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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGGCTGCACACGCCGTCATTCGCGACGGTTTCTCCGCAAGAGGTTTCAGGTTCCAGCCCAGCGGAAGTGCAGAATTTTGgtaacgactctgcttgtgtttttttttcgtcttcgaaaccaatgcttatgtttttcttcccgactcaaggagtaatcccatggaaatggaaccatgtgac...

Basic information

species Zea mays
transcript GRMZM2G090087_T03
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G090087_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os05g45960.1 (Oryza sativa), 5'ss of exon 2
GTGGCTGCACACGCCGTCATTCGCGACGGTTTCTCCGCAAGAGGTTTCAGGTTCCAGCCCAGCGGAAGTGCAGAATTTTGgtaacga---ctctgcttgtgttttt--ttttcgtcttcgaaaccaatgcttatgtttttcttcccgactcaaggagtaatcccatggaaatggaaccatgtgac
|||| ||||||||||| ||||||||||||| ||||| || ||  |||||||||| ||||| |||||||||||||||||||||||        |   ||| | || |  || | || || | |  || ||  | ||      |       | |   |||  |      |      |||||  |   
GTGGATGCACACGCCGCCATTCGCGACGGTGTCTCCTCAGGAAATTTCAGGTTCGAGCCCGGCGGAAGTGCAGAATTTTGgtaagagagctcccatttggggttctgcttattgtttttgtacacattgaatctggagggatatta---ttagttagtgcttgtgatgttgcaaaaccaattc--
















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|211124834|gb|FL408235.1|FL408235
EST:     GTCTCCGCAAGAGGTTTCAGGTTCCAGCCCAGCGGAAGTGCAGAATTTTG                         TGCAGGGCAGCTGGACAGCATCTGCTAACTGGAACTGGATAGTCGATCCCC
genomic: TTCTCCGCAAGAGGTTTCAGGTTCCAGCCCAGCGGAAGTGCAGAATTTTGgtaacgactc ... agttgttcagTGCAGGGCAGCTGGACAGCATCTGCTAACTGGAACTGGATAGTCGATCCCC
EST: gi|211368406|gb|FL377758.1|FL377758
EST:     GTCTCCGCAAGAGGTTTCAGGTTCCAGCCCAGCGGAAGTGCAGAATTTTG                         TGCAGGGCAGCTGGACAGCATCTGCTAACTGGAACTGGATAGTCGATCCCC
genomic: TTCTCCGCAAGAGGTTTCAGGTTCCAGCCCAGCGGAAGTGCAGAATTTTGgtaacgactc ... agttgttcagTGCAGGGCAGCTGGACAGCATCTGCTAACTGGAACTGGATAGTCGATCCCC
EST: gi|211082384|gb|FL402151.1|FL402151
EST:     GTCTCCGCAAGAGGTTTCAGGTTCCAGCCCAGCGGAAGTGCAGAATTTTG                         TGCAGGGCAGCTGGACAGCATCTGCTAACTGGAACTGGATAGTCGATCCCC
genomic: TTCTCCGCAAGAGGTTTCAGGTTCCAGCCCAGCGGAAGTGCAGAATTTTGgtaacgactc ... agttgttcagTGCAGGGCAGCTGGACAGCATCTGCTAACTGGAACTGGATAGTCGATCCCC
EST: gi|148958687|gb|EC904955.2|EC904955
EST:     TTCTCCGCAAGAGGTTTCAGGTTCCAGCCCAGCGGAAGTGCAGAATTTTG                         TGCAGGGCAGCTGGACAGCATCTGCTAACTGGAACTGGATAGTCGATCCCC
genomic: TTCTCCGCAAGAGGTTTCAGGTTCCAGCCCAGCGGAAGTGCAGAATTTTGgtaacgactc ... agttgttcagTGCAGGGCAGCTGGACAGCATCTGCTAACTGGAACTGGATAGTCGATCCCC
EST: gi|211219293|gb|FL379956.1|FL379956
EST:     GTCTCCGCAAGAGGTTTCAGGTTCCAGCCCAGCGGAAGTGCAGAATTTTG                         TGCAGGGCAGCTGGACAGCATCTGCTAACTGGAACTGGATAGTCGATCCCC
genomic: TTCTCCGCAAGAGGTTTCAGGTTCCAGCCCAGCGGAAGTGCAGAATTTTGgtaacgactc ... agttgttcagTGCAGGGCAGCTGGACAGCATCTGCTAACTGGAACTGGATAGTCGATCCCC
EST: gi|211040046|gb|FL419087.1|FL419087
EST:     GTCTCCGCAAGAGGTTTCAGGTTCCAGCCCAGCGGAAGTGCAGAATTTTG                         TGCAGGGCAGCTGGACAGCATCTGCTAACTGGAACTGGATAGTCGATCCCC
genomic: TTCTCCGCAAGAGGTTTCAGGTTCCAGCCCAGCGGAAGTGCAGAATTTTGgtaacgactc ... agttgttcagTGCAGGGCAGCTGGACAGCATCTGCTAACTGGAACTGGATAGTCGATCCCC
EST: gi|211089833|gb|FL381143.1|FL381143
EST:     GTCTCCGCAAGAGGTTTCAGGTTCCAGCCCAGCGGAAGTGCAGAATTTTG                         TGCAGGGCAGCTGGACAGCATCTGCTAACTGGAACTGGATAGTCGATCCCC
genomic: TTCTCCGCAAGAGGTTTCAGGTTCCAGCCCAGCGGAAGTGCAGAATTTTGgtaacgactc ... agttgttcagTGCAGGGCAGCTGGACAGCATCTGCTAACTGGAACTGGATAGTCGATCCCC
EST: gi|211332038|gb|FL380497.1|FL380497
EST:     GTCTCCGCAAGAGGTTTCAGGTTCCAGCCCAGCGGAAGTGCAGAATTTTG                         TGCAGGGCAGCTGGACAGCATCTGCTAACTGGAACTGGATAGTCGATCCCC
genomic: TTCTCCGCAAGAGGTTTCAGGTTCCAGCCCAGCGGAAGTGCAGAATTTTGgtaacgactc ... agttgttcagTGCAGGGCAGCTGGACAGCATCTGCTAACTGGAACTGGATAGTCGATCCCC
EST: gi|94472231|gb|EB701189.1|EB701189
EST:     TTCTCCGCAAGAGGTTTCAGGTTCCAGCCCAGCGGAAGTGCAGAATTTTG                         TGCAGGGCAGCTGGACAGCATCTGCTAACTGGAACTGGATAGTCGATCCCC
genomic: TTCTCCGCAAGAGGTTTCAGGTTCCAGCCCAGCGGAAGTGCAGAATTTTGgtaacgactc ... agttgttcagTGCAGGGCAGCTGGACAGCATCTGCTAACTGGAACTGGATAGTCGATCCCC
EST: gi|211484357|gb|FL369749.1|FL369749
EST:     GTCTCCGCAAGAGGTTTCAGGTTCCAGCCCAGCGGAAGTGCAGAATTTTG                         TGCAGGGCAGCTGGACAGCATCTGCTAACTGGAACTGGATAGTCGATCCCC
genomic: TTCTCCGCAAGAGGTTTCAGGTTCCAGCCCAGCGGAAGTGCAGAATTTTGgtaacgactc ... agttgttcagTGCAGGGCAGCTGGACAGCATCTGCTAACTGGAACTGGATAGTCGATCCCC
EST: gi|211535838|gb|FL377068.1|FL377068
EST:     GTCTCCGCAAGAGGTTTCAGGTTCCAGCCCAGCGGAAGTGCAGAATTTTG                         TGCAGGGCAGCTGGACAGCATCTGCTAACTGGAACTGGATAGTCGATCCCC
genomic: TTCTCCGCAAGAGGTTTCAGGTTCCAGCCCAGCGGAAGTGCAGAATTTTGgtaacgactc ... agttgttcagTGCAGGGCAGCTGGACAGCATCTGCTAACTGGAACTGGATAGTCGATCCCC
EST: gi|211390609|gb|FL418018.1|FL418018
EST:     TTCTCCGCAAGAGGTTTCAGGTTCCAGCCCAGCGGAAGTGCAGAATTTTG                         TGCAGGGCAGCTGGACAGCATCTGCTAACTGGAACTGGASTAGTCGATCCC
genomic: TTCTCCGCAAGAGGTTTCAGGTTCCAGCCCAGCGGAAGTGCAGAATTTTGgtaacgactc ... agttgttcagTGCAGGGCAGCTGGACAGCATCTGCTAACTGGAACTGGA-TAGTCGATCCC
EST: gi|211059652|gb|FL374524.1|FL374524
EST:     GTCTCCGCAAGAGGTTTCAGGTTCCAGCCCAGCGGAAGTGCAGAATTTTG                         TGCAGGGCAGCTGGACAGCATCTGCTAACTGGAACTGGATAGTCGATCCCC
genomic: TTCTCCGCAAGAGGTTTCAGGTTCCAGCCCAGCGGAAGTGCAGAATTTTGgtaacgactc ... agttgttcagTGCAGGGCAGCTGGACAGCATCTGCTAACTGGAACTGGATAGTCGATCCCC
EST: gi|211002755|gb|FL375715.1|FL375715
EST:     TTCTCCGCAAGAGGTTTCAGGTTCCAGCCCAGCGGAAGTGCA-A-TTTTG                         TGCAGGGCAGCTGGACAGCATCTGCTAACTGGAACTGGATAGTCGATCCCC
genomic: TTCTCCGCAAGAGGTTTCAGGTTCCAGCCCAGCGGAAGTGCAGAATTTTGgtaacgactc ... agttgttcagTGCAGGGCAGCTGGACAGCATCTGCTAACTGGAACTGGATAGTCGATCCCC
EST: gi|60399068|gb|DN231882.1|DN231882
EST:     TTCTCCGCAAGAGGTTTCAGGTTCCAGCCCAGCGGAAGTGCAGAATTTTG                         TGCAGGGCAGCTGGACAGCATCTGCTAACTGGAACTGGATAGTCGATCCCC
genomic: TTCTCCGCAAGAGGTTTCAGGTTCCAGCCCAGCGGAAGTGCAGAATTTTGgtaacgactc ... agttgttcagTGCAGGGCAGCTGGACAGCATCTGCTAACTGGAACTGGATAGTCGATCCCC
EST: gi|60346857|gb|DN213830.1|DN213830
EST:     TTCTCCGCAAGAGGTTTCAGGTTCCAGCCCAGCGGAAGTGCAGAATTTTG                         TGCAGGGCAGCTGGACAGCATCTGCTAACTGGAACTGGATAGTCGATCCCC
genomic: TTCTCCGCAAGAGGTTTCAGGTTCCAGCCCAGCGGAAGTGCAGAATTTTGgtaacgactc ... agttgttcagTGCAGGGCAGCTGGACAGCATCTGCTAACTGGAACTGGATAGTCGATCCCC
EST: gi|28576035|gb|CB281927.1|CB281927
EST:     TTCTCCGCAAGAGGTTTCAGGTTCCAGCCCAGCGGAAGTGCAGAATTTTG                         TGCAGGGCAGCTGGACAGCATCTGCTAACTGGAACTGGATAGTCGATCCCC
genomic: TTCTCCGCAAGAGGTTTCAGGTTCCAGCCCAGCGGAAGTGCAGAATTTTGgtaacgactc ... agttgttcagTGCAGGGCAGCTGGACAGCATCTGCTAACTGGAACTGGATAGTCGATCCCC
EST: gi|211261878|gb|FL409707.1|FL409707
EST:     GTCTCCGCAAGAGGTTTCAGGTTCCAGCCCAGCGGAAGTGCAGAATTTTG                         TGCAGGGCAGCTGGACAGCATCTGCTAACTGGAACTGGATAGTCGATCCCC
genomic: TTCTCCGCAAGAGGTTTCAGGTTCCAGCCCAGCGGAAGTGCAGAATTTTGgtaacgactc ... agttgttcagTGCAGGGCAGCTGGACAGCATCTGCTAACTGGAACTGGATAGTCGATCCCC
EST: gi|149071327|gb|EE159720.2|EE159720
EST:     TTCTCCGCAAGAGGTTTCAGGTTCCAGCCCAGCGGAAGTGCAGAATTTTG                         TGCAGGGCAGCTGGACAGCATCTGCTAACTGGAACTGGATAGTCGATCCCC
genomic: TTCTCCGCAAGAGGTTTCAGGTTCCAGCCCAGCGGAAGTGCAGAATTTTGgtaacgactc ... agttgttcagTGCAGGGCAGCTGGACAGCATCTGCTAACTGGAACTGGATAGTCGATCCCC
EST: gi|211254108|gb|FL390493.1|FL390493
EST:     TTCTCCGCAAGAGGTTTCAGGTTCCAGCCCAGCGGAAGTGCAGAATTTTG                         TGCAGGGCAGCTGGACAGCATCTGCTAACTGGAACTGGATAGTCGATCCCC
genomic: TTCTCCGCAAGAGGTTTCAGGTTCCAGCCCAGCGGAAGTGCAGAATTTTGgtaacgactc ... agttgttcagTGCAGGGCAGCTGGACAGCATCTGCTAACTGGAACTGGATAGTCGATCCCC
EST: gi|211069274|gb|FL419947.1|FL419947
EST:     GTCTCCGCAAGAGGTTTCAGGTTCCAGCCCAGCGGAAGTGCAGAATTTTG                         TGCAGGGCAGCTGGACAGCATCTGCTAACTGGAACTGGATAGTCGATCCCC
genomic: TTCTCCGCAAGAGGTTTCAGGTTCCAGCCCAGCGGAAGTGCAGAATTTTGgtaacgactc ... agttgttcagTGCAGGGCAGCTGGACAGCATCTGCTAACTGGAACTGGATAGTCGATCCCC
EST: gi|60339011|gb|DN205984.1|DN205984
EST:     TTCTCCGCAAGAGGTTTCAGGTTCCAGCCCAGCGGAAGTGCAGAATTTTG                         TGCAGGGCAGCTGGACAGCATCTGCTAACTGGAACTGGATAGTCGATCCCC
genomic: TTCTCCGCAAGAGGTTTCAGGTTCCAGCCCAGCGGAAGTGCAGAATTTTGgtaacgactc ... agttgttcagTGCAGGGCAGCTGGACAGCATCTGCTAACTGGAACTGGATAGTCGATCCCC
EST: gi|211309737|gb|FL424540.1|FL424540
EST:     GTCTCCGCAAGANGTTTCAGGTTCCAGCCCAGCGGAAGTGCAGAATTTTG                         TGCAGGGCAGCTGGACAGCATCTGCTAACTGGAACTGGATAGTCGATCCCC
genomic: TTCTCCGCAAGAGGTTTCAGGTTCCAGCCCAGCGGAAGTGCAGAATTTTGgtaacgactc ... agttgttcagTGCAGGGCAGCTGGACAGCATCTGCTAACTGGAACTGGATAGTCGATCCCC
EST: gi|211337034|gb|FL418406.1|FL418406
EST:     GTCTCCGCAAGAGGTTTCAGGTTCCAGCCCAGCGGAAGTGCAGAATTTTG                         TGCAGGGCAGCTGGACAGCATCTGCTAACTGGAACTGGATAGTCGATCCCC
genomic: TTCTCCGCAAGAGGTTTCAGGTTCCAGCCCAGCGGAAGTGCAGAATTTTGgtaacgactc ... agttgttcagTGCAGGGCAGCTGGACAGCATCTGCTAACTGGAACTGGATAGTCGATCCCC
EST: gi|211524408|gb|FL405472.1|FL405472
EST:     GTCTCCGCAAGAGGTTTCAGGTTCCAGCCCAGCGGAAGTGCAGAATTTTG                         TGCAGGGCAGCTGGACAGCATCTGCTAACTGGAACTGGATAGTCGATCCCC
genomic: TTCTCCGCAAGAGGTTTCAGGTTCCAGCCCAGCGGAAGTGCAGAATTTTGgtaacgactc ... agttgttcagTGCAGGGCAGCTGGACAGCATCTGCTAACTGGAACTGGATAGTCGATCCCC

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: 309

GTGGCTGCACACGCCGTCATTCGCGACGGTTTCTCCGCAAGAGGTTTCAGGTTCCAGCCCAGCGGAAGTGCAGAATTTTGgtaacgactc ... agttgttcagTGCAGGGCAGCTGGACAGCATCTGCTAACTGGAACTGGATAGTCGATCCCCTGAACGGTGATAAATTCATCAAAGTTGCTGAGGTTCAGGGAACAGAAAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 153

GTGGCTGCACACGCCGTCATTCGCGACGGTTTCTCCGCAAGAGGTTTCAGGTTCCAGCCCAGCGGAAGTGCAGAATTTTGgtaacgactc ... agttgttcagTGCAGGGCAGCTGGACAGCATCTGCTAACTGGAACTGGATAGTCGATCCCCTGAACGGTGATAAATTCATCAAAGTTGCTGAGGTTCAGGGAACAGAAAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 106

GTGGCTGCACACGCCGTCATTCGCGACGGTTTCTCCGCAAGAGGTTTCAGGTTCCAGCCCAGCGGAAGTGCAGAATTTTGgtaacgactc ... agttgttcagTGCAGGGCAGCTGGACAGCATCTGCTAACTGGAACTGGATAGTCGATCCCCTGAACGGTGATAAATTCATCAAAGTTGCTGAGGTTCAGGGAACAGAAAT


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

GTGGCTGCACACGCCGTCATTCGCGACGGTTTCTCCGCAAGAGGTTTCAGGTTCCAGCCCAGCGGAAGTGCAGAATTTTGgtaacgactc ... agttgttcagTGCAGGGCAGCTGGACAGCATCTGCTAACTGGAACTGGATAGTCGATCCCCTGAACGGTGATAAATTCATCAAAGTTGCTGAGGTTCAGGGAACAGAAAT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGGCTGCACACGCCGTCATTCGCGACGGTTTCTCCGCAAGAGGTTTCAGGTTCCAGCCCAGCGGAAGTGCAGAATTTTGgtaacgactctgcttgtgtttttttttcgtcttcgaaaccaatgcttatgtttttcttcccgactcaaggagtaatcccatggaaatggaaccatgtgac

- - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - AAGAGG