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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acagtcgggggagctgtgtgtgtggttactacttactactcgaggccgcatttggtgtggatgataagttggcttgggcctgcgcctgattgatttgcagGTGGCTGCACACGCCGTCATTCGCGACGGTTTCTCCGCAAGAGGTTTCAGGTTCCAGCCCAGCGGAAGTGCAGAATTTTG

Basic information

species Zea mays
transcript GRMZM2G090087_T03
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G090087_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os05g45960.1 (Oryza sativa), 3'ss of exon 1
acagtcgggggagctgtgtgtgtggttactacttactactcgaggccgcatttggtgtggatga-taagttggcttgggcctgcgcctgattgatttgcagGTGGCTGCACACGCCGTCATTCGCGACGGTTTCTCCGCAAGAGGTTTCAGGTTCCAGCCCAGCGGAAGTGCAGAATTTTG
 |  |      | |  | | | |||   | |      | ||| ||      |||  |  ||||| || | | |  |   | |  |  ||||||||| |||||||| ||||||||||| ||||||||||||| ||||| || ||  |||||||||| ||||| |||||||||||||||||||
tcgctttttccaccgttttttttgggagcgatccggca-tcgtggttttggttgcgggcgatgaatatggtcgactcatcgtttgggtgattgattggcagGTGGATGCACACGCCGCCATTCGCGACGGTGTCTCCTCAGGAAATTTCAGGTTCGAGCCCGGCGGAAGTGCAGAATTTTG
















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:     CAGCACCTTGCCGCCGTCCGTCGATCTGCACCCTTTGCGTGCGTGTCCAG                         GTGGCTGCACACGCCGTCATTCGCGACGGTGTCTCCGCAAGAGGTTTCAGG
genomic: CAGCACCTTGCCGCCGTCCGTCGATCTGCACCCTTTGCGTGCGTGTCCAGgtgatcccgc ... tgatttgcagGTGGCTGCACACGCCGTCATTCGCGACGGTTTCTCCGCAAGAGGTTTCAGG
EST: gi|211368406|gb|FL377758.1|FL377758
EST:     CAGCACCTTGCCGCCGTCCGTCGATCTGCACCCTTTGCGTGCGTGTCCAG                         GTGGCTGCACACGCCGTCATTCGCGACGGTGTCTCCGCAAGAGGTTTCAGG
genomic: CAGCACCTTGCCGCCGTCCGTCGATCTGCACCCTTTGCGTGCGTGTCCAGgtgatcccgc ... tgatttgcagGTGGCTGCACACGCCGTCATTCGCGACGGTTTCTCCGCAAGAGGTTTCAGG
EST: gi|211082384|gb|FL402151.1|FL402151
EST:     CAGCACCTTGCCGCCGTCCGTCGATCTGCACCCTTTGCGTGCGTGTCCAG                         GTGGCTGCACACGCCGTCATTCGCGACGGTGTCTCCGCAAGAGGTTTCAGG
genomic: CAGCACCTTGCCGCCGTCCGTCGATCTGCACCCTTTGCGTGCGTGTCCAGgtgatcccgc ... tgatttgcagGTGGCTGCACACGCCGTCATTCGCGACGGTTTCTCCGCAAGAGGTTTCAGG
EST: gi|148958687|gb|EC904955.2|EC904955
EST:     CAGCACCTTGCCGCCGTCCGTCGATCTGCACCCTTTGCGTGCGTGTCCAG                         GTGGCTGCACACGCCGTCATTCGCGACGGTTTCTCCGCAAGAGGTTTCAGG
genomic: CAGCACCTTGCCGCCGTCCGTCGATCTGCACCCTTTGCGTGCGTGTCCAGgtgatcccgc ... tgatttgcagGTGGCTGCACACGCCGTCATTCGCGACGGTTTCTCCGCAAGAGGTTTCAGG
EST: gi|211219293|gb|FL379956.1|FL379956
EST:     CAGCACCTTGCCGCCGTCCGTCGATCTGCACCCTTTGCGTGCGTGTCCAG                         GTGGCTGCACACGCCGTCATTCGCGACGGTGTCTCCGCAAGAGGTTTCAGG
genomic: CAGCACCTTGCCGCCGTCCGTCGATCTGCACCCTTTGCGTGCGTGTCCAGgtgatcccgc ... tgatttgcagGTGGCTGCACACGCCGTCATTCGCGACGGTTTCTCCGCAAGAGGTTTCAGG
EST: gi|211040046|gb|FL419087.1|FL419087
EST:     CAGCACCTTGCCGCCGTCCGTCGATCTGCACCCTTTGCGTGCGTGTCCAG                         GTGGCTGCACACGCCGTCATTCGCGACGGTGTCTCCGCAAGAGGTTTCAGG
genomic: CAGCACCTTGCCGCCGTCCGTCGATCTGCACCCTTTGCGTGCGTGTCCAGgtgatcccgc ... tgatttgcagGTGGCTGCACACGCCGTCATTCGCGACGGTTTCTCCGCAAGAGGTTTCAGG
EST: gi|211311129|gb|FL384825.1|FL384825
EST:     CAGCACCTTGCCGCCGTCCGTCGATCTGCACCCTTTGCGTGCGTGTCCAG                         GTGGCTGCACACGCCGTCATTCGCGACGGTGTCTCCGCAAGAGGTTTCAGG
genomic: CAGCACCTTGCCGCCGTCCGTCGATCTGCACCCTTTGCGTGCGTGTCCAGgtgatcccgc ... tgatttgcagGTGGCTGCACACGCCGTCATTCGCGACGGTTTCTCCGCAAGAGGTTTCAGG
EST: gi|211089833|gb|FL381143.1|FL381143
EST:     CAGCACCTTGCCGCCGTCCGTCGATCTGCACCCTTTGCGTGCGTGTCCAG                         GTGGCTGCACACGCCGTCATTCGCGACGGTGTCTCCGCAAGAGGTTTCAGG
genomic: CAGCACCTTGCCGCCGTCCGTCGATCTGCACCCTTTGCGTGCGTGTCCAGgtgatcccgc ... tgatttgcagGTGGCTGCACACGCCGTCATTCGCGACGGTTTCTCCGCAAGAGGTTTCAGG
EST: gi|211332038|gb|FL380497.1|FL380497
EST:     CAGCACCTTGCCGCCGTCCGTCGATCTGCACCCTTTGCGTGCGTGTCCAG                         GTGGCTGCACACGCCGTCATTCGCGACGGTGTCTCCGCAAGAGGTTTCAGG
genomic: CAGCACCTTGCCGCCGTCCGTCGATCTGCACCCTTTGCGTGCGTGTCCAGgtgatcccgc ... tgatttgcagGTGGCTGCACACGCCGTCATTCGCGACGGTTTCTCCGCAAGAGGTTTCAGG
EST: gi|94472231|gb|EB701189.1|EB701189
EST:     CAGCACCTTGCCGCCGTCCGTCGATCTGCACCCTTTGCGTGCGTGTCCAG                         GTGGCTGCACACGCCGTCATTCGCGACGGTTTCTCCGCAAGAGGTTTCAGG
genomic: CAGCACCTTGCCGCCGTCCGTCGATCTGCACCCTTTGCGTGCGTGTCCAGgtgatcccgc ... tgatttgcagGTGGCTGCACACGCCGTCATTCGCGACGGTTTCTCCGCAAGAGGTTTCAGG
EST: gi|211484357|gb|FL369749.1|FL369749
EST:     CAGCACCTTGCTGCCGTCCGTCGATCTGCACCCTTTGCGTGCGTGTCCAG                         GTGGCTGCACACGCCGTCATTCGCGACGGTGTCTCCGCAAGAGGTTTCAGG
genomic: CAGCACCTTGCCGCCGTCCGTCGATCTGCACCCTTTGCGTGCGTGTCCAGgtgatcccgc ... tgatttgcagGTGGCTGCACACGCCGTCATTCGCGACGGTTTCTCCGCAAGAGGTTTCAGG
EST: gi|211535838|gb|FL377068.1|FL377068
EST:     CA-SACCTTGCCGCCGTCCGTCGATCTGCACCCTTTGCGTGCGTGTCCAG                         GTGGCTGCACACGCCGTCATTCGCGACGGTGTCTCCGCAAGAGGTTTCAGG
genomic: CAGCACCTTGCCGCCGTCCGTCGATCTGCACCCTTTGCGTGCGTGTCCAGgtgatcccgc ... tgatttgcagGTGGCTGCACACGCCGTCATTCGCGACGGTTTCTCCGCAAGAGGTTTCAGG
EST: gi|211390609|gb|FL418018.1|FL418018
EST:     CAGCACCTTGCCGCCGTCCGTCGATCTGCACCCTTTGCGTGCGTGTCCAG                         GTGGCTGCACACGCCGTCATTCG--ACGGTTTCTCCGCAAGAGGTTTCAGG
genomic: CAGCACCTTGCCGCCGTCCGTCGATCTGCACCCTTTGCGTGCGTGTCCAGgtgatcccgc ... tgatttgcagGTGGCTGCACACGCCGTCATTCGCGACGGTTTCTCCGCAAGAGGTTTCAGG
EST: gi|211059652|gb|FL374524.1|FL374524
EST:     CAGCACCTTGCCGCCGTCCGTCGATCTGCACCCTTTGCGTGCGTGTCCAG                         GTGGCTGCACACGCCGTCATTCGCGACGGTGTCTCCGCAAGAGGTTTCAGG
genomic: CAGCACCTTGCCGCCGTCCGTCGATCTGCACCCTTTGCGTGCGTGTCCAGgtgatcccgc ... tgatttgcagGTGGCTGCACACGCCGTCATTCGCGACGGTTTCTCCGCAAGAGGTTTCAGG
EST: gi|211002755|gb|FL375715.1|FL375715
EST:     CAGCACCTTGCCGCCGTCCGTCGATCTGCACCCTTTGCGTGCGTGTCCAG                         GTGGCTGCACACGCCGTCATTCGCGACGGTTTCTCCGCAAGAGGTTTCAGG
genomic: CAGCACCTTGCCGCCGTCCGTCGATCTGCACCCTTTGCGTGCGTGTCCAGgtgatcccgc ... tgatttgcagGTGGCTGCACACGCCGTCATTCGCGACGGTTTCTCCGCAAGAGGTTTCAGG
EST: gi|60399068|gb|DN231882.1|DN231882
EST:     CAGCACCTTGCCGCCGTCCGTCGATCTGCACCCTTTGCGTGCGTGTCCAG                         GTGGCTGCACACGCCGTCATTCGCGACGGTTTCTCCGCAAGAGGTTTCAGG
genomic: CAGCACCTTGCCGCCGTCCGTCGATCTGCACCCTTTGCGTGCGTGTCCAGgtgatcccgc ... tgatttgcagGTGGCTGCACACGCCGTCATTCGCGACGGTTTCTCCGCAAGAGGTTTCAGG
EST: gi|60346857|gb|DN213830.1|DN213830
EST:     CAGCACCTTGCCGCCGTCCGTCGATCTGCACCCTTTGCGTGCGTGTCCAG                         GTGGCTGCACACGCCGTCATTCGCGACGGTTTCTCCGCAAGAGGTTTCAGG
genomic: CAGCACCTTGCCGCCGTCCGTCGATCTGCACCCTTTGCGTGCGTGTCCAGgtgatcccgc ... tgatttgcagGTGGCTGCACACGCCGTCATTCGCGACGGTTTCTCCGCAAGAGGTTTCAGG
EST: gi|28576035|gb|CB281927.1|CB281927
EST:     CAGCACCTTGCCGCCGTCCGTCGATCTGCACCCTTTGCGTGCGTGTCCAG                         GTGGCTGCACACGCCGTCATTCGCGACGGTTTCTCCGCAAGAGGTTTCAGG
genomic: CAGCACCTTGCCGCCGTCCGTCGATCTGCACCCTTTGCGTGCGTGTCCAGgtgatcccgc ... tgatttgcagGTGGCTGCACACGCCGTCATTCGCGACGGTTTCTCCGCAAGAGGTTTCAGG
EST: gi|211261878|gb|FL409707.1|FL409707
EST:     CAGCACCTTGCCGCCGTCCGTCGATCTGCACCCTTTGCGTGCGTGTCCAG                         GTGGCTGCACACGCCGTCATTCGCGACGGTGTCTCCGCAAGAGGTTTCAGG
genomic: CAGCACCTTGCCGCCGTCCGTCGATCTGCACCCTTTGCGTGCGTGTCCAGgtgatcccgc ... tgatttgcagGTGGCTGCACACGCCGTCATTCGCGACGGTTTCTCCGCAAGAGGTTTCAGG
EST: gi|211521602|gb|FL412476.1|FL412476
EST:     CAGCACCTTGCCGCCGTCCGTCGATCTGCACCCTTTGCGTGCGTGTCCAG                         GTGGCTGCACACGCCGTCATTCGCGACGGTGTCTCCGCAAGAGGTTTCAGG
genomic: CAGCACCTTGCCGCCGTCCGTCGATCTGCACCCTTTGCGTGCGTGTCCAGgtgatcccgc ... tgatttgcagGTGGCTGCACACGCCGTCATTCGCGACGGTTTCTCCGCAAGAGGTTTCAGG
EST: gi|149071327|gb|EE159720.2|EE159720
EST:     CAGCACCTTGCCGCCGTCCGTCGATCTGCACCCTTTGCGTGCGTGTCCAG                         GTGGCTGCACACGCCGTCATTCGCGACGGTTTCTCCGCAAGAGGTTTCAGG
genomic: CAGCACCTTGCCGCCGTCCGTCGATCTGCACCCTTTGCGTGCGTGTCCAGgtgatcccgc ... tgatttgcagGTGGCTGCACACGCCGTCATTCGCGACGGTTTCTCCGCAAGAGGTTTCAGG
EST: gi|211254108|gb|FL390493.1|FL390493
EST:     CAGCACCTTGCCGCCGTCCGTCGATCTGCACCCTTTGCGTGCGTGTCCAG                         GTGGCTGCACACGCCGTCATTCGCGACGGTTTCTCCGCAAGAGGTTTCAGG
genomic: CAGCACCTTGCCGCCGTCCGTCGATCTGCACCCTTTGCGTGCGTGTCCAGgtgatcccgc ... tgatttgcagGTGGCTGCACACGCCGTCATTCGCGACGGTTTCTCCGCAAGAGGTTTCAGG
EST: gi|211069274|gb|FL419947.1|FL419947
EST:     CAGCACCTTGCCGCCGTCCGTCGATCTGCACCCTTTGCGTGCGTGTCCAG                         GTGGCTGCACACGCCGTCATTCGCGACGGTGTCTCCGCAAGAGGTTTCAGG
genomic: CAGCACCTTGCCGCCGTCCGTCGATCTGCACCCTTTGCGTGCGTGTCCAGgtgatcccgc ... tgatttgcagGTGGCTGCACACGCCGTCATTCGCGACGGTTTCTCCGCAAGAGGTTTCAGG
EST: gi|60339011|gb|DN205984.1|DN205984
EST:     CAGCACCTTGCCGCCGTCCGTCGATCTGCACCCTTTGCGTGCGTGTCCAG                         GTGGCTGCACACGCCGTCATTCGCGACGGTTTCTCCGCAAGAGGTTTCAGG
genomic: CAGCACCTTGCCGCCGTCCGTCGATCTGCACCCTTTGCGTGCGTGTCCAGgtgatcccgc ... tgatttgcagGTGGCTGCACACGCCGTCATTCGCGACGGTTTCTCCGCAAGAGGTTTCAGG
EST: gi|211309737|gb|FL424540.1|FL424540
EST:     CAGCACCTTGCCGCCGTCCGTCGATCTGCACCCTTTGCGTGCGTGTCCAG                         GTGGCTGCACACGCCGTCATTCGCGACGGTGTCTCCGCAAGANGTTTCAGG
genomic: CAGCACCTTGCCGCCGTCCGTCGATCTGCACCCTTTGCGTGCGTGTCCAGgtgatcccgc ... tgatttgcagGTGGCTGCACACGCCGTCATTCGCGACGGTTTCTCCGCAAGAGGTTTCAGG
EST: gi|211337034|gb|FL418406.1|FL418406
EST:     CAGCACCTTGCCGCCGTCCGTCGATCTGCACCCTTTGCGTGCGTGTCCAG                         GTGGCTGCACACGCCGTCATTCGCGACGGTGTCTCCGCAAGAGGTTTCAGG
genomic: CAGCACCTTGCCGCCGTCCGTCGATCTGCACCCTTTGCGTGCGTGTCCAGgtgatcccgc ... tgatttgcagGTGGCTGCACACGCCGTCATTCGCGACGGTTTCTCCGCAAGAGGTTTCAGG
EST: gi|211524408|gb|FL405472.1|FL405472
EST:     CAGCACCTTGCCGCCGTCCGTCGATCTGCACCCTTTGCGTGCGTGTCCAG                         GTGGCTGCACACGCCGTCATTCGCGACGGTGTCTCCGCAAGAGGTTTCAGG
genomic: CAGCACCTTGCCGCCGTCCGTCGATCTGCACCCTTTGCGTGCGTGTCCAGgtgatcccgc ... tgatttgcagGTGGCTGCACACGCCGTCATTCGCGACGGTTTCTCCGCAAGAGGTTTCAGG

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), 48 (downstream exon)
Score: 292

AGTGAGGAGCGCACTGAAGCCAGCCGCCGATGAGTCGCCTCCTCTCGCGGCAGCACCTTGCCGCCGTCCGTCGATCTGCACCCTTTGCGTGCGTGTCCAGgtgatcccgc ... tgatttgcagGTGGCTGCACACGCCGTCATTCGCGACGGTTTCTCCGCAAGAGGTTTCAGGTTCCAGCCCAGCGGAAGTGCAGAATTTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 157

AGTGAGGAGCGCACTGAAGCCAGCCGCCGATGAGTCGCCTCCTCTCGCGGCAGCACCTTGCCGCCGTCCGTCGATCTGCACCCTTTGCGTGCGTGTCCAGgtgatcccgc ... tgatttgcagGTGGCTGCACACGCCGTCATTCGCGACGGTTTCTCCGCAAGAGGTTTCAGGTTCCAGCCCAGCGGAAGTGCAGAATTTTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 138

AGTGAGGAGCGCACTGAAGCCAGCCGCCGATGAGTCGCCTCCTCTCGCGGCAGCACCTTGCCGCCGTCCGTCGATCTGCACCCTTTGCGTGCGTGTCCAGgtgatcccgc ... tgatttgcagGTGGCTGCACACGCCGTCATTCGCGACGGTTTCTCCGCAAGAGGTTTCAGGTTCCAGCCCAGCGGAAGTGCAGAATTTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 125

AGTGAGGAGCGCACTGAAGCCAGCCGCCGATGAGTCGCCTCCTCTCGCGGCAGCACCTTGCCGCCGTCCGTCGATCTGCACCCTTTGCGTGCGTGTCCAGgtgatcccgc ... tgatttgcagGTGGCTGCACACGCCGTCATTCGCGACGGTTTCTCCGCAAGAGGTTTCAGGTTCCAGCCCAGCGGAAGTGCAGAATTTTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccgcatttggtgtggatgataagttggcttgggcctgcgcctgattgatttgcagGTGGCTGCACACGCCGTCATTCGCGACGGTTTCTCCGCAAGAGGTTTCAGGTTCCAGCCCAGCGGAAGTGCAGAATTTTG
                                          gattgat  putative branch site (score: 125)
                                           attgattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acagtcgggggagctgtgtgtgtggttactacttactactcgaggccgcatttggtgtggatgataagttggcttgggcctgcgcctgattgatttgcagGTGGCTGCACACGCCGTCATTCGCGACGGTTTCTCCGCAAGAGGTTTCAGGTTCCAGCCCAGCGGAAGTGCAGAATTTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - -ggagctg
- - - - - - - - - - - - - - - - - - - - - - gccgcat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - gtggatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcctgcg