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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tactcaagatttcgaactgcattattttgctttgttattttaaattcttaacattttctgtggaagttactgatcatttgatgaacctctgctgggacagAAATTATGCAAAGCATGCGTCTTGCTGGATGGATTGAATCGAGGCTTGCCGAAACTAGGCATTGGAAGTACCAAAGCAGGTGCTAGAGCTGACAGTGATG

Basic information

species Zea mays
transcript GRMZM2G402242_T03
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G402242_T03 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os01g41565.1 (Oryza sativa), 3'ss of exon 9
--tactcaagatttcgaactgcattattttgctttgttattttaaattcttaacattttctgtggaagttactgatcatttgatgaacctctgctggg-acagAAATTATGCAAAGCATGCGTCTTGCTGGATGGATTGAATCGAGGCTTGCCGAAACTAGGCATTGGAAGTACCAAAGCAGGTGCTAGAGCTGACAGTGATG
   |||||        | ||   | ||  ||  |   |    | |||||     |||| |  ||    ||||||| |||  | |||   |||| |      ||||||||||||||||||||||||||||||| |||||||||||||||||||| ||||||||||| || || |||||||  |  ||| ||| ||| |||||  
ctcactcatataaaaaagctatctaatgatg--tgactggcatgaattcccctgatttccaatgctt-ttactgaacatcagttgacattctggtcttcgtagAAATTATGCAAAGCATGCGTCTTGCTGGACGGATTGAATCGAGGCTTGCCAAAACTAGGCATAGGGAGGACCAAAGGCGTAGCTGGAGGTGATAGTGACT

upper sequence: GRMZM2G402242_T03 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os02g52470.2 (Oryza sativa), 3'ss of exon 10
tactcaagatttcgaactgcattattttgctttgttattt---taaattcttaacattttctgtggaagt----tactgatcatttgatgaacctctgctgggacagAAATTATGCAAAGCATGCGTCTTGCTGGATGGATTGAATCGAGGCTTGCCGAAACTAGGCATTGGAAGTACCAAAGCAGGTGCTAGAGCTGACAGTGATG
      | |  | ||||    |||  |     ||| |||    | |||||     |||| |  ||    |     ||||| |||  | ||||  ||||       ||||||||||||||||||| ||||||||||| ||||||||||||||||| || ||||||||||| || || |||||||    |||| ||| |||  ||||  
-----gaaacctggaacc-tgttagctaatgatgtgattggcatgaattcccctgatttccaatgcttttactgaactgaacatc-gttgaaattctggccttgtagAAATTATGCAAAGCATGTGTCTTGCTGGACGGATTGAATCGAGGCTTACCAAAACTAGGCATAGGCAGGACCAAAGGCATTGCTGGAGGTGATGGTGACT
















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|91877954|gb|EB407911.1|EB407911
EST:     GGATGCCAGAGCAAGGAACGTGTGAACGATGTGGCTACATTTTTAGTCAG                         AAATTATGCAAAGCATGCGTCTTGCTGGATGGATTGAATCGAGGCTTGCCG
genomic: GGATGCCAGAGCAAGGAACGTGTGAACGATGTGGCTACATTTCTAGTCAGgtatcgtcat ... gctgggacagAAATTATGCAAAGCATGCGTCTTGCTGGATGGATTGAATCGAGGCTTGCCG
EST: gi|71761950|gb|DR959887.1|DR959887
EST:     GGATGCCAGAGCAAGGAACGTGTGAACGATGTGGCTACATTTTTAGTCAG                         AAATTATGCAAAGCATGCGTCTTGCTGGATGGATTGAATCGAGGCTTGCCG
genomic: GGATGCCAGAGCAAGGAACGTGTGAACGATGTGGCTACATTTCTAGTCAGgtatcgtcat ... gctgggacagAAATTATGCAAAGCATGCGTCTTGCTGGATGGATTGAATCGAGGCTTGCCG
EST: gi|67014256|gb|CO443005.1|CO443005
EST:     GGATGCCAGAGCAAGGAACGTGTGAACGATGTGGCTACATTTCTAGTCAG                         AAATTATGCAAAGCATGCGTCTTGCTGGATGGATTGAATCGAGGCTTGCCG
genomic: GGATGCCAGAGCAAGGAACGTGTGAACGATGTGGCTACATTTCTAGTCAGgtatcgtcat ... gctgggacagAAATTATGCAAAGCATGCGTCTTGCTGGATGGATTGAATCGAGGCTTGCCG
EST: gi|50337085|gb|CO532211.1|CO532211
EST:     GGATGCCAGAGCAAGGAACGTGTGAACGATGTGGCTACATTTCTAGTCAG                         AAATTATGCAAAGCATGCGTCTTGCTGGATGGATTGAATCGAGGCTTGCCG
genomic: GGATGCCAGAGCAAGGAACGTGTGAACGATGTGGCTACATTTCTAGTCAGgtatcgtcat ... gctgggacagAAATTATGCAAAGCATGCGTCTTGCTGGATGGATTGAATCGAGGCTTGCCG
EST: gi|91872706|gb|EB402663.1|EB402663
EST:     GGATGCCAGAGCAAGGAACGTGTGAACGATGTGGCTACATTTCTAGTCAG                         AAATTATGCAAAGCATGCGTCTTGCTGGATGGATTGAATCGAGGCTTGCCG
genomic: GGATGCCAGAGCAAGGAACGTGTGAACGATGTGGCTACATTTCTAGTCAGgtatcgtcat ... gctgggacagAAATTATGCAAAGCATGCGTCTTGCTGGATGGATTGAATCGAGGCTTGCCG
EST: gi|60350684|gb|DN217657.1|DN217657
EST:     GGATGCCAGAGCAAGGAACGTGTGAACGATGTGGCTACATTTCTAGTCAG                         AAATTATGCAAAGCATGCGTCTTGCTGGATGGATTGAATCGAGGCTTGCCG
genomic: GGATGCCAGAGCAAGGAACGTGTGAACGATGTGGCTACATTTCTAGTCAGgtatcgtcat ... gctgggacagAAATTATGCAAAGCATGCGTCTTGCTGGATGGATTGAATCGAGGCTTGCCG
EST: gi|91878573|gb|EB408530.1|EB408530
EST:     GGATGCCAGAGCAAGGAACGTGTGAACGATGTGGCTACATTTCTAGTCAG                         AAATTATGCAAAGCATGCGTCTTGCTGGAGGGATTGAATCGAGGCTTGCCG
genomic: GGATGCCAGAGCAAGGAACGTGTGAACGATGTGGCTACATTTCTAGTCAGgtatcgtcat ... gctgggacagAAATTATGCAAAGCATGCGTCTTGCTGGATGGATTGAATCGAGGCTTGCCG
EST: gi|50323939|gb|CO519065.1|CO519065
EST:     GGATGCCAGAGCAAGGAACGTGTGAACGATGTGGCTACATTTTTAGTCAG                         AAATTATGCAAAGCATGCGTCTTGCTGGATGGATTGAATCGAGGCTTGCCG
genomic: GGATGCCAGAGCAAGGAACGTGTGAACGATGTGGCTACATTTCTAGTCAGgtatcgtcat ... gctgggacagAAATTATGCAAAGCATGCGTCTTGCTGGATGGATTGAATCGAGGCTTGCCG
EST: gi|101389613|gb|EB816739.1|EB816739
EST:     GGATGCCAGAGCAAGGAACGTGTGAACGATGTGGCTACATTTCTAGTCAG                         AAATTATGCAAAGCATGCGTCTTGCTGGATGGATTGAATCGAGGCTTGCCG
genomic: GGATGCCAGAGCAAGGAACGTGTGAACGATGTGGCTACATTTCTAGTCAGgtatcgtcat ... gctgggacagAAATTATGCAAAGCATGCGTCTTGCTGGATGGATTGAATCGAGGCTTGCCG
EST: gi|71770542|gb|DR968479.1|DR968479
EST:     GGATGCCAGAGCAAGGAACGTGTGAACGATGTGGCTACATTTCTAGTCAG                         AAATTATGCAAAGCATGCGTCTTGCTGGATGGATTGAATCGAGGCTTGCCG
genomic: GGATGCCAGAGCAAGGAACGTGTGAACGATGTGGCTACATTTCTAGTCAGgtatcgtcat ... gctgggacagAAATTATGCAAAGCATGCGTCTTGCTGGATGGATTGAATCGAGGCTTGCCG

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: 70

ACTAGACATCATAAAATCCGGTGAAAATTTCAGAATCTCCACAACAACAAGGATGCCAGAGCAAGGAACGTGTGAACGATGTGGCTACATTTCTAGTCAGgtatcgtcat ... gctgggacagAAATTATGCAAAGCATGCGTCTTGCTGGATGGATTGAATCGAGGCTTGCCGAAACTAGGCATTGGAAGTACCAAAGCAGGTGCTAGAGCTGACAGTGATG


Block sizes: 46 (upstream exon), 44 (downstream exon)
Score: 30

ACTAGACATCATAAAATCCGGTGAAAATTTCAGAATCTCCACAACAACAAGGATGCCAGAGCAAGGAACGTGTGAACGATGTGGCTACATTTCTAGTCAGgtatcgtcat ... gctgggacagAAATTATGCAAAGCATGCGTCTTGCTGGATGGATTGAATCGAGGCTTGCCGAAACTAGGCATTGGAAGTACCAAAGCAGGTGCTAGAGCTGACAGTGATG


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 24

ACTAGACATCATAAAATCCGGTGAAAATTTCAGAATCTCCACAACAACAAGGATGCCAGAGCAAGGAACGTGTGAACGATGTGGCTACATTTCTAGTCAGgtatcgtcat ... gctgggacagAAATTATGCAAAGCATGCGTCTTGCTGGATGGATTGAATCGAGGCTTGCCGAAACTAGGCATTGGAAGTACCAAAGCAGGTGCTAGAGCTGACAGTGATG


Block sizes: 47 (upstream exon), 45 (downstream exon)
Score: 50

ACTAGACATCATAAAATCCGGTGAAAATTTCAGAATCTCCACAACAACAAGGATGCCAGAGCAAGGAACGTGTGAACGATGTGGCTACATTTCTAGTCAGgtatcgtcat ... gctgggacagAAATTATGCAAAGCATGCGTCTTGCTGGATGGATTGAATCGAGGCTTGCCGAAACTAGGCATTGGAAGTACCAAAGCAGGTGCTAGAGCTGACAGTGATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttaacattttctgtggaagttactgatcatttgatgaacctctgctgggacagAAATTATGCAAAGCATGCGTCTTGCTGGATGGATTGAATCGAGGCTTGCCGAAACTAGGCATTGGAAGTACCAAAGCAGGTGCTAGAGCTGACAGTGATG
                                        cctctgct  CT-rich tract
     acatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tactcaagatttcgaactgcattattttgctttgttattttaaattcttaacattttctgtggaagttactgatcatttgatgaacctctgctgggacagAAATTATGCAAAGCATGCGTCTTGCTGGATGGATTGAATCGAGGCTTGCCGAAACTAGGCATTGGAAGTACCAAAGCAGGTGCTAGAGCTGACAGTGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA