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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGTTAGTGAATATGCTGTAACTGGAAATGATGCTGGCCGAGGAACACTAATAGCTGCTTTAGCTGAAGCTGCATTTCTCATTGGATTAGAAAGGAACAGgtttttgtaacattatttctggtttggctcctgcttgatggtagattgtattgcagacttatctgttttgatttgaaactttttccatgcag

Basic information

species Zea mays
transcript GRMZM2G180889_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G180889_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os03g20420.1 (Oryza sativa), 5'ss of exon 14
TTGTTAGTGAATATGCTGTAACTGGAAATGATGCTGGCCGAGGAACACTAATAGCTGCTTTAGCTGAAGCTGCATTTCTCATTGGATTAGAAAGGAACAGgtttttgtaacattatttctggtttggctcctgcttgatgg--tagattgtattgcagacttatctgttttgatttga-aactttttccatgcag----------
|||||||||||||||| || ||||||||||||||||||||||||||| || |||||||| |||| ||||||||||||||||||||||||||||| ||||||| |||    | |  ||| |||  |  ||   || || |    | |||   |||    || |   |      |||||  ||  ||  | ||  ||          
TTGTTAGTGAATATGCGGTGACTGGAAATGATGCTGGCCGAGGAACATTAGTAGCTGCTCTAGCAGAAGCTGCATTTCTCATTGGATTAGAAAGAAACAGgtctttt--gcctcttttatggcatttctagggcctgttcactttgatgccattttcaacct---taccaaaatttggtaaagttgccaataaagtggctacatt

upper sequence: GRMZM2G180889_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA03G27470.1 (Glycine max), 5'ss of exon 11
---TTGTTAGTGAATATGCTGTAACTGGAAATGATGCTGGCCGAGGAACACTAATAGCTGCTTTAGCTGAAGCTGCATTTCTCATTGGATTAGAAAGGAACAGgttt-ttgtaacattatttctg---gtttggctcctgcttgatggtagattgtattgc---agacttatctg--ttttgatttgaaactttttcc-atgcag
   ||||||||||||||||||| |    || |||||| |     ||||  ||  | |||||| | ||||||||||||||||| |||||| |||||| ||||| ||||  | ||| |  | |||       || | | | | || |||     || | ||||   |  | |||     |||| ||||  |  ||| |   ||||||
TTTTTGTTAGTGAATATGCTGTGA---AAAGTGATGCAGCAAATGGAAATCTCTTGGCTGCTGTGGCTGAAGCTGCATTTCTTATTGGACTAGAAAAGAACAAgtttgctataaaaaaaattcaatgtacttcgtttcagttttatgaagtttttttttgccttaaccgtataaagtttttcatttatatttttctttgatgcag

upper sequence: GRMZM2G180889_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA03G00630.1 (Glycine max), 5'ss of exon 13
TTGTTAGTGAATATGCTGTAACTGGAAATGATGCTGGCCGAGGAACACTAATAGCTGCTTTAGCTGAAGCTGCATTTCTCATTGGATTAGAAAGGAACAGgtt---tttgtaacattatttctggtttggctcctgcttgatgg--tagattgtattgcagacttatctgttttgatttgaaactttttccatgcag---------------
|||||||||| ||||||||        ||||||||||    ||||| ||  | |||||| | ||||||||||||||||| |||||| |||||||||| |||||   ||| ||||   | || |    |   |  |  |  |||   ||| | || | |||   | |  | |  | | |||    | |||| ||                   
TTGTTAGTGAGTATGCTGTTTGGAAGGATGATGCTGGAAATGGAACTCTTCTGGCTGCTGTGGCTGAAGCTGCATTTCTTATTGGACTAGAAAGGAATAGgttggatttataactacaattttccaataaattttattctatgaactagttggtgtagcactttgaattatcataaattgcttatgtttctatttgttgtttttttttacag

upper sequence: GRMZM2G180889_T01 (Zea mays), 5'ss of exon 2
lower sequence: AT3G10740.1 (Arabidopsis thaliana), 5'ss of exon 14
TTGTTAGTGAATATGCTGTAACTGGAAATGATGCTGGCCGAGGAACACTAATAGCTGCTTTAGCTGAAGCTGCATTTCTCATTGGATTAGAAAGGAACAGgtttttgtaacattatttctggtttggctcctgcttgatggtagattgtattgcagacttatctgttttgatttgaaactttttccatgcag
|||| |||||||||||||| |||||||| ||||||||   |||||  ||  | ||  || | || |||||||| |||||||||||  | |||| ||| |||||    |   ||| | |||     ||||      | |    | |   |     |   | | |         ||   ||||||| ||     
TTGTCAGTGAATATGCTGTTACTGGAAAAGATGCTGGTACAGGAAGCCTTCTTGCCTCTCTTGCAGAAGCTGCGTTTCTCATTGGTCTTGAAAAGAATAGgttccctttgaatt-tctcttcccaggctttgatctcaactaaaaacatcaaataagttaaac------atcttatgactttttgcag----

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|32840433|gb|CD980114.1|CD980114
EST:     ATAGCTGCTTTAGCTGAAGCTGCATTTCTCATTGGATTAGAAAGGAACAG                         CGACGTGGTTGAGATGGCAAGTTGTGCTCCACTCCTTGTAAACGACAATGA
genomic: ATAGCTGCTTTAGCTGAAGCTGCATTTCTCATTGGATTAGAAAGGAACAGgtttttgtaa ... ttccatgcagCGACGTGGTTGAGATGGCAAGTTGTGCTCCACTCTTTGTAAACGACAATGA
EST: gi|32841988|gb|CD981669.1|CD981669
EST:     ATAGCTGCTTTAGCTGAAGCTGCATTTCTCATTGGATTAGAAAGGAACAG                         CGACGTGGTTGAGATGGCAAGTTGTGCTCCACTCCTTGTAAACGACAATGA
genomic: ATAGCTGCTTTAGCTGAAGCTGCATTTCTCATTGGATTAGAAAGGAACAGgtttttgtaa ... ttccatgcagCGACGTGGTTGAGATGGCAAGTTGTGCTCCACTCTTTGTAAACGACAATGA
EST: gi|26558128|gb|CA830363.1|CA830363
EST:     ATAGCTGCTTTAGCTGAAGCTGCATTTCTCATTGGATTAGAAAGGAACAG                         CGACGTGGTTGAGATGGCAAGTTGTGCTCCACTCTTTGTAAACGACAATGA
genomic: ATAGCTGCTTTAGCTGAAGCTGCATTTCTCATTGGATTAGAAAGGAACAGgtttttgtaa ... ttccatgcagCGACGTGGTTGAGATGGCAAGTTGTGCTCCACTCTTTGTAAACGACAATGA
EST: gi|21987659|gb|BQ779187.1|BQ779187
EST:     ATAGCTGCTTTAGCTGAAGCTGCATTTCTCATTGGATTAGAAAGGAACAG                         CGACGTGGTTGAGATGGCAAGTTGTGCTCCACTCTTTGTAAACGACAATGA
genomic: ATAGCTGCTTTAGCTGAAGCTGCATTTCTCATTGGATTAGAAAGGAACAGgtttttgtaa ... ttccatgcagCGACGTGGTTGAGATGGCAAGTTGTGCTCCACTCTTTGTAAACGACAATGA
EST: gi|32842541|gb|CD982222.1|CD982222
EST:     ATAGCTGCTTTAGCTGAAGCTGCATTTCTCATTGGATTAGAAAGGAACAG                         CGACGTGGTTGAGATGGCAAGTTGTGCTCCACTCCTTGTAAACGACAATGA
genomic: ATAGCTGCTTTAGCTGAAGCTGCATTTCTCATTGGATTAGAAAGGAACAGgtttttgtaa ... ttccatgcagCGACGTGGTTGAGATGGCAAGTTGTGCTCCACTCTTTGTAAACGACAATGA
EST: gi|32842248|gb|CD981929.1|CD981929
EST:     ATTTCTCATTGGATTAGAAAGGAACAG                         CGACGTGGTTGAGATGGCAAGTTGTGCTCCACTCCTTGTAAACGACAATGA
genomic: ATTTCTCATTGGATTAGAAAGGAACAGgtttttgtaa ... ttccatgcagCGACGTGGTTGAGATGGCAAGTTGTGCTCCACTCTTTGTAAACGACAATGA
EST: gi|32842540|gb|CD982221.1|CD982221
EST:     ATAGCTGCTTTAGCTGAAGCTGCATTTCTCATTGGATTAGAAAGGAACAG                         CGACGTGGTTGAGATGGCAAGTTGTGCTCCACTCCTTGTAACCGACAATGA
genomic: ATAGCTGCTTTAGCTGAAGCTGCATTTCTCATTGGATTAGAAAGGAACAGgtttttgtaa ... ttccatgcagCGACGTGGTTGAGATGGCAAGTTGTGCTCCACTCTTTGTAAACGACAATGA
EST: gi|32842247|gb|CD981928.1|CD981928
EST:     ATAGCTGCTTTAGCTGAAGCTGCATTTCTCATTGGATTAGAAAGGAACAG                         CGACGTGGTTGAGATGGCAAGTTGTGCTCCACTCCTTGTAAACGACAATGA
genomic: ATAGCTGCTTTAGCTGAAGCTGCATTTCTCATTGGATTAGAAAGGAACAGgtttttgtaa ... ttccatgcagCGACGTGGTTGAGATGGCAAGTTGTGCTCCACTCTTTGTAAACGACAATGA
EST: gi|32841989|gb|CD981670.1|CD981670
EST:     TTTCTCATTGGATTAGAAAGGAACAG                         CGACGTGGTTGAGATGGCAAGTTGTGCTCCACTCCTTGTAAACGACAATGA
genomic: TTTCTCATTGGATTAGAAAGGAACAGgtttttgtaa ... ttccatgcagCGACGTGGTTGAGATGGCAAGTTGTGCTCCACTCTTTGTAAACGACAATGA

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), 45 (downstream exon)
Score: 29

TTGTTAGTGAATATGCTGTAACTGGAAATGATGCTGGCCGAGGAACACTAATAGCTGCTTTAGCTGAAGCTGCATTTCTCATTGGATTAGAAAGGAACAGgtttttgtaa ... ttccatgcagCGACGTGGTTGAGATGGCAAGTTGTGCTCCACTCTTTGTAAACGACAATGACCAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 357

TTGTTAGTGAATATGCTGTAACTGGAAATGATGCTGGCCGAGGAACACTAATAGCTGCTTTAGCTGAAGCTGCATTTCTCATTGGATTAGAAAGGAACAGgtttttgtaa ... ttccatgcagCGACGTGGTTGAGATGGCAAGTTGTGCTCCACTCTTTGTAAACGACAATGACCAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 250

TTGTTAGTGAATATGCTGTAACTGGAAATGATGCTGGCCGAGGAACACTAATAGCTGCTTTAGCTGAAGCTGCATTTCTCATTGGATTAGAAAGGAACAGgtttttgtaa ... ttccatgcagCGACGTGGTTGAGATGGCAAGTTGTGCTCCACTCTTTGTAAACGACAATGACCAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 213

TTGTTAGTGAATATGCTGTAACTGGAAATGATGCTGGCCGAGGAACACTAATAGCTGCTTTAGCTGAAGCTGCATTTCTCATTGGATTAGAAAGGAACAGgtttttgtaa ... ttccatgcagCGACGTGGTTGAGATGGCAAGTTGTGCTCCACTCTTTGTAAACGACAATGACCAAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGTTAGTGAATATGCTGTAACTGGAAATGATGCTGGCCGAGGAACACTAATAGCTGCTTTAGCTGAAGCTGCATTTCTCATTGGATTAGAAAGGAACAGgtttttgtaacattatttctggtttggctcctgcttgatggtagattgtattgcagacttatctgttttgatttgaaactttttccatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA