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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctcactgtagtgtttgatattacaagccgatttctcattccatccctcagctccataactagagagtaatgatggtaacagatcttattctctttgcagACATGCTATTCAATTGATATCACCTGCCAGCGTGGTCTCAAAGACTAATGGAAGAGAGAAAATCTGCAAG

Basic information

species Zea mays
transcript GRMZM2G018697_T02
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G018697_T02 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os01g62040.2 (Oryza sativa), 3'ss of exon 9
tctcactgtagtgtttgatattacaagccgatttctcattccatccctcagctccataactagagagtaatgatggtaa-------cagatcttattctctttgcagACATGCTATTCAATTGATATCACCTGCCAGCGTGGTCTCAAAGACTAATGGAAGAGAGAAAATCTGCAAG
       |    |   | | ||||   ||  ||||    | |  |  | |||    | | | |||| |  |  || | |        | |||||       |||||| |||||||||||  || |||||||||||||||| ||  ||||| ||||||| ||||| || ||| |||||
-------gagtggaccggtcttaccttccagtttcagtgttctactataagcatttttaattgagattgctactgatgaacgactgtatatcttgaatctcttgcagGCATGCTATTCAGCTGCTATCACCTGCCAGCGTAGTTGCAAAGGCTAATGGGAGAGAAAAGATCAGCAAG

upper sequence: GRMZM2G018697_T02 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os07g08170.1 (Oryza sativa), 3'ss of exon 10
--tctcactgtagtg--tttgatattacaagccgatttctcattccatccctcagctccataactagagagtaatgatggtaacagatcttattctctttgcagACATGCTATTCAATTGATATCACCTGCCAGCGTGGTCTCAAAGACTAATGGAAGAGAGAAAATCTGCAAG
  | | | | | ||   |||  | ||| || |      |||||   |   || ||     || | | |||  || ||| |||||| || ||        || || ||||||||||| ||| ||||||| ||||| || ||  ||||| ||||||| |||||||| ||| |||||
attttaaattttgtagttttagttttataaccaccaagctcatctta---ctgaggcagctagcga-agatgaacgattgtaacacatgttgaatctcatgtagGCATGCTATTCAGTTGCTATCACCCGCCAGTGTAGTTGCAAAGGCTAATGGGAGAGAGAAGATCAGCAAG
















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|149086326|gb|EE175867.2|EE175867
EST:     GAAGAAAGTCTTGCTTATTTAGGCGAGATCGGACAGCAGACATCTTTGAG                         ACATGCTATTCAATTGATATCACCTGCCAGCGTGGTCTCAAAGACTAATGG
genomic: GAAGAAAGTCTTGCTTATTTAGGCGAGATCGGACAGCAGACATCTTTGAGgttagatttt ... ctctttgcagACATGCTATTCAATTGATATCACCTGCCAGCGTGGTCTCAAAGACTAATGG
EST: gi|60340836|gb|DN207809.1|DN207809
EST:     GAAGAAAGTCTTGCTTATTTAGGCGAGATCGGACAGCAGACATCTTTGAG                         ACATGCTATTCAATTGATATCACCTGCCAGCGTGGTCTCGAAGACTAATGG
genomic: GAAGAAAGTCTTGCTTATTTAGGCGAGATCGGACAGCAGACATCTTTGAGgttagatttt ... ctctttgcagACATGCTATTCAATTGATATCACCTGCCAGCGTGGTCTCAAAGACTAATGG
EST: gi|211320429|gb|FL002694.1|FL002694
EST:     GAAGAAAGTCTTGCTTATTTAGGCGAGATCGGACAGCAGACATCTTTGAG                         ACATGCTATTCAATTGATATCACCTGCCAGCGTGGTCTCAAAGACTAATGG
genomic: GAAGAAAGTCTTGCTTATTTAGGCGAGATCGGACAGCAGACATCTTTGAGgttagatttt ... ctctttgcagACATGCTATTCAATTGATATCACCTGCCAGCGTGGTCTCAAAGACTAATGG
EST: gi|61118430|gb|DN559391.1|DN559391
EST:     GAAGAAAGTCTTGCTTATTTAGGCGAGATCGGACAGCAGACATCTTTGAG                         ACATGCTATTCAATTGATATCACCTGCCAGCGTGGTCTCAAAGACTAATGG
genomic: GAAGAAAGTCTTGCTTATTTAGGCGAGATCGGACAGCAGACATCTTTGAGgttagatttt ... ctctttgcagACATGCTATTCAATTGATATCACCTGCCAGCGTGGTCTCAAAGACTAATGG
EST: gi|50328442|gb|CO523568.1|CO523568
EST:     GAAGAAAGTCTTGCTTATTTAGGCGAGATCGGACAGCAGACATCTTTGAG                         ACATGCTATTCAATTGATATCACCTGCCAGCGTGGTCTCAAAGACTAATGG
genomic: GAAGAAAGTCTTGCTTATTTAGGCGAGATCGGACAGCAGACATCTTTGAGgttagatttt ... ctctttgcagACATGCTATTCAATTGATATCACCTGCCAGCGTGGTCTCAAAGACTAATGG
EST: gi|13126371|gb|BG316941.1|BG316941
EST:     GAAGAAAGTCTTGCTTATTTAGGCGAGATCGGACAGCAGACATCTTTGAG                         ACATGCTATTCAATTGATATC
genomic: GAAGAAAGTCTTGCTTATTTAGGCGAGATCGGACAGCAGACATCTTTGAGgttagatttt ... ctctttgcagACATGCTATTCAATTGATATC
EST: gi|61118429|gb|DN559390.1|DN559390
EST:     GAAGAAAGTCTTGCTTATTTAGGCGAGATCGGACAGCAGACATCTTTGAG                         ACATGCTATTCAATTGATATCACCTGCCAGCGTGGTCTCAAAGACTAATGG
genomic: GAAGAAAGTCTTGCTTATTTAGGCGAGATCGGACAGCAGACATCTTTGAGgttagatttt ... ctctttgcagACATGCTATTCAATTGATATCACCTGCCAGCGTGGTCTCAAAGACTAATGG
EST: gi|211320427|gb|FL002692.1|FL002692
EST:     GAAGAAAGTCTTGCTTATTTAGGCGAGATCGGACAGCAGACATCTTTGAG                         ACATGCTATTCAATTGATATCACCTGCCAGCGTGGTCTCAAAGACTAATGG
genomic: GAAGAAAGTCTTGCTTATTTAGGCGAGATCGGACAGCAGACATCTTTGAGgttagatttt ... ctctttgcagACATGCTATTCAATTGATATCACCTGCCAGCGTGGTCTCAAAGACTAATGG
EST: gi|31612365|gb|CD568987.1|CD568987
EST:     GAAGAAAGTCTTGCTTATTTAGGCGAGATCGGACAGCAGACATCTTTGAG                         ACATGCTATTCAATTGATATCACCTGCCAGCGTGGTCTCAAAGACTAATGG
genomic: GAAGAAAGTCTTGCTTATTTAGGCGAGATCGGACAGCAGACATCTTTGAGgttagatttt ... ctctttgcagACATGCTATTCAATTGATATCACCTGCCAGCGTGGTCTCAAAGACTAATGG
EST: gi|76287195|gb|DV026763.1|DV026763
EST:     G-AGAAAGTCTTGTTTATTTAGGCGAGATCGGACAGCAGACATCTTTGAG                         ACATGCTATTCAATTGATATCACCTGCCAGCGTGGTCTCAAAGACTAATGG
genomic: GAAGAAAGTCTTGCTTATTTAGGCGAGATCGGACAGCAGACATCTTTGAGgttagatttt ... ctctttgcagACATGCTATTCAATTGATATCACCTGCCAGCGTGGTCTCAAAGACTAATGG
EST: gi|149051700|gb|EE155813.2|EE155813
EST:     GAAGAAAGTCTTGCTTATTTAGGCGAGATCGGACAGCAGACATCTTTGAG                         ACATGCTATTCAATTGATATCACCTGCCAGCGTGGTCTCAAAGACTAATGG
genomic: GAAGAAAGTCTTGCTTATTTAGGCGAGATCGGACAGCAGACATCTTTGAGgttagatttt ... ctctttgcagACATGCTATTCAATTGATATCACCTGCCAGCGTGGTCTCAAAGACTAATGG

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: 43 (upstream exon), 49 (downstream exon)
Score: 42

ATATTGGCTATCCGAGCACAAGTGGAGGAGATTGATATGGATGAAGAAAGTCTTGCTTATTTAGGCGAGATCGGACAGCAGACATCTTTGAGgttagatttt ... ctctttgcagACATGCTATTCAATTGATATCACCTGCCAGCGTGGTCTCAAAGACTAATGGAAGAGAGAAAATCTGCAAG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 31

ATATTGGCTATCCGAGCACAAGTGGAGGAGATTGATATGGATGAAGAAAGTCTTGCTTATTTAGGCGAGATCGGACAGCAGACATCTTTGAGgttagatttt ... ctctttgcagACATGCTATTCAATTGATATCACCTGCCAGCGTGGTCTCAAAGACTAATGGAAGAGAGAAAATCTGCAAG


Block sizes: 44 (upstream exon), 47 (downstream exon)
Score: 29

ATATTGGCTATCCGAGCACAAGTGGAGGAGATTGATATGGATGAAGAAAGTCTTGCTTATTTAGGCGAGATCGGACAGCAGACATCTTTGAGgttagatttt ... ctctttgcagACATGCTATTCAATTGATATCACCTGCCAGCGTGGTCTCAAAGACTAATGGAAGAGAGAAAATCTGCAAG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 35

ATATTGGCTATCCGAGCACAAGTGGAGGAGATTGATATGGATGAAGAAAGTCTTGCTTATTTAGGCGAGATCGGACAGCAGACATCTTTGAGgttagatttt ... ctctttgcagACATGCTATTCAATTGATATCACCTGCCAGCGTGGTCTCAAAGACTAATGGAAGAGAGAAAATCTGCAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctcagctccataactagagagtaatgatggtaacagatcttattctctttgcagACATGCTATTCAATTGATATCACCTGCCAGCGTGGTCTCAAAGACTAATGGAAGAGAGAAAATCTGCAAG
                            tggtaac  putative branch site (score: 35)
                                      tcttattctctttgc  putative PPT
                                     atcttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctcactgtagtgtttgatattacaagccgatttctcattccatccctcagctccataactagagagtaatgatggtaacagatcttattctctttgcagACATGCTATTCAATTGATATCACCTGCCAGCGTGGTCTCAAAGACTAATGGAAGAGAGAAAATCTGCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- -cactgta
- - - - - gtgtttg
- - - - - - - - - - - -caagccg
- - - - - - - - - - - - - - - - - - - - - - - - -agctcca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aatgatg