Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acatggtttgaagatctagattaacgtggttgaagaaatatggttcactagtataagtaatccattacagaagctatggcttatgtagctaatgaaacagGGAGTTTAAGGAGAAGAACAAAGTGGACAAGATAGTTGTGTTGTGGACTGCAAACACTGAAAGGTATAGCAATGTGTGCGCTGGTCTCAACGACACGATG

Basic information

species Zea mays
transcript GRMZM2G155242_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G155242_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os03g09250.2 (Oryza sativa), 3'ss of exon 4
acatggtttgaagatctagattaacgtggttgaagaaatatggttcactagta--taagtaatccatta-cagaagctatggc--ttatgtagctaatgaaacagGGAGTTTAAGGAGAAGAACAAAGTGGACAAGATAGTTGTGTTGTGGACTGCAAACACTGAAAGGTATAGCAATGTGTGCGCTGGTCTCAACGACACGATG
   | |||  |   |||  |||||  |||||| |  || |||    ||| ||   || | |  |  | | ||  ||  |||    || | |   || | ||| |||||||| ||||| |||| ||||||||||||| | || ||||||||||||||||||||||||||||| |||||||| || | ||| ||||| ||||| |||
---tagttccag--tctgcattaagatggttggaacaacatgacaaacttgtgactatgaatgctgtaaacattagacatgatattttttttattacttaaatagGGAGTTCAAGGAAAAGAGCAAAGTGGACAAGGTGGTGGTGTTGTGGACTGCAAACACTGAAAGGTACAGCAATGTCTGTGTTGGGCTCAATGACACAATG

upper sequence: GRMZM2G155242_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA18G02210.2 (Glycine max), 3'ss of exon 4
--acatggtttgaagatctagattaacgtggttgaagaaatatggttcactagtataagtaatccattacagaagctatggcttatgtagctaatgaaacagGGAGTTTAAGGAGAAGAACAAAGTGGACAAGATAGTTGTGTTGTGGACTGCAAACACTGAAAGGTATAGCAATGTGTGCGCTGGTCTCAACGACACGATG
  | |||   |    || |  ||  || |   |  | | |||      ||    || |    |   |||   | | | |  ||   || |  |   |  ||||| |||||||||    | ||||||||||||| | |||||  |||||||||| ||||| || |||||||||||| ||   |  || || || ||||| |||
gtatatgtcct----atttcaatctacatacatacatacataca---tacatacatgatctgtatcttattcaggttctaact---gttgacatgaactcagGGCGTTTAAGGAAGCCACCAAAGTGGACAAGGTGGTTGTCCTGTGGACTGCCAACACAGAGAGGTATAGCAATTTGGTTGTAGGCCTTAATGACACCATG

upper sequence: GRMZM2G155242_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT2G22240.1 (Arabidopsis thaliana), 3'ss of exon 3
acatggtttgaagatctagattaacgtggttgaagaaatatggt-tcac-tagtataagtaatccattacagaagctatggct-tatgtagctaatgaaacagGGAGTTTAAGGAGAAGAACAAAGTGGACAAGATAGTTGTGTTGTGGACTGCAAACACTGAAAGGTATAGCAATGTGTGCGCTGGTCTCAACGACACGATG
                                     |||| || | || ||| | || || |   |||   |   ||| | | | | |   || |     ||||||||||||||||||||||||||||| ||| | |||||||| |||||||||||||| ||  | ||||||||||||   |  || || ||||| |||| |
-----------------------------------gtatatagtcttacatagcaaaattagttagttagttagtgtattgatgtgtttgaatattt--ttagGGAGTTTAAGGAGAAGAACAAAGTGGATAAGTTGGTTGTGTTATGGACTGCAAACACAGAGCGTTATAGCAATGTGATTGTAGGACTTAACGATACGACG

upper sequence: GRMZM2G155242_T01 (Zea mays), 3'ss of exon 4
lower sequence: PP1S267_10V6.1 (Physcomitrella patens), 3'ss of exon 4
-----------------aca-tggtttgaagatctagattaacgtggttgaagaaatatggttcactagtataagtaatccattacagaagctatggcttatgtagctaatgaaacagGGAGTTTAAGGAGAAGAACAAAGTGGACAAGATAGTTGTGTTGTGGACTGCAAACACTGAAAGGTATAGCAATGTGTGCGCTGGTCTCAACGACACGATG
                 | | |  ||   ||  ||| |     ||   |  |||  || ||   | |  |   |   || | ||    | |||  ||   |   |  |       |||||| |||||||   ||||||| ||||||||||| |||||| |||||||||| ||||| ||| | || ||  |||||  || ||||||||| ||||||| |
gtagggcgtccgattctatacttcttccgagccctacagcc-tgtttctagagagttacggaa-attgatcgcatcgatgcgtt-tgaatgctgaggtcaaaaca-ttgtgattgcagGGACTTTAAGGCTCAGAACAAGGTGGACAAGATCGTTGTGCTGTGGACTGCTAACACCGAACGATACAGTGATGTGATCGTTGGTCTCAATGACACGAAG

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|149095755|gb|EE181394.2|EE181394
EST:     ATCAAGGGCACCAAGAAAGAACAGGTGGAGCAGATCATCAAGGATATCAG                         GGAGTTTAAGGAGAAGAACAAAGTGGACAAGATAGTTGTGTTGTGGACTGC
genomic: ATCAAGGGCACCAAGAAAGAACAGGTGGAGCAGATCATCAAGGATATCAGgtatatggat ... aatgaaacagGGAGTTTAAGGAGAAGAACAAAGTGGACAAGATAGTTGTGTTGTGGACTGC
EST: gi|32908546|gb|CF013359.1|CF013359
EST:     GGTGGAGCAGATCATCAAGGATATCAG                         GGAGTTTAAGGAGAAGAACAAAGTGGACAAGATAGTTGTGTTGTGGACTGC
genomic: GGTGGAGCAGATCATCAAGGATATCAGgtatatggat ... aatgaaacagGGAGTTTAAGGAGAAGAACAAAGTGGACAAGATAGTTGTGTTGTGGACTGC
EST: gi|31353688|gb|CD438045.1|CD438045
EST:     ATCAAGGGCACCAAGAAAGAACAGGTGGAGCAGATCATCAAGGATATCAG                         GGAGTTTAAGGAGAAGAACAAAGTGGACAAGATAGTTGTGTTGTGGACTGC
genomic: ATCAAGGGCACCAAGAAAGAACAGGTGGAGCAGATCATCAAGGATATCAGgtatatggat ... aatgaaacagGGAGTTTAAGGAGAAGAACAAAGTGGACAAGATAGTTGTGTTGTGGACTGC
EST: gi|31349014|gb|CD433371.1|CD433371
EST:     ATCAAGGGCACCAAGAAAGAACAGGTGGAGCAGATCATCAAGGATATCAG                         GGAGTTTAAGGAGAAGAACAAAGTGGACAAGATAGTTGTGTTGTGGACTGC
genomic: ATCAAGGGCACCAAGAAAGAACAGGTGGAGCAGATCATCAAGGATATCAGgtatatggat ... aatgaaacagGGAGTTTAAGGAGAAGAACAAAGTGGACAAGATAGTTGTGTTGTGGACTGC
EST: gi|211029042|gb|FL245288.1|FL245288
EST:     CAAGGATATTAG                         GGAGTTTAAGGAGAAGAACAAAGTGGACAAGATAGTTGTGTTGTGGACTGC
genomic: CAAGGATATCAGgtatatggat ... aatgaaacagGGAGTTTAAGGAGAAGAACAAAGTGGACAAGATAGTTGTGTTGTGGACTGC
EST: gi|211037207|gb|FK948216.1|FK948216
EST:     ATCAAGGGCACCAAGAAAGAACAGGTGGAGCAGATCATCAAGGATATCAG                         GGAGTTTAAGGAGAAGAACAAAGTGGACAAGATAGTTGTGTTGTGGACTGC
genomic: ATCAAGGGCACCAAGAAAGAACAGGTGGAGCAGATCATCAAGGATATCAGgtatatggat ... aatgaaacagGGAGTTTAAGGAGAAGAACAAAGTGGACAAGATAGTTGTGTTGTGGACTGC
EST: gi|4776520|gb|AI665523.1|AI665523
EST:     ATCAAGGGCACCAAGAAAGAACAGGTGGAGCAGATCATCAAGGATATCAG                         GGAGTTTAAGGAGAAGAACAAAGTGGACAAGATAGTTGTGTTGTGGACTGC
genomic: ATCAAGGGCACCAAGAAAGAACAGGTGGAGCAGATCATCAAGGATATCAGgtatatggat ... aatgaaacagGGAGTTTAAGGAGAAGAACAAAGTGGACAAGATAGTTGTGTTGTGGACTGC
EST: gi|6536588|gb|AW224901.1|AW224901
EST:     AGGTGGAGCAGATCATCAAGGATATCAG                         GGAGTTTAAGGAGAAGAACAAAGTGGACAAGATAGTTGTGTTGTGGACTGC
genomic: AGGTGGAGCAGATCATCAAGGATATCAGgtatatggat ... aatgaaacagGGAGTTTAAGGAGAAGAACAAAGTGGACAAGATAGTTGTGTTGTGGACTGC
EST: gi|149103373|gb|EE288760.2|EE288760
EST:     ATCAAGGGCACCAAGAAAGAACAGGTGGAGCAGATCATCAAGGATATCAG                         GGAGTTTAAGGA
genomic: ATCAAGGGCACCAAGAAAGAACAGGTGGAGCAGATCATCAAGGATATCAGgtatatggat ... aatgaaacagGGAGTTTAAGGA

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: 48 (upstream exon), 49 (downstream exon)
Score: 504

ATGATCCGGACTTCATCGCGGCTAACCAGGGCTCTCGCGCCAACAGTGTCATCAAGGGCACCAAGAAAGAACAGGTGGAGCAGATCATCAAGGATATCAGgtatatggat ... aatgaaacagGGAGTTTAAGGAGAAGAACAAAGTGGACAAGATAGTTGTGTTGTGGACTGCAAACACTGAAAGGTATAGCAATGTGTGCGCTGGTCTCAACGACACGATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 42

ATGATCCGGACTTCATCGCGGCTAACCAGGGCTCTCGCGCCAACAGTGTCATCAAGGGCACCAAGAAAGAACAGGTGGAGCAGATCATCAAGGATATCAGgtatatggat ... aatgaaacagGGAGTTTAAGGAGAAGAACAAAGTGGACAAGATAGTTGTGTTGTGGACTGCAAACACTGAAAGGTATAGCAATGTGTGCGCTGGTCTCAACGACACGATG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 21

ATGATCCGGACTTCATCGCGGCTAACCAGGGCTCTCGCGCCAACAGTGTCATCAAGGGCACCAAGAAAGAACAGGTGGAGCAGATCATCAAGGATATCAGgtatatggat ... aatgaaacagGGAGTTTAAGGAGAAGAACAAAGTGGACAAGATAGTTGTGTTGTGGACTGCAAACACTGAAAGGTATAGCAATGTGTGCGCTGGTCTCAACGACACGATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 194

ATGATCCGGACTTCATCGCGGCTAACCAGGGCTCTCGCGCCAACAGTGTCATCAAGGGCACCAAGAAAGAACAGGTGGAGCAGATCATCAAGGATATCAGgtatatggat ... aatgaaacagGGAGTTTAAGGAGAAGAACAAAGTGGACAAGATAGTTGTGTTGTGGACTGCAAACACTGAAAGGTATAGCAATGTGTGCGCTGGTCTCAACGACACGATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cactagtataagtaatccattacagaagctatggcttatgtagctaatgaaacagGGAGTTTAAGGAGAAGAACAAAGTGGACAAGATAGTTGTGTTGTGGACTGCAAACACTGAAAGGTATAGCAATGTGTGCGCTGGTCTCAACGACACGATG
                                         agctaat  putative branch site (score: 194)
      tataagtaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acatggtttgaagatctagattaacgtggttgaagaaatatggttcactagtataagtaatccattacagaagctatggcttatgtagctaatgaaacagGGAGTTTAAGGAGAAGAACAAAGTGGACAAGATAGTTGTGTTGTGGACTGCAAACACTGAAAGGTATAGCAATGTGTGCGCTGGTCTCAACGACACGATG

- - - - - - - - - - - - -gtggttg
- - - - - - - - - - - - - - - - aagaaata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cagaagc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcttatg