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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tactatatcttactaaggattaaccattgtagtacttgcataaattaaaaatgtttgcttatctcttggtgatcaaatttgagtggttctgtctttgcagGAAAGAAAGGTGCCATTTGATTGGTTACCAGCCAATGGATCCACATTTAAGATCCCAGTATAAGGCCACCCTCAAAGAATCGGTTGGTCCTGCTCCAGTT

Basic information

species Zea mays
transcript GRMZM2G021864_T01
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G021864_T01 (Zea mays), 3'ss of exon 14
lower sequence: LOC_Os10g10190.1 (Oryza sativa), 3'ss of exon 14
-----tactatatcttactaaggattaaccattg-tagtacttgcataaattaaaaatgtttgcttatctcttggtgatcaaatttgagtggttctgtctttgcagGAAAGAAAGGTGCCATTTGATTGGTTACCAGCCAATGGATCCACATTTAAGATCCCAGTATAAGGCCACCCTCAAAGAATCGGTTGGTCCTGCTCCAGTT
     ||| ||    ||  | |  ||||       |||| | ||| |   |  |   ||  ||| |   | ||  | ||      |  ||  |   |  ||||||||||||||| ||| ||||| || |||||||||||| |||||||||| ||||||||||||||||||||  | |||||||| || |    |||||  ||    
gatgttaccatcctgtatcatgtcttaagtgcaaatagtgcatgcct---tggattctgcatgcatccatttttctcattctgcctatgtaat---gcatttgcagGAAAGAAAAGTGTCATTTAATAGGTTACCAGCCAGTGGATCCACAATTAAGATCCCAGTATAAGGCTGCTCTCAAAGATTCAGGGAATCCTGGACCTAAG
















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|78022987|gb|DV491374.1|DV491374
EST:     TTGTTTATTCGGCTAGAAACAAGACTTAGACAAATTATTATTGATTTCTG                         GAAAGAAAGGTGCCATTTGATTGGTTACCAGCCAATGGATCCACATTTAAG
genomic: TTGTTTATTCGGCTAGAAACAAGACTTAGACAAATTATTATTGATTTCTGgtaagtgctt ... gtctttgcagGAAAGAAAGGTGCCATTTGATTGGTTACCAGCCAATGGATCCACATTTAAG
EST: gi|32931903|gb|CF036715.1|CF036715
EST:     TTGTTTATTCGGCTAGAAACAGGACTTAGACAAATTATTATTGATTTCTG                         GAAAGAAAGGTGCCATTTGATTGGTTACCAGCCAATGGATCCACATTTAAG
genomic: TTGTTTATTCGGCTAGAAACAAGACTTAGACAAATTATTATTGATTTCTGgtaagtgctt ... gtctttgcagGAAAGAAAGGTGCCATTTGATTGGTTACCAGCCAATGGATCCACATTTAAG
EST: gi|211458170|gb|FL127582.1|FL127582
EST:     TATTGATTTCTG                         GAAAGAAAGGTGCCATTTGATTGGTTACCAGCCAATGGATCCACATTTAAG
genomic: TATTGATTTCTGgtaagtgctt ... gtctttgcagGAAAGAAAGGTGCCATTTGATTGGTTACCAGCCAATGGATCCACATTTAAG
EST: gi|89758497|gb|DY687658.1|DY687658
EST:     TTGTTTATTCGGCTAGAAACAAGACTTAGACAAATTATTATTGATTTCTG                         GAAAGAAAGGTGCCATTTGATTGGTTACCAGCCAATGGATCCACATTTAAG
genomic: TTGTTTATTCGGCTAGAAACAAGACTTAGACAAATTATTATTGATTTCTGgtaagtgctt ... gtctttgcagGAAAGAAAGGTGCCATTTGATTGGTTACCAGCCAATGGATCCACATTTAAG
EST: gi|211460681|gb|FL127583.1|FL127583
EST:     TTGTTTATTCGGCTAGAAACAAGACTTAGACAAATTATTATTGATTTCTG                         GAAAGAAAGGTGCCATTTGATTGGTTACCAGCCAATGGATCCACATTTAAG
genomic: TTGTTTATTCGGCTAGAAACAAGACTTAGACAAATTATTATTGATTTCTGgtaagtgctt ... gtctttgcagGAAAGAAAGGTGCCATTTGATTGGTTACCAGCCAATGGATCCACATTTAAG
EST: gi|32934210|gb|CF039022.1|CF039022
EST:     TTGTTTATTCGGCTAGAAACAAGACTTAGACAAATTATTATTGATTTCTG                         GAAAGAAAGGTGCCATTTGATTGGTTACCAGCCAATGGATCCACATTTAAG
genomic: TTGTTTATTCGGCTAGAAACAAGACTTAGACAAATTATTATTGATTTCTGgtaagtgctt ... gtctttgcagGAAAGAAAGGTGCCATTTGATTGGTTACCAGCCAATGGATCCACATTTAAG
EST: gi|211404582|gb|FL228991.1|FL228991
EST:     TTGTTTATTCGGCTAGAAACAAGACTTAGACAAATTATTATTGATTTCTG                         GAAAGAAAGGTGCCATTTGATTGGTTAC-AGCCAATGGATCCACATTTAAG
genomic: TTGTTTATTCGGCTAGAAACAAGACTTAGACAAATTATTATTGATTTCTGgtaagtgctt ... gtctttgcagGAAAGAAAGGTGCCATTTGATTGGTTACCAGCCAATGGATCCACATTTAAG
EST: gi|211460682|gb|FL127584.1|FL127584
EST:     TTGTTTATTCGGCTAGAAACAAGACTTAGACAAATTATTATTGATTTCTG                         GAAAGAAAGGTGCCATTTGATTGGTTACCAGCCAATGGATCCACATTTAAG
genomic: TTGTTTATTCGGCTAGAAACAAGACTTAGACAAATTATTATTGATTTCTGgtaagtgctt ... gtctttgcagGAAAGAAAGGTGCCATTTGATTGGTTACCAGCCAATGGATCCACATTTAAG
EST: gi|32930527|gb|CF035339.1|CF035339
EST:     TTGTTTATTCGGCTAGAAACAAGGCTTAGACAAATTACTATTGATTTCTG                         GAAAGAAAGGAGCCATTTGATTGGTTACCAGCCAATGGATCCACATTTAAG
genomic: TTGTTTATTCGGCTAGAAACAAGACTTAGACAAATTATTATTGATTTCTGgtaagtgctt ... gtctttgcagGAAAGAAAGGTGCCATTTGATTGGTTACCAGCCAATGGATCCACATTTAAG
EST: gi|5915604|gb|AW053245.1|AW053245
EST:     TTGTTTATTCGGCTAGAAACAAGACTTAGACAAATTATTATTGATTTCTG                         GAAAGAAAGGTGCCATTTGATTGGTTACCAGCCAATGGATCCACATTTAAG
genomic: TTGTTTATTCGGCTAGAAACAAGACTTAGACAAATTATTATTGATTTCTGgtaagtgctt ... gtctttgcagGAAAGAAAGGTGCCATTTGATTGGTTACCAGCCAATGGATCCACATTTAAG
EST: gi|5361116|gb|AI795731.1|AI795731
EST:     TTGTTTATTCGGCTAGAAACAAGACTTAGACAAATTATTATTGATTTCTG                         GAAAGAAAGGTGCCATTTGATTGGTTACCAGCCAATGGATCCACATTTAAG
genomic: TTGTTTATTCGGCTAGAAACAAGACTTAGACAAATTATTATTGATTTCTGgtaagtgctt ... gtctttgcagGAAAGAAAGGTGCCATTTGATTGGTTACCAGCCAATGGATCCACATTTAAG
EST: gi|211404583|gb|FL228992.1|FL228992
EST:     TTGTTTATTCGGCTAGAAACAAGACTTAGACAAATTATTATTGAYTTCTG                         GAAAGAAAGGTGCCATTTGATTGGTTACCAGCCAATGGATCCACATTTAAG
genomic: TTGTTTATTCGGCTAGAAACAAGACTTAGACAAATTATTATTGATTTCTGgtaagtgctt ... gtctttgcagGAAAGAAAGGTGCCATTTGATTGGTTACCAGCCAATGGATCCACATTTAAG
EST: gi|78106768|gb|DV525186.1|DV525186
EST:     TTGTTTATTCGGCTAGAAACAAGACTTAGACAAATTATTATTGATTTCTG                         GAAAGAAAGGTGCCATTTGATTGGTTACCCGCCAATGGATCCCCATTTAAG
genomic: TTGTTTATTCGGCTAGAAACAAGACTTAGACAAATTATTATTGATTTCTGgtaagtgctt ... gtctttgcagGAAAGAAAGGTGCCATTTGATTGGTTACCAGCCAATGGATCCACATTTAAG
EST: gi|91054831|gb|EB165249.1|EB165249
EST:     TTGTTTATTCGGCTAGAAACAAGACTTAGACAAATTATTATTGATTTCTG                         GAAAGAAAGGTGCCATTTGATTGGTTACCAGCCAATGGATCCACATTTAAG
genomic: TTGTTTATTCGGCTAGAAACAAGACTTAGACAAATTATTATTGATTTCTGgtaagtgctt ... gtctttgcagGAAAGAAAGGTGCCATTTGATTGGTTACCAGCCAATGGATCCACATTTAAG
EST: gi|12968788|gb|BG265825.1|BG265825
EST:     TTGTTTATTCGGCTAGAAACAAGACTTAGACAAATTATTATTGATTTCTG                         GAAAGAAAGGTGCCATTTGATTGGTTACCAGCCAATGGATCCACATTTAAG
genomic: TTGTTTATTCGGCTAGAAACAAGACTTAGACAAATTATTATTGATTTCTGgtaagtgctt ... gtctttgcagGAAAGAAAGGTGCCATTTGATTGGTTACCAGCCAATGGATCCACATTTAAG

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: 76

CAAATTTTATTGAACCAGCACATGACAAACAAGATTTTGAGAGGACACCATTGTTTATTCGGCTAGAAACAAGACTTAGACAAATTATTATTGATTTCTGgtaagtgctt ... gtctttgcagGAAAGAAAGGTGCCATTTGATTGGTTACCAGCCAATGGATCCACATTTAAGATCCCAGTATAAGGCCACCCTCAAAGAATCGGTTGGTCCTGCTCCAGTT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 51

CAAATTTTATTGAACCAGCACATGACAAACAAGATTTTGAGAGGACACCATTGTTTATTCGGCTAGAAACAAGACTTAGACAAATTATTATTGATTTCTGgtaagtgctt ... gtctttgcagGAAAGAAAGGTGCCATTTGATTGGTTACCAGCCAATGGATCCACATTTAAGATCCCAGTATAAGGCCACCCTCAAAGAATCGGTTGGTCCTGCTCCAGTT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 53

CAAATTTTATTGAACCAGCACATGACAAACAAGATTTTGAGAGGACACCATTGTTTATTCGGCTAGAAACAAGACTTAGACAAATTATTATTGATTTCTGgtaagtgctt ... gtctttgcagGAAAGAAAGGTGCCATTTGATTGGTTACCAGCCAATGGATCCACATTTAAGATCCCAGTATAAGGCCACCCTCAAAGAATCGGTTGGTCCTGCTCCAGTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 70

CAAATTTTATTGAACCAGCACATGACAAACAAGATTTTGAGAGGACACCATTGTTTATTCGGCTAGAAACAAGACTTAGACAAATTATTATTGATTTCTGgtaagtgctt ... gtctttgcagGAAAGAAAGGTGCCATTTGATTGGTTACCAGCCAATGGATCCACATTTAAGATCCCAGTATAAGGCCACCCTCAAAGAATCGGTTGGTCCTGCTCCAGTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaaaatgtttgcttatctcttggtgatcaaatttgagtggttctgtctttgcagGAAAGAAAGGTGCCATTTGATTGGTTACCAGCCAATGGATCCACATTTAAGATCCCAGTATAAGGCCACCCTCAAAGAATCGGTTGGTCCTGCTCCAGTT
                                         ttctgtcttt  CT-rich tract
                          atcaaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tactatatcttactaaggattaaccattgtagtacttgcataaattaaaaatgtttgcttatctcttggtgatcaaatttgagtggttctgtctttgcagGAAAGAAAGGTGCCATTTGATTGGTTACCAGCCAATGGATCCACATTTAAGATCCCAGTATAAGGCCACCCTCAAAGAATCGGTTGGTCCTGCTCCAGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - tacttgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gatcaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggttct