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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactggatctgataattatttaagatagaacttgttacacatataagataattatcctgcatatactgaaaataaactgacactgatatctcaatctttctttgatagGCTTTCAACTATCAACAAATGCTTCTCTGCAGAGACTGTTGAGGATATCATAAAAGCATTT

Basic information

species Zea mays
transcript GRMZM2G042818_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G042818_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os01g54860.1 (Oryza sativa), 3'ss of exon 9
gtactggatctgataat-tatttaagatagaacttgttacacatataagataattatcctgcatatactgaaaataaactgacactgatatctcaatctttctttgatagGCTTTCAACTATCAACAAATGCTTCTCTGCAGAGACTGTTGAGGATATCATAAAAGCATTT
||    || |||||    | ||  | ||  |||||| | | |||  |   | ||||| ||     || ||||| |||| ||||||||  ||  ||||||| ||| ||||||||  |||||||||||||||| |||||||| |||||| | ||||| ||||||||||| |||
gt-taagaactgatgtccttttccaaatgtaacttgctgcgcatgcat--ttattattctat---tattgaaa-taaattgacactggaatgacaatcttacttcgatagGCTCCCAACTATCAACAAATGTTTCTCTGCTGAGACTATCGAGGACATCATAAAAGCTTTT
















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|29544823|gb|CB605431.1|CB605431
EST:     TGATGAAGATAGTATATTGAATAA                         GCTTTCAACTATCAACAAATGCTTCTCTGCAGAGACTGTTGAGGATATCAT
genomic: TGATGAAGATAGTATATTGAATAAgtactggatc ... tctttgatagGCTTTCAACTATCAACAAATGCTTCTCTGCAGAGACTGTTGAGGATATCAT
EST: gi|37400624|gb|CF637668.1|CF637668
EST:     GAAGAATTTTCAACAGATGTTCAAACTGATGAAGATAGTATATTGAATAA                         GCTTTCAACTATCAACAAATGCTTCTCTGCAGAGACTGTTGAGGATATCAT
genomic: GAAGAATTTTCAACAGATGTTCAAACTGATGAAGATAGTATATTGAATAAgtactggatc ... tctttgatagGCTTTCAACTATCAACAAATGCTTCTCTGCAGAGACTGTTGAGGATATCAT
EST: gi|15177481|gb|BI398420.1|BI398420
EST:     GAAGAATTTTCAACAGATGTTCAAACTGATGAAGATAGTATATTGAATAA                         GCTTTCAACTATCAACAAATGCTTCTCTGCAGAGACTGTTGAAGATATCAT
genomic: GAAGAATTTTCAACAGATGTTCAAACTGATGAAGATAGTATATTGAATAAgtactggatc ... tctttgatagGCTTTCAACTATCAACAAATGCTTCTCTGCAGAGACTGTTGAGGATATCAT
EST: gi|148959114|gb|EC905254.2|EC905254
EST:     GAAGAATTTTCAACAGATGTTCAAACTGATGAAGATAGTATATTGAATAA                         GCTTTCAACTATCAACAAATGCTTCTCTGCAGAGACTGTTGAGGATATCAT
genomic: GAAGAATTTTCAACAGATGTTCAAACTGATGAAGATAGTATATTGAATAAgtactggatc ... tctttgatagGCTTTCAACTATCAACAAATGCTTCTCTGCAGAGACTGTTGAGGATATCAT
EST: gi|45568357|gb|CK986026.1|CK986026
EST:     CAGATGTTCAAACTGATGAAGATAGTATATTGAATAA                         GCTTTCAACTATCAACAAATGCTTCTCTGCAGAGACTGTTGAGGATATCAT
genomic: CAGATGTTCAAACTGATGAAGATAGTATATTGAATAAgtactggatc ... tctttgatagGCTTTCAACTATCAACAAATGCTTCTCTGCAGAGACTGTTGAGGATATCAT
EST: gi|149000045|gb|EE037146.2|EE037146
EST:     GAAGAATTTTCAACAGATGTTCAAACTGATGAAGATAGTATATTGAATAA                         GCTTTCA-CTATCAACAAATGCTTCTCTGCAGAGACTG
genomic: GAAGAATTTTCAACAGATGTTCAAACTGATGAAGATAGTATATTGAATAAgtactggatc ... tctttgatagGCTTTCAACTATCAACAAATGCTTCTCTGCAGAGACTG
EST: gi|37392700|gb|CF633603.1|CF633603
EST:     AGATGTACAAACTGATGAAGATAGTATATGGAATAA                         GCTTTCAACTATCAACAAATGCTTCTCTGCAGAGACTGTTGAGGATATCAT
genomic: AGATGTTCAAACTGATGAAGATAGTATATTGAATAAgtactggatc ... tctttgatagGCTTTCAACTATCAACAAATGCTTCTCTGCAGAGACTGTTGAGGATATCAT
EST: gi|60352184|gb|DN219157.1|DN219157
EST:     GAAGAATTTTCAACAGATGTTCAAACTGATGAAGATAGTATATTGAATAA                         GCTTTCAACTATCAACAAATGCTTCTCTGCAGAGACTGTTGAGGATATCAT
genomic: GAAGAATTTTCAACAGATGTTCAAACTGATGAAGATAGTATATTGAATAAgtactggatc ... tctttgatagGCTTTCAACTATCAACAAATGCTTCTCTGCAGAGACTGTTGAGGATATCAT
EST: gi|30052459|gb|AI065748.2|AI065748
EST:     GAAGAATTTTCAACAGATGTGCAANCTGATGAAGATAGTATATTGAATAA                         GCTTTCAACTATCAA
genomic: GAAGAATTTTCAACAGATGTTCAAACTGATGAAGATAGTATATTGAATAAgtactggatc ... tctttgatagGCTTTCAACTATCAA
EST: gi|32930057|gb|CF034869.1|CF034869
EST:     GAAGAATTTTCAACAGATGTTCAAACTGATGAAGATAGTATATTGAATAA                         GCTTTCAACTATCAACAAATGCTTCTCTGCAGAGACTGTTGAGGATATCAT
genomic: GAAGAATTTTCAACAGATGTTCAAACTGATGAAGATAGTATATTGAATAAgtactggatc ... tctttgatagGCTTTCAACTATCAACAAATGCTTCTCTGCAGAGACTGTTGAGGATATCAT
EST: gi|71304194|gb|DR788217.1|DR788217
EST:     GAAGAATTTTCAACAGATGTTCAAACTGATGAAGATAGTATATTGAATAA                         GCTTTCAACTATCAACAAATGCTTCTCTGCAGAGACTGTTGAGGATATCAT
genomic: GAAGAATTTTCAACAGATGTTCAAACTGATGAAGATAGTATATTGAATAAgtactggatc ... tctttgatagGCTTTCAACTATCAACAAATGCTTCTCTGCAGAGACTGTTGAGGATATCAT
EST: gi|29544214|gb|CB604594.1|CB604594
EST:     TGTTCAAACTGATGAAGATAGTATATTGAATAA                         GCTTTCAACTATCAACAAATGCTTCTCTGCAGAGACTGTTGAGGATATCAT
genomic: TGTTCAAACTGATGAAGATAGTATATTGAATAAgtactggatc ... tctttgatagGCTTTCAACTATCAACAAATGCTTCTCTGCAGAGACTGTTGAGGATATCAT
EST: gi|40303747|gb|CK348134.1|CK348134
EST:     GAAGAATTTTCAACAGATGTTCAAACTGATGAAGATAGTATATTGAATAA                         GCTTTCAACTATCAACAAATGCTTCTCTGCAGAGACTGTTGAGGATATCAT
genomic: GAAGAATTTTCAACAGATGTTCAAACTGATGAAGATAGTATATTGAATAAgtactggatc ... tctttgatagGCTTTCAACTATCAACAAATGCTTCTCTGCAGAGACTGTTGAGGATATCAT
EST: gi|149089063|gb|EE178226.2|EE178226
EST:     GAAGAATTTTCAACAGATGTTCAAACTGATGAAGATAGTATATTGAATAA                         GCTTTCAACTATCAACAAATGCTTCTCTGCAGAGACTGTTGAGGATATCAT
genomic: GAAGAATTTTCAACAGATGTTCAAACTGATGAAGATAGTATATTGAATAAgtactggatc ... tctttgatagGCTTTCAACTATCAACAAATGCTTCTCTGCAGAGACTGTTGAGGATATCAT
EST: gi|91053743|gb|EB164161.1|EB164161
EST:     GAAGAATTTTCAACAGATGTTCAAACTGATGAAGATAGTATATTGAATAA                         GCTTTCAACTATCAACAAATGCTTCTCTGCAGAGACTGTTGAGGATATCAT
genomic: GAAGAATTTTCAACAGATGTTCAAACTGATGAAGATAGTATATTGAATAAgtactggatc ... tctttgatagGCTTTCAACTATCAACAAATGCTTCTCTGCAGAGACTGTTGAGGATATCAT
EST: gi|74239819|gb|DT647733.1|DT647733
EST:     GAAGAATTTTCAACAGATGTTCAAACTGATGAAGATAGTATATTGAATAA                         GCTTTCAACTATCAACAAATGCTTCTCTGCAGAGACTGTTGAGGATATCAT
genomic: GAAGAATTTTCAACAGATGTTCAAACTGATGAAGATAGTATATTGAATAAgtactggatc ... tctttgatagGCTTTCAACTATCAACAAATGCTTCTCTGCAGAGACTGTTGAGGATATCAT
EST: gi|148959115|gb|EE010592.2|EE010592
EST:     AAGA-TTTTCAACAGATGTTCAAACTGATGAAGATAGTATATTTGA-TAA                         GCTTTCAACTA
genomic: AAGAATTTTCAACAGATGTTCAAACTGATGAAGATAGTATATT-GAATAAgtactggatc ... tctttgatagGCTTTCAACTA
EST: gi|211149870|gb|FL475634.1|FL475634
EST:     TCAAACTGATGAAGATAGTATATTGAATAA                         GCTTTCAACTATCAACAAATGCTTCTCTGCAGAGACTGTTGAGGATATCAT
genomic: TCAAACTGATGAAGATAGTATATTGAATAAgtactggatc ... tctttgatagGCTTTCAACTATCAACAAATGCTTCTCTGCAGAGACTGTTGAGGATATCAT
EST: gi|74238393|gb|DT646307.1|DT646307
EST:     GAAGAATTTTCAACAGATGTTCAAACTGATGAAGATAGTATATTGAATAA                         GCTTTTCA-CTATCAACAAATGCTTCTCTGCAGAGACTGTTGAGGATATCA
genomic: GAAGAATTTTCAACAGATGTTCAAACTGATGAAGATAGTATATTGAATAAgtactggatc ... tctttgatagGCTTT-CAACTATCAACAAATGCTTCTCTGCAGAGACTGTTGAGGATATCA
EST: gi|37379687|gb|CF626591.1|CF626591
EST:     AATTTTCAACAGATGTTCAAACTGATGAAGATAGTATA-TGAATNAA                         GCTTTCAACTATCAACAAATGTTTCTCTGCAGAGACTGTTGAGGATATCA
genomic: AATTTTCAACAGATGTTCAAACTGATGAAGATAGTATATTGAAT-AAgtactggatc ... tctttgatagGCTTTCAACTATCAACAAATGCTTCTCTGCAGAGACTGTTGAGGATATCA
EST: gi|71762792|gb|DR960729.1|DR960729
EST:     GAAGAATTTTCAACAGATGTTCAAACTGATGAAGATAGTATATTGAATAA                         GCTTTCAACTATCAACAAATGCTTCTCTGCAGAGACTGTTGAGGATATCAT
genomic: GAAGAATTTTCAACAGATGTTCAAACTGATGAAGATAGTATATTGAATAAgtactggatc ... tctttgatagGCTTTCAACTATCAACAAATGCTTCTCTGCAGAGACTGTTGAGGATATCAT

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), 48 (downstream exon)
Score: 145

GTCTACTGGATTTGGACACAGGTGCTGAGTCTGCAGTCCGAGCTGTTATTGAAGAATTTTCAACAGATGTTCAAACTGATGAAGATAGTATATTGAATAAgtactggatc ... tctttgatagGCTTTCAACTATCAACAAATGCTTCTCTGCAGAGACTGTTGAGGATATCATAAAAGCATTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 216

GTCTACTGGATTTGGACACAGGTGCTGAGTCTGCAGTCCGAGCTGTTATTGAAGAATTTTCAACAGATGTTCAAACTGATGAAGATAGTATATTGAATAAgtactggatc ... tctttgatagGCTTTCAACTATCAACAAATGCTTCTCTGCAGAGACTGTTGAGGATATCATAAAAGCATTT


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 202

GTCTACTGGATTTGGACACAGGTGCTGAGTCTGCAGTCCGAGCTGTTATTGAAGAATTTTCAACAGATGTTCAAACTGATGAAGATAGTATATTGAATAAgtactggatc ... tctttgatagGCTTTCAACTATCAACAAATGCTTCTCTGCAGAGACTGTTGAGGATATCATAAAAGCATTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 368

GTCTACTGGATTTGGACACAGGTGCTGAGTCTGCAGTCCGAGCTGTTATTGAAGAATTTTCAACAGATGTTCAAACTGATGAAGATAGTATATTGAATAAgtactggatc ... tctttgatagGCTTTCAACTATCAACAAATGCTTCTCTGCAGAGACTGTTGAGGATATCATAAAAGCATTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcctgcatatactgaaaataaactgacactgatatctcaatctttctttgatagGCTTTCAACTATCAACAAATGCTTCTCTGCAGAGACTGTTGAGGATATCATAAAAGCATTT
                                   tctcaatctttcttt  CT-rich tract
       atatactgaaaataaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactggatctgataattatttaagatagaacttgttacacatataagataattatcctgcatatactgaaaataaactgacactgatatctcaatctttctttgatagGCTTTCAACTATCAACAAATGCTTCTCTGCAGAGACTGTTGAGGATATCATAAAAGCATTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT