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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgagacaataacaaattctctagaagatcaacttctcttcacacttttcagttctctagctactttgtctctttatagtaacaccatacttattctcagGGCCTACCGGGCATTTTACATTCTAAACTGGATTTACCGTTATTTCACGGAGGGTCATCACAGCAGATGGATCC

Basic information

species Zea mays
transcript GRMZM2G408989_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G408989_T03 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os05g45310.1 (Oryza sativa), 3'ss of exon 3
------atgagacaataacaaattctctagaagatcaacttctcttcacacttttcagttctctagctactttgtctctttatagtaacaccatacttattct-cagGGCCTACCGGGCATTTTACATTCTAAACTGGATTTACCGTTATTTCACGGAGGGTCATCACAGCAGATGGATCC
      ||  |  | ||    || || || |   | |||   ||  ||  ||| |  |||| |     | || ||||||||  |||  ||| |||||| || | |||||||||||| ||||||||||| |||||||||||||||||||| ||||| |||||||| ||||||||||||||||
gtccagattcgg-attagggcatgctttaaatagtgaacga-tcgacatgcttctaggttccc-----agttggtctctttcaagtctcacaatacttgttttgcagGGCCTACCGTGCATTTTACATCCTAAACTGGATTTACCGTTACTTCACTGAGGGTCACCACAGCAGATGGATCC

upper sequence: GRMZM2G408989_T03 (Zea mays), 3'ss of exon 2
lower sequence: Vv10s0003g01700.t01 (Vitis vinifera), 3'ss of exon 3
atgagacaataacaaattctctagaagatcaacttctcttcacacttttcagttctctagctactttgtctctttatagtaac-accatacttattct-cagGGCCTACCGGGCATTTTACATTCTAAACTGGATTTACCGTTATTTCACGGAGGGTCATCACAGCAGATGGATCC
   | |||       |   | ||  | || | |        |||       ||  |  |  |||||||        |   ||| |  ||| | | ||| ||||||||| || ||||| ||||| || |||||||||||||||||||||||||||   |||   ||| |||||||  
--aacacatgtttgcaccatatatcacataagcaaaaagagacataaacttgtatttaatatactttgggataaacttccaactaatatattcaatctgcagGGCCTATCGTGCATTATACATCCTCAACTGGATTTACCGTTATTTCACGGAGCAACATTTTAGCCGATGGATAG
















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|211036981|gb|FL384634.1|FL384634
EST:     AGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGG                         GGCCTACCGGGCATTTTACATTTCTAA-CTGGATTTACCGTTATTTCACGG
genomic: AGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGGgtatggattg ... ttattctcagGGCCTACCGGGCATTTTACATT-CTAAACTGGATTTACCGTTATTTCACGG
EST: gi|16920990|gb|BM074929.1|BM074929
EST:     TGTTATCTTCCTTGG                         GGCCTACCGGGCATTTTACATTCTAAACTGGATTTACCGTTATTTCACGGA
genomic: TGTTTTCTTCCTTGGgtatggattg ... ttattctcagGGCCTACCGGGCATTTTACATTCTAAACTGGATTTACCGTTATTTCACGGA
EST: gi|91871430|gb|EB401416.1|EB401416
EST:     AGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGG                         GGCCTACCGGGCATTTTACATTCTAAACTGGATTTACCGTTATTTCACGGA
genomic: AGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGGgtatggattg ... ttattctcagGGCCTACCGGGCATTTTACATTCTAAACTGGATTTACCGTTATTTCACGGA
EST: gi|91871428|gb|EB401415.1|EB401415
EST:     AGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGG                         GGCCTACCGGGCATTTTACATTCTAAACTGGATTTACCGTTATTTCACGGA
genomic: AGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGGgtatggattg ... ttattctcagGGCCTACCGGGCATTTTACATTCTAAACTGGATTTACCGTTATTTCACGGA
EST: gi|78023775|gb|DV492162.1|DV492162
EST:     AGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGG                         GGCCTACCGGGCATTTTACATTCTAAACTGGATTTACCGTTATTTCACGGA
genomic: AGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGGgtatggattg ... ttattctcagGGCCTACCGGGCATTTTACATTCTAAACTGGATTTACCGTTATTTCACGGA
EST: gi|78023788|gb|DV492175.1|DV492175
EST:     AGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGG                         GGCCTACCGGGCATTTTACATTCTAAACTGGATTTACCGTTATTTCACGGA
genomic: AGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGGgtatggattg ... ttattctcagGGCCTACCGGGCATTTTACATTCTAAACTGGATTTACCGTTATTTCACGGA
EST: gi|50330722|gb|CO525848.1|CO525848
EST:     AGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGG                         GGCCTACCGGGCATTTTACATTCTAAACTGGATTTACCGTTATTTCACGGA
genomic: AGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGGgtatggattg ... ttattctcagGGCCTACCGGGCATTTTACATTCTAAACTGGATTTACCGTTATTTCACGGA
EST: gi|16922820|gb|BM075812.1|BM075812
EST:     GTGGATAACTTAACTGGACAATATGTTATCTTCCTTGG                         GGCCTACCGGGCATTTTACATTCTAAACTGGATTTACCGTTATTTCACGGA
genomic: GTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGGgtatggattg ... ttattctcagGGCCTACCGGGCATTTTACATTCTAAACTGGATTTACCGTTATTTCACGGA
EST: gi|60344375|gb|DN211348.1|DN211348
EST:     AGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGG                         GGCCTACCGGGCATTTTACATTCTAAACTGGATTTACCGTTATTTCACGGA
genomic: AGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGGgtatggattg ... ttattctcagGGCCTACCGGGCATTTTACATTCTAAACTGGATTTACCGTTATTTCACGGA
EST: gi|14245658|gb|BG874240.1|BG874240
EST:     GCAGAAATGTGGATAACTTAACTGGGCAATATGTTTTCTTCCTTGG                         GGCCTACCGGGCATTTTACATTCTAAACTGGATTTACCGTTATTTCACGGA
genomic: GCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGGgtatggattg ... ttattctcagGGCCTACCGGGCATTTTACATTCTAAACTGGATTTACCGTTATTTCACGGA
EST: gi|24769505|gb|CA404634.1|CA404634
EST:     AGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGG                         GGCCTACCGGGCATTTTACATTCTAAACTGGATTTACCGTTATTTCACGGA
genomic: AGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGGgtatggattg ... ttattctcagGGCCTACCGGGCATTTTACATTCTAAACTGGATTTACCGTTATTTCACGGA
EST: gi|31354771|gb|CD439128.1|CD439128
EST:     AGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGG                         GGCCTACCGGGCATTTTACATTCTAAACTGGATTTACCGTTATTTCACGGA
genomic: AGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGGgtatggattg ... ttattctcagGGCCTACCGGGCATTTTACATTCTAAACTGGATTTACCGTTATTTCACGGA
EST: gi|32912106|gb|CF016918.1|CF016918
EST:     AGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGG                         GGCCTACCGGGCATTTTACATTCTAAACTGGATTTACCGTTATTTCACGGA
genomic: AGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGGgtatggattg ... ttattctcagGGCCTACCGGGCATTTTACATTCTAAACTGGATTTACCGTTATTTCACGGA
EST: gi|60342889|gb|DN209862.1|DN209862
EST:     AGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGG                         GGCCTACCGGGCATTTTACATTCTAAACTGGATTTACCGTTATTTCACGGA
genomic: AGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGGgtatggattg ... ttattctcagGGCCTACCGGGCATTTTACATTCTAAACTGGATTTACCGTTATTTCACGGA
EST: gi|211379193|gb|FL377345.1|FL377345
EST:     AGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGG                         GGCCTACCGGGCATTTTACATTCTAAACTGGATTTTACCNGT-ATTTCAAG
genomic: AGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGGgtatggattg ... ttattctcagGGCCTACCGGGCATTTTACATTCTAAACTGGATTT-ACC-GTTATTTCACG
EST: gi|18165355|gb|BM335194.1|BM335194
EST:     AGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGG                         GGCCTACCGGGCATTTTACATTCTAAACTGGATTTACCGTTATTTCACGGA
genomic: AGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGGgtatggattg ... ttattctcagGGCCTACCGGGCATTTTACATTCTAAACTGGATTTACCGTTATTTCACGGA
EST: gi|78080744|gb|DV509156.1|DV509156
EST:     AGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGG                         GGCCTACCGGGCATTTTACATTCTAAACTGGATTTACCGTTATTTCACGGA
genomic: AGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGGgtatggattg ... ttattctcagGGCCTACCGGGCATTTTACATTCTAAACTGGATTTACCGTTATTTCACGGA

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: 47 (upstream exon), 48 (downstream exon)
Score: 61

CGATCTATTTAGAGGCAGTGGCAATTCTCCCACAGTTAGTGTTACTCCAGAGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGGgtatggattg ... ttattctcagGGCCTACCGGGCATTTTACATTCTAAACTGGATTTACCGTTATTTCACGGAGGGTCATCACAGCAGATGGATCC


Block sizes: 41 (upstream exon), 49 (downstream exon)
Score: 46

CGATCTATTTAGAGGCAGTGGCAATTCTCCCACAGTTAGTGTTACTCCAGAGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGGgtatggattg ... ttattctcagGGCCTACCGGGCATTTTACATTCTAAACTGGATTTACCGTTATTTCACGGAGGGTCATCACAGCAGATGGATCC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 41

CGATCTATTTAGAGGCAGTGGCAATTCTCCCACAGTTAGTGTTACTCCAGAGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGGgtatggattg ... ttattctcagGGCCTACCGGGCATTTTACATTCTAAACTGGATTTACCGTTATTTCACGGAGGGTCATCACAGCAGATGGATCC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 63

CGATCTATTTAGAGGCAGTGGCAATTCTCCCACAGTTAGTGTTACTCCAGAGAAGCAGAAATGTGGATAACTTAACTGGACAATATGTTTTCTTCCTTGGgtatggattg ... ttattctcagGGCCTACCGGGCATTTTACATTCTAAACTGGATTTACCGTTATTTCACGGAGGGTCATCACAGCAGATGGATCC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttcagttctctagctactttgtctctttatagtaacaccatacttattctcagGGCCTACCGGGCATTTTACATTCTAAACTGGATTTACCGTTATTTCACGGAGGGTCATCACAGCAGATGGATCC
                               tagtaac  putative branch site (score: 63)
                                            cttattctc  putative PPT
                           tttatagtaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgagacaataacaaattctctagaagatcaacttctcttcacacttttcagttctctagctactttgtctctttatagtaacaccatacttattctcagGGCCTACCGGGCATTTTACATTCTAAACTGGATTTACCGTTATTTCACGGAGGGTCATCACAGCAGATGGATCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - -taacaaa
- - - - - - - - - - - - - - - - - - -cttcaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aacacca