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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAAGATAGTAAACCCCCGTATCATCCTGTTGGACTGCCCTGTTGAGTATAAGAAAGGAGAAAATCAGACCAACGCTGAGTTGATGAAGGAAGAAGATTGgtaagagatatccatgtaccacaatgattttacctaaatacaatgcatgcataattttaaagtaatttggtagaattctaaggtatattatgtggcaaactttattgcag

Basic information

species Zea mays
transcript GRMZM2G069765_T01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G069765_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os06g34690.1 (Oryza sativa), 5'ss of exon 9
GAAAGATAGTAAACCCCCGTATCATCCTGTTGGACTGCCCTGTTGAGTATAAGAAAGGAGAAAATCAGACCAACGCTGAGTTGATGAAGGAAGAAGATTGgtaagagatatccatgtaccacaatgattttacctaaatacaatgcatgcataattttaaagtaatttg-gtagaattctaaggtatattatgtggcaaactttattgcag
| |||||||| |||||||| || |||||  |||| |||||||||||||| |||||||||||||| |||||||| |||||  |||||||||||||||||||||||| |||    ||  |    |||| |||| || |  |  | ||  || |  ||| |   |  |||   | |   |   | || ||| | |||   | |   |||| |||
GGAAGATAGTCAACCCCCGCATTATCCTTCTGGATTGCCCTGTTGAGTACAAGAAAGGAGAAAACCAGACCAATGCTGAACTGATGAAGGAAGAAGATTGgtaagggatgg--ataaattcaaatg-ttttgccaatttgaattgt-tgaactattgtggtgctattgaagcaatgtagcatggaataatttgtaa-atatgctatttcag
















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|32934292|gb|CF039104.1|CF039104
EST:     AAGAAAGGAGAAAATCAGACCAACGCTGAGTTGATGAAGGAAGAAGATTG                         GCAGGTTCTGTTAGAGATGGAGGAAGAATACATAAAGAACCTGTGCGGTCA
genomic: AAGAAAGGAGAAAATCAGACCAACGCTGAGTTGATGAAGGAAGAAGATTGgtaagagata ... tttattgcagGCAGGTTCTGTTAGAGATGGAGGAAGAATACATAAAGAACCTGTGCGGTCA
EST: gi|32930780|gb|CF035592.1|CF035592
EST:     AAGAAAGGAGAAAATCAGACCAACGCTGAGTTGATGAAGGAAGAAGATTG                         GCAGGTTCTGTTAGAGATGGAGGAAGAATACATAAAGAACCTGTGCGGTCA
genomic: AAGAAAGGAGAAAATCAGACCAACGCTGAGTTGATGAAGGAAGAAGATTGgtaagagata ... tttattgcagGCAGGTTCTGTTAGAGATGGAGGAAGAATACATAAAGAACCTGTGCGGTCA
EST: gi|22472423|gb|BU036903.1|BU036903
EST:     AAGAAAGGAGAAAATCAGACCAACGCTGAGTTGATGAAGGAAGAAGATTG                         GCAGGTTCTGTTAGAGATGGAGGAAGAATACATAAAGAACCTGTGCGGTCA
genomic: AAGAAAGGAGAAAATCAGACCAACGCTGAGTTGATGAAGGAAGAAGATTGgtaagagata ... tttattgcagGCAGGTTCTGTTAGAGATGGAGGAAGAATACATAAAGAACCTGTGCGGTCA
EST: gi|67025927|gb|CO454676.1|CO454676
EST:     AAGAAAGGAGAAAATCAGACCAACGCTGAGTTGATGAAGGAAGAAGATTG                         GCAGGTTCTGTTAGAGATGGAGGAAGAATACATAAAGAACCTGTGCGGTCA
genomic: AAGAAAGGAGAAAATCAGACCAACGCTGAGTTGATGAAGGAAGAAGATTGgtaagagata ... tttattgcagGCAGGTTCTGTTAGAGATGGAGGAAGAATACATAAAGAACCTGTGCGGTCA
EST: gi|32935251|gb|CF040063.1|CF040063
EST:     AAGAAAGGAGAAAATCAGACCAACGCTGAGTTGATGAAGGAAGAAGATTG                         GCAGGTTCTGTTAGAGATGGAGGAAGAATACATAAAGAACCTGTGCGGTCA
genomic: AAGAAAGGAGAAAATCAGACCAACGCTGAGTTGATGAAGGAAGAAGATTGgtaagagata ... tttattgcagGCAGGTTCTGTTAGAGATGGAGGAAGAATACATAAAGAACCTGTGCGGTCA
EST: gi|33098179|gb|CF058139.1|CF058139
EST:     AAGAAAGGAGAAAATCAGACCGACGCTGAGTTGATGAAGGAAGAAGATTG                         GCAGGTTCTGTTAGAGATGGAGGAAGAATACATAAAGAACCTGTGCGGTCA
genomic: AAGAAAGGAGAAAATCAGACCAACGCTGAGTTGATGAAGGAAGAAGATTGgtaagagata ... tttattgcagGCAGGTTCTGTTAGAGATGGAGGAAGAATACATAAAGAACCTGTGCGGTCA
EST: gi|22545904|gb|BU098263.1|BU098263
EST:     GACCAACGCTGAGTTGATGAAGGAAGAAGATTG                         GCAGGTTCTGTTAGAGATGGAGGAAGAATACATAAAGAACCTGTGCGGTCA
genomic: GACCAACGCTGAGTTGATGAAGGAAGAAGATTGgtaagagata ... tttattgcagGCAGGTTCTGTTAGAGATGGAGGAAGAATACATAAAGAACCTGTGCGGTCA
EST: gi|67040881|gb|CO467136.1|CO467136
EST:     AAGAAAGGAGAAAATCAGACCAACGCTGAGTTGATGAAGGAAGAAGATTG                         GCAGGTTCTGCTAGAGATGGAGGAAGAATACATAAAGAACCTGTGCGGTCA
genomic: AAGAAAGGAGAAAATCAGACCAACGCTGAGTTGATGAAGGAAGAAGATTGgtaagagata ... tttattgcagGCAGGTTCTGTTAGAGATGGAGGAAGAATACATAAAGAACCTGTGCGGTCA
EST: gi|20802750|gb|BQ293800.1|BQ293800
EST:     AAGAAAGGAGAAAATCAGACCAACGCTGAGTTGATGAAGGAAGAAGATTG                         GCAGGTTCTGTTAGAGATGGAGGAAGAATACATAAAGAACCTGTGCGGTCA
genomic: AAGAAAGGAGAAAATCAGACCAACGCTGAGTTGATGAAGGAAGAAGATTGgtaagagata ... tttattgcagGCAGGTTCTGTTAGAGATGGAGGAAGAATACATAAAGAACCTGTGCGGTCA
EST: gi|22819616|gb|BU499706.1|BU499706
EST:     CGCTGAGTTGATGAAGGAAGAAGATTG                         GCAGGTTCTGTTAGAGATGGAGGAAGAATACATAAAGAACCTGTGCGGTCC
genomic: CGCTGAGTTGATGAAGGAAGAAGATTGgtaagagata ... tttattgcagGCAGGTTCTGTTAGAGATGGAGGAAGAATACATAAAGAACCTGTGCGGT-C
EST: gi|67013717|gb|CO442466.1|CO442466
EST:     AAGAAAGGAGAAAATCAGACCAACGCTGAGTTGATGAAGGAAGAAGATTG                         GCAGGTTCTGCTAGAGATGGAGGAAGAATACATAAAGAACCTGTGCGGTCA
genomic: AAGAAAGGAGAAAATCAGACCAACGCTGAGTTGATGAAGGAAGAAGATTGgtaagagata ... tttattgcagGCAGGTTCTGTTAGAGATGGAGGAAGAATACATAAAGAACCTGTGCGGTCA
EST: gi|33093977|gb|CF053971.1|CF053971
EST:     AAGAAAGGAGAAAATCAGACCAACGCTGAGTTGATGAAGGAAGAAGATTG                         GCAGGTTCTGTTAGAGATGGAGGAAGAATACATAAAGAACCTGTGCGGTCA
genomic: AAGAAAGGAGAAAATCAGACCAACGCTGAGTTGATGAAGGAAGAAGATTGgtaagagata ... tttattgcagGCAGGTTCTGTTAGAGATGGAGGAAGAATACATAAAGAACCTGTGCGGTCA
EST: gi|33094806|gb|CF054800.1|CF054800
EST:     AAGAAAGGAGAAAATCAGACCAACGCTGAGTTGATGAAGGAAGAAGATTG                         GCAGGTTCTGTTAGAGATGGGGGAAGAATACATAAAGAACCTGTGCGGTCA
genomic: AAGAAAGGAGAAAATCAGACCAACGCTGAGTTGATGAAGGAAGAAGATTGgtaagagata ... tttattgcagGCAGGTTCTGTTAGAGATGGAGGAAGAATACATAAAGAACCTGTGCGGTCA
EST: gi|22542007|gb|BU092445.1|BU092445
EST:     AAGAAAGGAGAAAATCAGACCAACGCTGAGTTGATGAAGGAAGAAGATTG                         GCAGGTTCTGTTAGAGATGGAGGAAGAATACATAAAGAACCTGTGCGGTCA
genomic: AAGAAAGGAGAAAATCAGACCAACGCTGAGTTGATGAAGGAAGAAGATTGgtaagagata ... tttattgcagGCAGGTTCTGTTAGAGATGGAGGAAGAATACATAAAGAACCTGTGCGGTCA
EST: gi|32933658|gb|CF038470.1|CF038470
EST:     AAGAAAGGAGAAAATCAGACCAACGCTGAGTTGATGAAGGAAGAAGATTG                         GCAGGTTCTGTTAGAGATGGAGGAAGAATACATAAAGAACCTGTGCGGTCA
genomic: AAGAAAGGAGAAAATCAGACCAACGCTGAGTTGATGAAGGAAGAAGATTGgtaagagata ... tttattgcagGCAGGTTCTGTTAGAGATGGAGGAAGAATACATAAAGAACCTGTGCGGTCA

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: 347

GAAAGATAGTAAACCCCCGTATCATCCTGTTGGACTGCCCTGTTGAGTATAAGAAAGGAGAAAATCAGACCAACGCTGAGTTGATGAAGGAAGAAGATTGgtaagagata ... tttattgcagGCAGGTTCTGTTAGAGATGGAGGAAGAATACATAAAGAACCTGTGCGGTCAAATTCTAAAATTCAAGCCTGATTTAGTCATAACTGAGAAAGGGCTCAGT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 269

GAAAGATAGTAAACCCCCGTATCATCCTGTTGGACTGCCCTGTTGAGTATAAGAAAGGAGAAAATCAGACCAACGCTGAGTTGATGAAGGAAGAAGATTGgtaagagata ... tttattgcagGCAGGTTCTGTTAGAGATGGAGGAAGAATACATAAAGAACCTGTGCGGTCAAATTCTAAAATTCAAGCCTGATTTAGTCATAACTGAGAAAGGGCTCAGT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 141

GAAAGATAGTAAACCCCCGTATCATCCTGTTGGACTGCCCTGTTGAGTATAAGAAAGGAGAAAATCAGACCAACGCTGAGTTGATGAAGGAAGAAGATTGgtaagagata ... tttattgcagGCAGGTTCTGTTAGAGATGGAGGAAGAATACATAAAGAACCTGTGCGGTCAAATTCTAAAATTCAAGCCTGATTTAGTCATAACTGAGAAAGGGCTCAGT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 179

GAAAGATAGTAAACCCCCGTATCATCCTGTTGGACTGCCCTGTTGAGTATAAGAAAGGAGAAAATCAGACCAACGCTGAGTTGATGAAGGAAGAAGATTGgtaagagata ... tttattgcagGCAGGTTCTGTTAGAGATGGAGGAAGAATACATAAAGAACCTGTGCGGTCAAATTCTAAAATTCAAGCCTGATTTAGTCATAACTGAGAAAGGGCTCAGT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAAGATAGTAAACCCCCGTATCATCCTGTTGGACTGCCCTGTTGAGTATAAGAAAGGAGAAAATCAGACCAACGCTGAGTTGATGAAGGAAGAAGATTGgtaagagatatccatgtaccacaatgattttacctaaatacaatgcatgcataattttaaagtaatttggtagaattctaaggtatattatgtggcaaactttattgcag

- - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG