020883
EST:     TCCAATGTGTGGCTTCAGTGCACTGGCTGTTAAGGTCTTCCAGCAATATG                         GCGTCCCTGTCTGTGGTAGAGACATTCTTGGGGATCTTAAGCTCAAAGAGT
genomic: TCCAATGTGTGGCTTCAGTGCACTGGCTGTTAAGGTCTTCCAGCAATATGgtaagttggc ... ttgatttcagGCGTCCCTGTCTGTGGTAGAGACATTCTTGGGGATCTTAAGCTCAAAGAGT
EST: gi|211328326|gb|FL186217.1|FL186217
EST:     TCCAATGTGTGGCTTCAGTGCACTGGCTGTTAAGGTCTTCCAGCAATATG                         GCGTCCCTGTCTGTGGTAGAGACATTCTTGGGGATCTTAAGCTCAAAGAGT
genomic: TCCAATGTGTGGCTTCAGTGCACTGGCTGTTAAGGTCTTCCAGCAATATGgtaagttggc ... ttgatttcagGCGTCCCTGTCTGTGGTAGAGACATTCTTGGGGATCTTAAGCTCAAAGAGT
EST: gi|84980275|gb|DW530624.1|DW530624
EST:     TCCAATGTGTGGCTTCAGTGCACTGGCTGTTAAGGTCTTCCAGCAATATG                         GCGTCCCTGTCTGTGGTAGAGACATTCTTGGGGATCTTAAGCTCAAAGAGT
genomic: TCCAATGTGTGGCTTCAGTGCACTGGCTGTTAAGGTCTTCCAGCAATATGgtaagttggc ... ttgatttcagGCGTCCCTGTCTGTGGTAGAGACATTCTTGGGGATCTTAAGCTCAAAGAGT
EST: gi|211069174|gb|FL417736.1|FL417736
EST:     TCCAATGTGTGGCTTCAGTGCACTGGCTGTTAAGGTCTTCCAGCAATATG                         GCGTCCCTGTCTGTGGTAGAGACATTCTTGGGGATCTTAAGCTCAAAGAGT
genomic: TCCAATGTGTGGCTTCAGTGCACTGGCTGTTAAGGTCTTCCAGCAATATGgtaagttggc ... ttgatttcagGCGTCCCTGTCTGTGGTAGAGACATTCTTGGGGATCTTAAGCTCAAAGAGT
EST: gi|101389214|gb|EB816562.1|EB816562
EST:     TCCAATGTGTGGCTTCAGTGCACTGGCTGTTAAGGTCTTCCAGCAATATG                         GCGTCCCTGTCTGTGGTAGAGACATTCTTGGGGATCTTAAGCTCAAAGAGT
genomic: TCCAATGTGTGGCTTCAGTGCACTGGCTGTTAAGGTCTTCCAGCAATATGgtaagttggc ... ttgatttcagGCGTCCCTGTCTGTGGTAGAGACATTCTTGGGGATCTTAAGCTCAAAGAGT
EST: gi|93017643|gb|EB643163.1|EB643163
EST:     TCCAATGTGTGGCTTCAGTGCACTGGCTGTTAAGGTCTTCCAGCAATATG                         GCGTCCCTGTCTGTGGTAGAGACATTCTTGGGGATCTTAAGCTCAAAGAGT
genomic: TCCAATGTGTGGCTTCAGTGCACTGGCTGTTAAGGTCTTCCAGCAATATGgtaagttggc ... ttgatttcagGCGTCCCTGTCTGTGGTAGAGACATTCTTGGGGATCTTAAGCTCAAAGAGT
EST: gi|74236783|gb|DT644697.1|DT644697
EST:     TCCAATGTGTGGCTTCAGTGCACTGGCTGTTAAGGTCTTCCAGCAATATG                         GCGTCCCTGTCTGTGGTAGAGACATTCTTGGGGATCTTAAGCTCAAAGAGT
genomic: TCCAATGTGTGGCTTCAGTGCACTGGCTGTTAAGGTCTTCCAGCAATATGgtaagttggc ... ttgatttcagGCGTCCCTGTCTGTGGTAGAGACATTCTTGGGGATCTTAAGCTCAAAGAGT
EST: gi|84980198|gb|DW530547.1|DW530547
EST:     TCCAATGTGTGGCTTCAGTGCACTGGCTGTTAAGGTCTTCCAGCAATATG                         GCGTCCCTGTCTGTGGTAGAGACATTCTTGGGGATCTTAAGCTCAAAGAGT
genomic: TCCAATGTGTGGCTTCAGTGCACTGGCTGTTAAGGTCTTCCAGCAATATGgtaagttggc ... ttgatttcagGCGTCCCTGTCTGTGGTAGAGACATTCTTGGGGATCTTAAGCTCAAAGAGT

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: 48 (upstream exon), 49 (downstream exon)
Score: 49

GATATCAAGGAGAACCCAGTCTTGATCTACATGAAGGGTTTTCCTGAGTCTCCAATGTGTGGCTTCAGTGCACTGGCTGTTAAGGTCTTCCAGCAATATGgtaagttggc ... ttgatttcagGCGTCCCTGTCTGTGGTAGAGACATTCTTGGGGATCTTAAGCTCAAAGAGTGTGTTAAAGCCCACAC


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 55

GATATCAAGGAGAACCCAGTCTTGATCTACATGAAGGGTTTTCCTGAGTCTCCAATGTGTGGCTTCAGTGCACTGGCTGTTAAGGTCTTCCAGCAATATGgtaagttggc ... ttgatttcagGCGTCCCTGTCTGTGGTAGAGACATTCTTGGGGATCTTAAGCTCAAAGAGTGTGTTAAAGCCCACAC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 43

GATATCAAGGAGAACCCAGTCTTGATCTACATGAAGGGTTTTCCTGAGTCTCCAATGTGTGGCTTCAGTGCACTGGCTGTTAAGGTCTTCCAGCAATATGgtaagttggc ... ttgatttcagGCGTCCCTGTCTGTGGTAGAGACATTCTTGGGGATCTTAAGCTCAAAGAGTGTGTTAAAGCCCACAC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 31

GATATCAAGGAGAACCCAGTCTTGATCTACATGAAGGGTTTTCCTGAGTCTCCAATGTGTGGCTTCAGTGCACTGGCTGTTAAGGTCTTCCAGCAATATGgtaagttggc ... ttgatttcagGCGTCCCTGTCTGTGGTAGAGACATTCTTGGGGATCTTAAGCTCAAAGAGTGTGTTAAAGCCCACAC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATATCAAGGAGAACCCAGTCTTGATCTACATGAAGGGTTTTCCTGAGTCTCCAATGTGTGGCTTCAGTGCACTGGCTGTTAAGGTCTTCCAGCAATATGgtaagttggctctaattagtagatcgcaggatgatttgtttcgaatgcaggtaatagtaaatgacactttttaaattttaagctctatgttattgatttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT