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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAGGCTTTTTGTGAAGGCTCTGGGAAAGCCATCTGAAATATTGACAAAACTGAATGCAATGGCTGGATTTTCTCCAAATGAAGAAATTGAGCTGTACGAGgtgcttcacaattctgtatttatttctctagagtacacattctaacttgctgtatgcatgttttctgcctatgtgctccttgtgctcataaaatctgtta...

Basic information

species Zea mays
transcript GRMZM2G303655_T01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G303655_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os12g30540.1 (Oryza sativa), 5'ss of exon 19
TAGGCTTTTTGTGAAGGCTCTGGGAAAGCCATCTGAAATATTGACAAAACTGAATGCAATGGCTGGATTTTCTCCAAATGAAGAAATTGAGCTGTACGAGgtgcttcaca-attctgtatttatttctctagagtacacattctaacttgctgtatgcatgttttctgcctatgtgctccttgtgctcataaaatctgtta---
|||||||||||||||||||  |||||| |||||||||||  |||||||| |||||| ||||||||||||| |||||||||||||||||||||| || ||||||     || |||| ||  |   |  |   | |   | ||  | || ||||  ||  |    |  | |          |      ||  |  ||||  |    
TAGGCTTTTTGTGAAGGCTACGGGAAAACCATCTGAAATCCTGACAAAATTGAATGAAATGGCTGGATTTGCTCCAAATGAAGAAATTGAGCTATATGAGgtgagggtcatattcagttctcgatgattacgtggtaatatcattacatgctacataaaaccatcttactctcagagcac----agtcgcatgatctactcatg

upper sequence: GRMZM2G303655_T01 (Zea mays), 5'ss of exon 9
lower sequence: Vv13s0073g00610.t01 (Vitis vinifera), 5'ss of exon 19
TAGGCTTTTTGTGAAGGCTCTGGGAAAGCCATCTGAAATATTGACAAAACTGAATGCAATGGCTGGATTTTCTCCAAATGAAGAAATTGAGCTGTACGAGgtgcttcacaattctgtatttatttctctagagtacacattctaacttgctgtatgcatgttttctgcctatgtgctccttgtgctcataaaatctgtta
 ||||| ||||||||||     |||||||||  |||||||||| |||||||||||| | ||||||| |||  ||| |||||||| ||||| || |  |||||      || |  |  | ||     |  ||       ||| | | ||  |||  |  |||   |||  |   |  |  || || |   |          
GAGGCTATTTGTGAAGGGGAGTGGAAAGCCAATTGAAATATTGTCAAAACTGAATGAATTGGCTGGCTTTAGTCCCAATGAAGAGATTGAACTTTTTGAGgt------cagtcttccagttccagtttcag---ttgtattattattt--tgttggtttgtcccctga-tgcataata-ttatggttccag---------
















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|6536518|gb|AW224831.1|AW224831
EST:     TGAATGCAATGGCTGGATTTTCTCCAAATGAAGAAATTGAGCTGTACGAG                         GAAATTAAGTTTGAGCCAAATGTGATGTGCGAACATATTGACAAGNAAACT
genomic: TGAATGCAATGGCTGGATTTTCTCCAAATGAAGAAATTGAGCTGTACGAGgtgcttcaca ... tattctgcagGAAATTAAGTTTGAGCCAAATGTGATGTGCGAACATATTGACAAG-AAACT
EST: gi|31354456|gb|CD438813.1|CD438813
EST:     GATTTTCTCCAAATGAAGAAATTGAGCTGTACGAG                         GAAATTAAGTTTGAGCCAAATGTGATGTGCGAACATATTGACAAGAAACTT
genomic: GATTTTCTCCAAATGAAGAAATTGAGCTGTACGAGgtgcttcaca ... tattctgcagGAAATTAAGTTTGAGCCAAATGTGATGTGCGAACATATTGACAAGAAACTT
EST: gi|211335220|gb|FL322949.1|FL322949
EST:     GAATGCAATGGCTGGATTTTCTCCCAAATGAAGAAATTGAGCTGNACGAG                         GAAATTAAGTTTGAGCCAAATGTGATGTGCGAAACATATTGACA
genomic: GAATGCAATGGCTGGATTTTCTCC-AAATGAAGAAATTGAGCTGTACGAGgtgcttcaca ... tattctgcagGAAATTAAGTTTGAGCCAAATGTGATGTGCGAA-CATATTGACA
EST: gi|211531762|gb|FL336391.1|FL336391
EST:     TGAATGNAATGGNTGGATTTTCTCCCAATGAAGAAATTGAGCTGTACGAG                         GAAATTAAGTTTGAGCCA
genomic: TGAATGCAATGGCTGGATTTTCTCCAAATGAAGAAATTGAGCTGTACGAGgtgcttcaca ... tattctgcagGAAATTAAGTTTGAGCCA
EST: gi|211265134|gb|FL336164.1|FL336164
EST:     TGAATGCAATGGCTGGATTTTCTCCAAATGAAAAAATTGAGCTGTACGAG                         GAAATTAAGTTTGAGCCAAATGTGATGTG
genomic: TGAATGCAATGGCTGGATTTTCTCCAAATGAAGAAATTGAGCTGTACGAGgtgcttcaca ... tattctgcagGAAATTAAGTTTGAGCCAAATGTGATGTG
EST: gi|211148456|gb|FL367819.1|FL367819
EST:     TGAATGCAATGGCTGGATTTTCTCCAAATGAAGAAATTGAGCTGTACGAN                         GAAATTAAGTTTGAGCCAAATG
genomic: TGAATGCAATGGCTGGATTTTCTCCAAATGAAGAAATTGAGCTGTACGAGgtgcttcaca ... tattctgcagGAAATTAAGTTTGAGCCAAATG

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: 46 (upstream exon), 48 (downstream exon)
Score: 69

TAGGCTTTTTGTGAAGGCTCTGGGAAAGCCATCTGAAATATTGACAAAACTGAATGCAATGGCTGGATTTTCTCCAAATGAAGAAATTGAGCTGTACGAGgtgcttcaca ... tattctgcagGAAATTAAGTTTGAGCCAAATGTGATGTGCGAACATATTGACAAGAAACTTACTTTCCGCTCTAGTCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 85

TAGGCTTTTTGTGAAGGCTCTGGGAAAGCCATCTGAAATATTGACAAAACTGAATGCAATGGCTGGATTTTCTCCAAATGAAGAAATTGAGCTGTACGAGgtgcttcaca ... tattctgcagGAAATTAAGTTTGAGCCAAATGTGATGTGCGAACATATTGACAAGAAACTTACTTTCCGCTCTAGTCAG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 76

TAGGCTTTTTGTGAAGGCTCTGGGAAAGCCATCTGAAATATTGACAAAACTGAATGCAATGGCTGGATTTTCTCCAAATGAAGAAATTGAGCTGTACGAGgtgcttcaca ... tattctgcagGAAATTAAGTTTGAGCCAAATGTGATGTGCGAACATATTGACAAGAAACTTACTTTCCGCTCTAGTCAG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 56

TAGGCTTTTTGTGAAGGCTCTGGGAAAGCCATCTGAAATATTGACAAAACTGAATGCAATGGCTGGATTTTCTCCAAATGAAGAAATTGAGCTGTACGAGgtgcttcaca ... tattctgcagGAAATTAAGTTTGAGCCAAATGTGATGTGCGAACATATTGACAAGAAACTTACTTTCCGCTCTAGTCAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TAGGCTTTTTGTGAAGGCTCTGGGAAAGCCATCTGAAATATTGACAAAACTGAATGCAATGGCTGGATTTTCTCCAAATGAAGAAATTGAGCTGTACGAGgtgcttcacaattctgtatttatttctctagagtacacattctaacttgctgtatgcatgttttctgcctatgtgctccttgtgctcataaaatctgtta

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA