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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCCCGATCACCGCCATACGCGAGATCAAAATCCTGAAGAAGCTTCACCACCAGAACGTTATCAAGCTCAAGGAGATCGTCACCTCCCCAGgtggttacaaccacaagtaaaatgaactagatgtgtattcctactaaccttttttcctctgggctgatgattggatttggggaattgttgcag

Basic information

species Zea mays
transcript GRMZM2G019267_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G019267_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os01g72790.1 (Oryza sativa), 5'ss of exon 3
TTCCCGATCACCGCCATACGCGAGATCAAAATCCTGAAGAAGCTTCACCACCAGAACGTTATCAAGCTCAAGGAGATCGTCACCTCCCCAGgt-ggttaca--accacaagtaaaatgaactagatgtgtattcctactaaccttttttcctctgggctgatgattggatttggggaattgttgcag------
||||| ||||| ||||||||||||||||| ||  |||||||||| |||||||||||||||||| |||||||||||||||||||||| ||||||  ||| ||    | |||| |   |    |     |||||    ||  |     |||       | || | |||| ||||||  | |   |||        
TTCCCCATCACGGCCATACGCGAGATCAAGATTTTGAAGAAGCTCCACCACCAGAACGTTATCCAGCTCAAGGAGATCGTCACCTCTCCAGgttagtttcatcgtcgcaagcacggttggttttg-atgtatcagaaccgagtccattttt-----ggtgctaattgaatttggaaactatatgccttttcag
















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|71766382|gb|DR964319.1|DR964319
EST:     GCTTCACCACCAGAACGTTATCAAGCTCAAGGAGATCGTCACCTCCCCAG                         GCCCAGAGCGGGACGAGCAAGGGAAGCCAA
genomic: GCTTCACCACCAGAACGTTATCAAGCTCAAGGAGATCGTCACCTCCCCAGgtggttacaa ... attgttgcagGCCCAGAGCGGGACGAGCAAGGGAAGCCAA
EST: gi|71774594|gb|DR972472.1|DR972472
EST:     GCTTCACCACCAGAACGTTATCAAGCTCAAGGAGATCGTCACCTCCCCAG                         GCCCAGAGCGGGACGAGCAAGGGAAGCCAA
genomic: GCTTCACCACCAGAACGTTATCAAGCTCAAGGAGATCGTCACCTCCCCAGgtggttacaa ... attgttgcagGCCCAGAGCGGGACGAGCAAGGGAAGCCAA
EST: gi|211438447|gb|FL012009.1|FL012009
EST:     GCTTCACCACCAGAACGTTATCAAGCTCAAGGAGATCGTCACCTCCCCAG                         GCCCAGAGCGGGACGAGCAAGGGAAGCCAA
genomic: GCTTCACCACCAGAACGTTATCAAGCTCAAGGAGATCGTCACCTCCCCAGgtggttacaa ... attgttgcagGCCCAGAGCGGGACGAGCAAGGGAAGCCAA
EST: gi|78078029|gb|DV506444.1|DV506444
EST:     GCTTCACCACCAGAACGTTATCAAGCTCAAGGAGATCGTCACCTCCCCAG                         GCCCAGAGCGGGACGAGCAAGGGAAGCCAA
genomic: GCTTCACCACCAGAACGTTATCAAGCTCAAGGAGATCGTCACCTCCCCAGgtggttacaa ... attgttgcagGCCCAGAGCGGGACGAGCAAGGGAAGCCAA
EST: gi|29130258|gb|CB380962.1|CB380962
EST:     GCTTCACCACCAGAACGTTATCAAGCTCAAGGAGATCGTCACCTCCCCAG                         GCCCAGAGCGGGACGAGCAAGGGAAGCCAA
genomic: GCTTCACCACCAGAACGTTATCAAGCTCAAGGAGATCGTCACCTCCCCAGgtggttacaa ... attgttgcagGCCCAGAGCGGGACGAGCAAGGGAAGCCAA
EST: gi|148938174|gb|EC882457.2|EC882457
EST:     GCTTCACCACCAGAACGTTATCAAGCTCAAGGAGATCGTCACCTCCCCAG                         GCCCAGAGCGGGACGAGCAAGGGAAGCCAA
genomic: GCTTCACCACCAGAACGTTATCAAGCTCAAGGAGATCGTCACCTCCCCAGgtggttacaa ... attgttgcagGCCCAGAGCGGGACGAGCAAGGGAAGCCAA
EST: gi|211438457|gb|FL012019.1|FL012019
EST:     GCTTCACCACCAGAACGTTATCAAGCTCAAGGAGATCGTCACCTCCCCAG                         GCCCAGAGCGGGACGAGCAAGGGAAGCCAA
genomic: GCTTCACCACCAGAACGTTATCAAGCTCAAGGAGATCGTCACCTCCCCAGgtggttacaa ... attgttgcagGCCCAGAGCGGGACGAGCAAGGGAAGCCAA
EST: gi|211435860|gb|FL012004.1|FL012004
EST:     GCTTCACCACCAGAACGTTATCAAGCTCAAGGAGATCGTCACCTCCCCAG                         GCCCAGAGCGGGACGAGCAAGGGAAGCCAA
genomic: GCTTCACCACCAGAACGTTATCAAGCTCAAGGAGATCGTCACCTCCCCAGgtggttacaa ... attgttgcagGCCCAGAGCGGGACGAGCAAGGGAAGCCAA
EST: gi|149107723|gb|EE189597.2|EE189597
EST:     GCTTCACCACCAGAACGTTATCAAGCTCAAGGAGATCGTCACCTCCCCAG                         GCCCAGAGCGGGACGAGCAAGGGAAGCCAA
genomic: GCTTCACCACCAGAACGTTATCAAGCTCAAGGAGATCGTCACCTCCCCAGgtggttacaa ... attgttgcagGCCCAGAGCGGGACGAGCAAGGGAAGCCAA
EST: gi|211438453|gb|FL012015.1|FL012015
EST:     GCTTCACCACCAGAACGTTATCAAGCTCAAGGAGATCGTCACCTCCCCAG                         GCCCAGAGCGGGACGAGCAAGGGAAGCCAA
genomic: GCTTCACCACCAGAACGTTATCAAGCTCAAGGAGATCGTCACCTCCCCAGgtggttacaa ... attgttgcagGCCCAGAGCGGGACGAGCAAGGGAAGCCAA
EST: gi|71430764|gb|DR811814.1|DR811814
EST:     GCTTCACCACCAGAACGTTATCAAGCTCAAGGAGATCGTCACCTCCCCAG                         GCCCAGAGCGGGACGAGCAAGGGAAGCCAA
genomic: GCTTCACCACCAGAACGTTATCAAGCTCAAGGAGATCGTCACCTCCCCAGgtggttacaa ... attgttgcagGCCCAGAGCGGGACGAGCAAGGGAAGCCAA
EST: gi|149099519|gb|EE185557.2|EE185557
EST:     GCTTCACCACCAGAACGTTATCAAGCTCAAGGAGATCGTCACCTCCCCAG                         GCCCAGAGCGGGACGAGCAAGGGAAGCCAA
genomic: GCTTCACCACCAGAACGTTATCAAGCTCAAGGAGATCGTCACCTCCCCAGgtggttacaa ... attgttgcagGCCCAGAGCGGGACGAGCAAGGGAAGCCAA
EST: gi|148946782|gb|EC892051.2|EC892051
EST:     GCTTCACCACCAGAACGTTATCAAGCTCAAGGAGATCGTCACCTCCCCAG                         GCCCAGAGCGGGACGAGCAAGGGAAGCCAA
genomic: GCTTCACCACCAGAACGTTATCAAGCTCAAGGAGATCGTCACCTCCCCAGgtggttacaa ... attgttgcagGCCCAGAGCGGGACGAGCAAGGGAAGCCAA
EST: gi|211438455|gb|FL012017.1|FL012017
EST:     GCTTCACCACCAGAACGTTATCAAGCTCAAGGAGATCGTCACCTCCCCAG                         GCCCAGAGCGGGACGAGCAAGGGAAGCCAA
genomic: GCTTCACCACCAGAACGTTATCAAGCTCAAGGAGATCGTCACCTCCCCAGgtggttacaa ... attgttgcagGCCCAGAGCGGGACGAGCAAGGGAAGCCAA
EST: gi|211438449|gb|FL012011.1|FL012011
EST:     GCTTCACCACCAGAACGTTATCAAGCTCAAGGAGATCGTCACCTCCCCAG                         GCCCAGAGCGGGACGAGCAAGGGAAGCCAA
genomic: GCTTCACCACCAGAACGTTATCAAGCTCAAGGAGATCGTCACCTCCCCAGgtggttacaa ... attgttgcagGCCCAGAGCGGGACGAGCAAGGGAAGCCAA
EST: gi|148942610|gb|EC887630.2|EC887630
EST:     GCTTCACCACCAGAACGTTATCAAGCTCAAGGAGATCGTCACCTCCCCAG                         GCCCAGAGCGGGACGAGCAAGGGAAGCCAA
genomic: GCTTCACCACCAGAACGTTATCAAGCTCAAGGAGATCGTCACCTCCCCAGgtggttacaa ... attgttgcagGCCCAGAGCGGGACGAGCAAGGGAAGCCAA
EST: gi|148962681|gb|EE013583.2|EE013583
EST:     GCTTCACCACCAGAACGTTATCAAGCTCAAGGAGATCGTCACCTCCCCAG                         GCCCAGAGCGGGACGAGCAAGGGAAGCCAA
genomic: GCTTCACCACCAGAACGTTATCAAGCTCAAGGAGATCGTCACCTCCCCAGgtggttacaa ... attgttgcagGCCCAGAGCGGGACGAGCAAGGGAAGCCAA
EST: gi|148969561|gb|EE020392.2|EE020392
EST:     GCTTCACCACCAGAACGTTATCAAGCTCAAGGAGATCGTCACCTCCCCAG                         GCCCAGAGCGGGACGAGCAAGGGAAGCCAA
genomic: GCTTCACCACCAGAACGTTATCAAGCTCAAGGAGATCGTCACCTCCCCAGgtggttacaa ... attgttgcagGCCCAGAGCGGGACGAGCAAGGGAAGCCAA
EST: gi|211002224|gb|FL012020.1|FL012020
EST:     GCTTCACCACCAGAACGTTATCAAGCTCAAGGAGATCGTCACCTCCCCAG                         GCCCAGAGCGGGACGAGCAAGGGAAGCCAA
genomic: GCTTCACCACCAGAACGTTATCAAGCTCAAGGAGATCGTCACCTCCCCAGgtggttacaa ... attgttgcagGCCCAGAGCGGGACGAGCAAGGGAAGCCAA
EST: gi|211438454|gb|FL012016.1|FL012016
EST:     GCTTCACCACCAGAACGTTATCAAGCTCAAGGAGATCGTCACCTCCCCAG                         GCCCAGAGCGGGACGAGCAAGGGAAGCCAA
genomic: GCTTCACCACCAGAACGTTATCAAGCTCAAGGAGATCGTCACCTCCCCAGgtggttacaa ... attgttgcagGCCCAGAGCGGGACGAGCAAGGGAAGCCAA
EST: gi|211435853|gb|FL011997.1|FL011997
EST:     GCTTCACCACCAGAACGTTATCAAGCTCAATGAGATCGTCACCTCCCCAG                         GCCCAGAGCGGGACGAGCAAGGGAAGCCAA
genomic: GCTTCACCACCAGAACGTTATCAAGCTCAAGGAGATCGTCACCTCCCCAGgtggttacaa ... attgttgcagGCCCAGAGCGGGACGAGCAAGGGAAGCCAA
EST: gi|211438448|gb|FL012010.1|FL012010
EST:     GCTTCACCACCAGAACGTTATCAAGCTCAAGGAGATCGTCACCTCCCCAG                         GCCCAGAGCGGGACGAGCAAGGGAAG
genomic: GCTTCACCACCAGAACGTTATCAAGCTCAAGGAGATCGTCACCTCCCCAGgtggttacaa ... attgttgcagGCCCAGAGCGGGACGAGCAAGGGAAG
EST: gi|211438445|gb|FL012007.1|FL012007
EST:     GCTTCACCACCAGAACGTTATCAAGCTCAAGGAGATCGTCACCTCCCCAG                         GCCCAGAGCGGGACGAGCAAGGGAAGCCAA
genomic: GCTTCACCACCAGAACGTTATCAAGCTCAAGGAGATCGTCACCTCCCCAGgtggttacaa ... attgttgcagGCCCAGAGCGGGACGAGCAAGGGAAGCCAA
EST: gi|148954879|gb|EC900358.2|EC900358
EST:     GCTTCACCACCAGAACGTTATCAAGCTCAAGGAGATCGTCACCTCCCCAG                         GCCCAGAGCGGGACGAGCAAGGGAAGCCAA
genomic: GCTTCACCACCAGAACGTTATCAAGCTCAAGGAGATCGTCACCTCCCCAGgtggttacaa ... attgttgcagGCCCAGAGCGGGACGAGCAAGGGAAGCCAA
EST: gi|211438446|gb|FL012008.1|FL012008
EST:     GCTTCACCACCAGAACGTTATCAAGCTCAAGGAGATCGTCACCTCCCCAG                         GCCCAGAGCGGGACGAGCAAGGGAAGCCAA
genomic: GCTTCACCACCAGAACGTTATCAAGCTCAAGGAGATCGTCACCTCCCCAGgtggttacaa ... attgttgcagGCCCAGAGCGGGACGAGCAAGGGAAGCCAA
EST: gi|76914973|gb|DV165773.1|DV165773
EST:     GCTTCACCACCAGAACGTTATCAAGCTCAAGGAGATCGTCACCTCCCCAG                         GCCCAGAGCGGGACGAGCAAGGGAAGCCAA
genomic: GCTTCACCACCAGAACGTTATCAAGCTCAAGGAGATCGTCACCTCCCCAGgtggttacaa ... attgttgcagGCCCAGAGCGGGACGAGCAAGGGAAGCCAA
EST: gi|211438452|gb|FL012014.1|FL012014
EST:     GCTTCACCACCAGAACGTTATCAAGCTCAAGGAGATCGTCACCTCCCCAG                         GCCCAGAGCGGGACGAGCAAGGGAAGCCAA
genomic: GCTTCACCACCAGAACGTTATCAAGCTCAAGGAGATCGTCACCTCCCCAGgtggttacaa ... attgttgcagGCCCAGAGCGGGACGAGCAAGGGAAGCCAA
EST: gi|211438444|gb|FL012006.1|FL012006
EST:     GCTTCACCACCAGAACGTTATCAAGCTCAAGGAGATCGTCACCTCCCCAG                         GCCCAGAGCGGGACGAGCAAGGGAAGCCAA
genomic: GCTTCACCACCAGAACGTTATCAAGCTCAAGGAGATCGTCACCTCCCCAGgtggttacaa ... attgttgcagGCCCAGAGCGGGACGAGCAAGGGAAGCCAA
EST: gi|211435856|gb|FL012000.1|FL012000
EST:     GCTTCACCACCAGAACGTTATCAAGCTCAAGGAGATCGTCACCTCCCCAG                         GCCCAGAGCGGGACGAGCAAGGGAAGCCAA
genomic: GCTTCACCACCAGAACGTTATCAAGCTCAAGGAGATCGTCACCTCCCCAGgtggttacaa ... attgttgcagGCCCAGAGCGGGACGAGCAAGGGAAGCCAA
EST: gi|211435858|gb|FL012002.1|FL012002
EST:     GCTTCACCACCAGAACGTTATCAAGCTCAAGGAGATCGTCACCTCCCCAG                         GCCCAGAGCGGGACGAGCAAGGGAAGCCAA
genomic: GCTTCACCACCAGAACGTTATCAAGCTCAAGGAGATCGTCACCTCCCCAGgtggttacaa ... attgttgcagGCCCAGAGCGGGACGAGCAAGGGAAGCCAA
EST: gi|211002225|gb|FL012021.1|FL012021
EST:     GCTTCACCACCAGAACGTTATCAAGCTCAAGGAGATCGTCACCTCCCCAG                         GCCCAGAGCGGGACGAGCAAGGGAAGCCAA
genomic: GCTTCACCACCAGAACGTTATCAAGCTCAAGGAGATCGTCACCTCCCCAGgtggttacaa ... attgttgcagGCCCAGAGCGGGACGAGCAAGGGAAGCCAA
EST: gi|149087325|gb|EE176860.2|EE176860
EST:     GCTTCACCACCAGAACGTTATCAAGCTCAAGGAGATCGTCACCTCCCCAG                         GCCCAGAGCGGGACGAGCAAGGGAAGCCAA
genomic: GCTTCACCACCAGAACGTTATCAAGCTCAAGGAGATCGTCACCTCCCCAGgtggttacaa ... attgttgcagGCCCAGAGCGGGACGAGCAAGGGAAGCCAA
EST: gi|211435854|gb|FL011998.1|FL011998
EST:     GCTTCACCACCAGAACGTTATCAAGCTCAAGGAGATCGTCACCTCCCCAG                         GCCCAGAGCGGGACGAGCAAGGGAAGCCAA
genomic: GCTTCACCACCAGAACGTTATCAAGCTCAAGGAGATCGTCACCTCCCCAGgtggttacaa ... attgttgcagGCCCAGAGCGGGACGAGCAAGGGAAGCCAA
EST: gi|148955711|gb|EC901398.2|EC901398
EST:     GCTTCACCACCAGAACGTTATCAAGCTCAAGGAGATCGTCACCTCCCCAG                         GCCCAGAGCGGGACGAGCAAGGGAAGCCAA
genomic: GCTTCACCACCAGAACGTTATCAAGCTCAAGGAGATCGTCACCTCCCCAGgtggttacaa ... attgttgcagGCCCAGAGCGGGACGAGCAAGGGAAGCCAA
EST: gi|211438456|gb|FL012018.1|FL012018
EST:     GCTTCACCACCAGAACGTTATCAAGCTCAAGGAGATCGTCACCTCCCCAG                         GCCCAGAGCGGGACGAGCAAGGGAAGCCAA
genomic: GCTTCACCACCAGAACGTTATCAAGCTCAAGGAGATCGTCACCTCCCCAGgtggttacaa ... attgttgcagGCCCAGAGCGGGACGAGCAAGGGAAGCCAA
EST: gi|149106097|gb|EE291761.2|EE291761
EST:     GCTTCACCACCAGAACGTTATCAAGCTCAAGGAGATCGTCACCTCCCCAG                         GCCCAGAGCGGGACGAGCAAGGGAAGCCAA
genomic: GCTTCACCACCAGAACGTTATCAAGCTCAAGGAGATCGTCACCTCCCCAGgtggttacaa ... attgttgcagGCCCAGAGCGGGACGAGCAAGGGAAGCCAA

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), 47 (downstream exon)
Score: 434

TTCCCGATCACCGCCATACGCGAGATCAAAATCCTGAAGAAGCTTCACCACCAGAACGTTATCAAGCTCAAGGAGATCGTCACCTCCCCAGgtggttacaa ... attgttgcagGCCCAGAGCGGGACGAGCAAGGGAAGCCAA


Block sizes: 49 (upstream exon), 40 (downstream exon)
Score: 292

TTCCCGATCACCGCCATACGCGAGATCAAAATCCTGAAGAAGCTTCACCACCAGAACGTTATCAAGCTCAAGGAGATCGTCACCTCCCCAGgtggttacaa ... attgttgcagGCCCAGAGCGGGACGAGCAAGGGAAGCCAA


Block sizes: 49 (upstream exon), 33 (downstream exon)
Score: 255

TTCCCGATCACCGCCATACGCGAGATCAAAATCCTGAAGAAGCTTCACCACCAGAACGTTATCAAGCTCAAGGAGATCGTCACCTCCCCAGgtggttacaa ... attgttgcagGCCCAGAGCGGGACGAGCAAGGGAAGCCAA


Block sizes: 49 (upstream exon), 36 (downstream exon)
Score: 332

TTCCCGATCACCGCCATACGCGAGATCAAAATCCTGAAGAAGCTTCACCACCAGAACGTTATCAAGCTCAAGGAGATCGTCACCTCCCCAGgtggttacaa ... attgttgcagGCCCAGAGCGGGACGAGCAAGGGAAGCCAA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTCCCGATCACCGCCATACGCGAGATCAAAATCCTGAAGAAGCTTCACCACCAGAACGTTATCAAGCTCAAGGAGATCGTCACCTCCCCAGgtggttacaaccacaagtaaaatgaactagatgtgtattcctactaaccttttttcctctgggctgatgattggatttggggaattgttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC