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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGTTTCTATCTAGCTGGTGATTACACAAAGCAGAAATACCTGGCTTCCATGGAAGGTGCAGTCCTATCCGGGAAGCTTTGCGCCCAGTCCATTGTGCAGgtaaataaatatactcaccgtggtcctggttgtgcataaaagcatcagatttctgtgttgttggatttatttcggtatgatacatgttttgcagctaatgaattaacatttactgcttccag

Basic information

species Zea mays
transcript GRMZM2G410515_T01
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G410515_T01 (Zea mays), 5'ss of exon 14
lower sequence: LOC_Os03g08570.1 (Oryza sativa), 5'ss of exon 14
AGGTTTCTATCTAGCTGGTGATTACACAAAGCAGAAATACCTGGCTTCCATGGAAGGTGCAGTCCTATCCGGGAAGCTTTGCGCCCAGTCCATTGTGCAGgtaaataaatatactcaccgtggtcctggttgtgcataaaagcatcagatttctgt-gttgt-tggatttatttcggtatgatacatgttttgcag-ctaatgaattaacatttactgcttccag
||| ||||||||||||||||| |||||||||||||||||  ||||||| ||||| |||||||| ||||| ||||||||||| || |||||  | ||| |||||||      | ||| || |||| ||| |||| |||| | |||||||| || | | ||||| | | |  | |||   ||||| || |||||| || ||||||| ||| || || ||| || |||
AGGGTTCTATCTAGCTGGTGACTACACAAAGCAGAAATATTTGGCTTCGATGGAGGGTGCAGTTCTATCTGGGAAGCTTTGTGCTCAGTCTGTAGTGGAGgtaaacgc---tgctctccatggttctgtttgtacatagatgcatcagacttgtattgttgtcttggtgcagttcacaatgattca-gttttgtaggctaatgagttatcacttgctgatttcag

upper sequence: GRMZM2G410515_T01 (Zea mays), 5'ss of exon 14
lower sequence: GLYMA11G36810.1 (Glycine max), 5'ss of exon 13
AGGTTTCTATCTAGCTGGTGATTACACAAAGCAGAAATACCTGGCTTCCATGGAAGGTGCAGTCCTATCCGGGAAGCTTTGCGCCCAGTCCATTGTGCAGgtaaataaatatactcaccgtggtcctggttgtgcataaaagcatcagatttctgtgttgttggatttatttcggtatgatacatgttttgcagctaatgaattaacatttactgcttccag
|||||||||| ||||||| ||||||||||| || |||||  | ||||| |||||||| || || || || ||||||||||| || ||| | ||||| |||||||| |  | | | ||      ||   ||    ||   |  ||| ||       |||  ||   | ||| |   |    |    ||| |   |  |  |||                    
AGGTTTCTATTTAGCTGGAGATTACACAAAACAAAAATATTTAGCTTCAATGGAAGGCGCTGTTCTTTCTGGGAAGCTTTGTGCACAGGCTATTGTACAGgtaaa-atctgt-cacaaaaatatctatgtaactcagcgattcattagcaagaaatgtgattatctatatataaatgctttcttagttattttgtgagagaa--------------------

upper sequence: GRMZM2G410515_T01 (Zea mays), 5'ss of exon 14
lower sequence: GLYMA18G00720.1 (Glycine max), 5'ss of exon 13
AGGTTTCTATCTAGCTGGTGATTACACAAAGCAGAAATACCTGGCTTCCATGGAAGGTGCAGTCCTATCCGGGAAGCTTTGCGCCCAGTCCATTGTGCAGgtaaataaatatactcaccgtggtcctggttgtgcataaaagcatcagatttctgtgttgttggatttatttcggtatgatacatgttttgcagctaatgaattaacatttactgcttccag
|||||||||| ||||||| ||||||||||| || |||||  | ||||| |||||||| || || || || ||||||||||| || ||| | ||||| ||||||||  |    || ||      ||   ||    |  |   |||  | |||     |   |  |||     ||  ||| ||||||| |||   | ||||    | | |              
AGGTTTCTATTTAGCTGGAGATTACACAAAACAAAAATATTTAGCTTCAATGGAAGGCGCTGTTCTTTCTGGGAAGCTTTGTGCACAGGCTATTGTACAGgtaaa--atctgacacaaaaatatctatgtaactcgca---gcaatacattagcaagaaatgtgat---aatctatat-atacatgctttcttggtaattttgtgagag-------------

upper sequence: GRMZM2G410515_T01 (Zea mays), 5'ss of exon 14
lower sequence: AT4G14210.2 (Arabidopsis thaliana), 5'ss of exon 14
AGGTTTCTATCTAGCTGGTGATTACACAAAGCAGAAATACCTGGCTTCCATGGAAGGTGCAGTCCTATCCGGGAAGCTTTGCGCCCAGTCCATTGTGCAGgtaaataaatatactcaccgtggtcctggttgtgcataaaagcatcagatttctgtgttgttggatt-tatt-tcggtatgatacatgttttgcagctaatgaattaacatt-tactgcttccag--------------------------------------------
||| |||||  ||||||| ||||||||||| ||||| ||| | |||||||||||||| || ||||| || || ||  | ||| | ||||| ||||| |||||||| |   |  ||  || |     | |||   ||   || | |    | | | | |||||||| | |||   |  ||        ||||  | | |  ||  | |  ||| ||||| |||| |                                            
AGGATTCTACTTAGCTGGAGATTACACAAAACAGAAGTACTTAGCTTCCATGGAAGGCGCTGTCCTCTCTGGCAAATTCTGCTCTCAGTCTATTGTTCAGgtaaaca--caagcttgccattcaaatagttaacca-gtaaccttgttctctgtttcttgttggaatatatcgccaataaccggtcggtttacctgattttgtctcactattatactg-ttccggttatgtagagaaattgctaaagtcagaatttactggttatacag

upper sequence: GRMZM2G410515_T01 (Zea mays), 5'ss of exon 14
lower sequence: Vv09s0002g00100.t01 (Vitis vinifera), 5'ss of exon 14
AGGTTTCTATCTAGCTGGTGATTACACAAAGCAGAAATACCTGGCTTCCATGGAAGGTGCAGTCCTATCCGGGAAGCTTTGCGCCCAGTCCATTGTGCAGgtaaataaatatactcaccgtggtcctggttgtgcataaaagcatcagatttctgtgttgttggatttatttcggtatgatacatgttttgcagctaatgaattaacatttactgcttccag--
 || || ||| ||||||| || |||||||| || |||||| | ||||| ||||||||||| || || || ||||||||||| || ||| | |||||  ||||||       | | ||| |     ||        |||   |||||| |||| |   | |||  |           |  |  |||  ||  | | | | || |  || |||| |  || ||   
GGGCTTTTATTTAGCTGGGGACTACACAAAACAAAAATACTTAGCTTCAATGGAAGGTGCTGTTCTGTCAGGGAAGCTTTGTGCACAGGCTATTGTAAAGgtaac------ttcccacaggaagact-----ccaatatttgcatcaaatttgtac-tggttaaa-----------aaaagtcatacttctctgatga-gagtatacttttattattttcaaac

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|211500355|gb|FL431278.1|FL431278
EST:     TGGAAGGTGCAGTCTTATCCGGGAAGCTTTGCGCCCAGTCCATAGTGCAG                         GATTATAGCAGGCTCGCACTCAGGAGCCAGAAAAGCCTACAATCAGGAGAA
genomic: TGGAAGGTGCAGTCCTATCCGGGAAGCTTTGCGCCCAGTCCATTGTGCAGgtaaataaat ... ctgcttccagGATTATAGCAGGCTCACACTCAGGAGCCAGAAAAGCCTACAATCAGGAGAA
EST: gi|4680986|gb|AI629656.1|AI629656
EST:     GTCCTATCCGGGAAGCTTTGCGCCCAGTCCATTGTGCAG                         GATTATAGCAGGCTCACACTCAGGAGCCAGAAAAGCCTACAATCAGGAGAA
genomic: GTCCTATCCGGGAAGCTTTGCGCCCAGTCCATTGTGCAGgtaaataaat ... ctgcttccagGATTATAGCAGGCTCACACTCAGGAGCCAGAAAAGCCTACAATCAGGAGAA
EST: gi|13515793|gb|BG518069.1|BG518069
EST:     TGGAAGGTGCAGTCCTATCCGGGAAGCTTTGCGCCCAGTCCATTGTGCAG                         GATTATAGCAGGCTCACACTCAGGAGCCAGAAAAGCCTACAATCAGGAGAA
genomic: TGGAAGGTGCAGTCCTATCCGGGAAGCTTTGCGCCCAGTCCATTGTGCAGgtaaataaat ... ctgcttccagGATTATAGCAGGCTCACACTCAGGAGCCAGAAAAGCCTACAATCAGGAGAA
EST: gi|16379611|gb|BI993047.1|BI993047
EST:     TGGAAGGTGCAGTCCTATCCGGGAAGCTTTGCGCCCAGTCCATTGTGCAG                         GATTATAGCAGGCTCACACTCAGGAGCCAGAAAAGCCTACAATCAGGAGAA
genomic: TGGAAGGTGCAGTCCTATCCGGGAAGCTTTGCGCCCAGTCCATTGTGCAGgtaaataaat ... ctgcttccagGATTATAGCAGGCTCACACTCAGGAGCCAGAAAAGCCTACAATCAGGAGAA
EST: gi|6031292|gb|AW076149.1|AW076149
EST:     TGGAAGGTGCAGTCCTATCCGGGAAGCTTTGTGCCCAGTCCATAGTGCAG                         GATTATAGCAGGCTCGCACTCAGGAGCCAGAAAAGCCTACAATCAGGAGAA
genomic: TGGAAGGTGCAGTCCTATCCGGGAAGCTTTGCGCCCAGTCCATTGTGCAGgtaaataaat ... ctgcttccagGATTATAGCAGGCTCACACTCAGGAGCCAGAAAAGCCTACAATCAGGAGAA
EST: gi|113704041|gb|EE681545.1|EE681545
EST:     TGGAAGGTGCAGTCTTATCCGGGAAGCTTTGCGCCCAGTCCATAGTGCAG                         GATTATAGCAGGCTCGCACTCAGGAGCCAGAAAAGCCTACAATCAGGAGAA
genomic: TGGAAGGTGCAGTCCTATCCGGGAAGCTTTGCGCCCAGTCCATTGTGCAGgtaaataaat ... ctgcttccagGATTATAGCAGGCTCACACTCAGGAGCCAGAAAAGCCTACAATCAGGAGAA
EST: gi|17930938|gb|BM267898.1|BM267898
EST:     TGGAAGGTGCAGTCCTATCCGGGAAGCTTTGCGCCCAGTCCATTGTGCAG                         GATTATAGCAGGCTCACACTCAGGAGCCAGAAAAGCCTACAATCAGGAGAA
genomic: TGGAAGGTGCAGTCCTATCCGGGAAGCTTTGCGCCCAGTCCATTGTGCAGgtaaataaat ... ctgcttccagGATTATAGCAGGCTCACACTCAGGAGCCAGAAAAGCCTACAATCAGGAGAA
EST: gi|4573270|gb|AI586829.1|AI586829
EST:     TGGAAGGTGCAGTCCTATCCGGGAAGCTTTGCGCCCAGTCCATTGTGCAG                         GATTATAGCAGGCTCACACTCAGGAGCCAGAAAAGCCTACAATCAGGAGAA
genomic: TGGAAGGTGCAGTCCTATCCGGGAAGCTTTGCGCCCAGTCCATTGTGCAGgtaaataaat ... ctgcttccagGATTATAGCAGGCTCACACTCAGGAGCCAGAAAAGCCTACAATCAGGAGAA
EST: gi|211500354|gb|FL431277.1|FL431277
EST:     TGGAAGGTGCAGTCTTATCCGGGAAGCTTTGCGCCCAGTCCATAGTGCAG                         GATTATAGCAGGCTCGCACTCAGGAGCCAGAAAAGCCTACAATCAGGAGAA
genomic: TGGAAGGTGCAGTCCTATCCGGGAAGCTTTGCGCCCAGTCCATTGTGCAGgtaaataaat ... ctgcttccagGATTATAGCAGGCTCACACTCAGGAGCCAGAAAAGCCTACAATCAGGAGAA
EST: gi|89248324|gb|DY620110.1|DY620110
EST:     TGGAAGGTGCAGTCCTATCCGGGAAGCTTTGCGCCCAGTCCATTGTGCAG                         GATTATAGCAGGCTCACACTCAGGAGCCAGAAAAGCCTACAATCAGGAGAA
genomic: TGGAAGGTGCAGTCCTATCCGGGAAGCTTTGCGCCCAGTCCATTGTGCAGgtaaataaat ... ctgcttccagGATTATAGCAGGCTCACACTCAGGAGCCAGAAAAGCCTACAATCAGGAGAA
EST: gi|4573271|gb|AI586830.1|AI586830
EST:     TGGAAGGTGCAGTCCTATCCGGGAAGCTTTGCGCCCAGTCCATTGTGCAG                         GATTATAGCAGGCTCACACTCAGGAGCCAGAAAAGCCTACAATCAGGAGAA
genomic: TGGAAGGTGCAGTCCTATCCGGGAAGCTTTGCGCCCAGTCCATTGTGCAGgtaaataaat ... ctgcttccagGATTATAGCAGGCTCACACTCAGGAGCCAGAAAAGCCTACAATCAGGAGAA
EST: gi|71765382|gb|DR963319.1|DR963319
EST:     TGGAAGGTGCAGTCCTATCCGGGAAGCTTTGCGCCCAGTCCATTGTGCAG                         GATTATAGCAGGCTCACACTCAGGAGCCAGAAAAGCCTACAATCAGGAGAA
genomic: TGGAAGGTGCAGTCCTATCCGGGAAGCTTTGCGCCCAGTCCATTGTGCAGgtaaataaat ... ctgcttccagGATTATAGCAGGCTCACACTCAGGAGCCAGAAAAGCCTACAATCAGGAGAA
EST: gi|92087932|gb|EB484163.1|EB484163
EST:     GGAAGGTGCAGTCCTATCCGGGAAGCTTTGTGCCCAGTCCATAGTGCAG                         GATTATAGCAGGCTCGCACTCAGGAGCCAGAAAAGCCTACAATCAGGAGAA
genomic: GGAAGGTGCAGTCCTATCCGGGAAGCTTTGCGCCCAGTCCATTGTGCAGgtaaataaat ... ctgcttccagGATTATAGCAGGCTCACACTCAGGAGCCAGAAAAGCCTACAATCAGGAGAA
EST: gi|5871340|gb|AW017811.1|AW017811
EST:     TGGAAGGTGCAGTCCTATCCGGGAAGCTTTGTGCCCAGTCCATAGTGCAG                         GATTATAGCAGGCTCGCACTCAGGAGCCAGAAAAGCCTACAATCAGGAGAA
genomic: TGGAAGGTGCAGTCCTATCCGGGAAGCTTTGCGCCCAGTCCATTGTGCAGgtaaataaat ... ctgcttccagGATTATAGCAGGCTCACACTCAGGAGCCAGAAAAGCCTACAATCAGGAGAA

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: 18

AGGTTTCTATCTAGCTGGTGATTACACAAAGCAGAAATACCTGGCTTCCATGGAAGGTGCAGTCCTATCCGGGAAGCTTTGCGCCCAGTCCATTGTGCAGgtaaataaat ... ctgcttccagGATTATAGCAGGCTCACACTCAGGAGCCAGAAAAGCCTACAATCAGGAGAAGTTCCCGTCCCATCTTAGTTGTAGTTGGCTTTAGCTATCGTCATCCCCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 103

AGGTTTCTATCTAGCTGGTGATTACACAAAGCAGAAATACCTGGCTTCCATGGAAGGTGCAGTCCTATCCGGGAAGCTTTGCGCCCAGTCCATTGTGCAGgtaaataaat ... ctgcttccagGATTATAGCAGGCTCACACTCAGGAGCCAGAAAAGCCTACAATCAGGAGAAGTTCCCGTCCCATCTTAGTTGTAGTTGGCTTTAGCTATCGTCATCCCCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 69

AGGTTTCTATCTAGCTGGTGATTACACAAAGCAGAAATACCTGGCTTCCATGGAAGGTGCAGTCCTATCCGGGAAGCTTTGCGCCCAGTCCATTGTGCAGgtaaataaat ... ctgcttccagGATTATAGCAGGCTCACACTCAGGAGCCAGAAAAGCCTACAATCAGGAGAAGTTCCCGTCCCATCTTAGTTGTAGTTGGCTTTAGCTATCGTCATCCCCA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 37

AGGTTTCTATCTAGCTGGTGATTACACAAAGCAGAAATACCTGGCTTCCATGGAAGGTGCAGTCCTATCCGGGAAGCTTTGCGCCCAGTCCATTGTGCAGgtaaataaat ... ctgcttccagGATTATAGCAGGCTCACACTCAGGAGCCAGAAAAGCCTACAATCAGGAGAAGTTCCCGTCCCATCTTAGTTGTAGTTGGCTTTAGCTATCGTCATCCCCA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGGTTTCTATCTAGCTGGTGATTACACAAAGCAGAAATACCTGGCTTCCATGGAAGGTGCAGTCCTATCCGGGAAGCTTTGCGCCCAGTCCATTGTGCAGgtaaataaatatactcaccgtggtcctggttgtgcataaaagcatcagatttctgtgttgttggatttatttcggtatgatacatgttttgcagctaatgaattaacatttactgcttccag

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