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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AACTGATTTGGGATTGATATCACAATGTTGCTTAACCAAGCATGTTTTTAAGATCAGCAAACAGTACTTGGCAAATGTCTCACTGAAAATTAATGTTAAGgtacttaccaccttggttatacatcaaatacagttcagaacagcaactttataagagaaatggctcgatattgactaatgataccatcaaattcag

Basic information

species Zea mays
transcript AC189879.3_FGT003
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC189879.3_FGT003 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os06g39640.1 (Oryza sativa), 5'ss of exon 13
AACTGATTTGGGATTGATATCACAATGTTGCTTAACCAAGCATGTTTTTAAGATCAGCAAACAGTACTTGGCAAATGTCTCACTGAAAATTAATGTTAAGgtacttaccacct--tggttatacatcaaatac--agtt------cagaacagcaactttataagagaaatggctcgatattgactaatgataccatcaaattcag-------------
|||||| ||||| |||||||||||||||||||||||||| |||||||| ||||||||||| |||||| |||||||||||||||| ||||| |||||||||||||  |  || |       |  ||   |||||  || |      || ||  | |   | ||     ||   |      |   | |  | || || |  | ||| |             
AACTGACTTGGGGTTGATATCACAATGTTGCTTAACCAAACATGTTTTCAAGATCAGCAAGCAGTACCTGGCAAATGTCTCACTTAAAATCAATGTTAAGgtaccaaatacttataaaccaagcagttaatacttagcttgtctacacaaatgtagtgtaatgcagtaagcagacttgcagc-attgctaatgccttgcatttcggagttgtgatacag

upper sequence: AC189879.3_FGT003 (Zea mays), 5'ss of exon 12
lower sequence: Vv11s0016g04620.t01 (Vitis vinifera), 5'ss of exon 13
AACTGATTTGGGATTGATATCACAATGTTGCTTAACCAAGCATGTTTTTAAGATCAGCAAACAGTACTTGGCAAATGTCTCACTGAAAATTAATGTTAAGgtacttaccaccttgg--ttatacatcaaatacagttcagaacagcaactttataagagaaatggctcgatattgactaatgataccatcaaattcag-------------
 || ||| |||| ||||| || || || ||  | || ||  |||| |  ||||| ||||| |||||| ||||||| || ||||| ||||| |||||||||||   | |   ||     || |    | | |  | | |  || |  |  ||  | |  | || |      | |   ||||   |    ||    |                
CACAGATCTGGGGTTGATTTCTCAGTGCTGTCTTACTAAAAATGTCTACAAGATTAGCAACCAGTACCTGGCAAACGTGTCACTTAAAATCAATGTTAAGgtctgtccagactgaaacttctgtggcgattctactacttaaaaatagattgcttattgcaaagttaatgtttcctctaagcttggtttcgggatttttctttttccccag

upper sequence: AC189879.3_FGT003 (Zea mays), 5'ss of exon 12
lower sequence: PP1S7_194V6.1 (Physcomitrella patens), 5'ss of exon 11
AACTGATTTGGGATTGATATCACAATGTTGCTTAACCAAGCATGTTTTTAAGATCAGCAAACAGTACTTGGCAAATGTCTCACTGAAAATTAATGTTAAGgtacttaccaccttggttatacatcaa--atacagttcagaacagcaactttataagagaaatggctcgatattgactaatgataccatcaaattcag-------------------------------------------------------------
 ||||   ||||| || | ||||||||||| || || |||||||| || ||||| ||||| ||||| || ||||||||  | || ||||||||||| |||||| ||   | || |||  ||  |  |  ||  | |||||  |    |   | |      | ||     |||   |||  |  |    |  |||  ||                                                             
GACTGTCCTGGGAGTGGTTTCACAATGTTGTTTGACTAAGCATGTCTTCAAGATGAGCAAGCAGTATTTAGCAAATGTGGCCCTCAAAATTAATGTGAAGgtaatt-ttaactaggtcgtaactagactatgtatttcaggtctttcatactgttttgtcagtg---ttatacctactccttgtcgtcttgaatatagaaacgtgggtctttataagactgatttatgattctaattgtgtccattgtacacttcacag

upper sequence: AC189879.3_FGT003 (Zea mays), 5'ss of exon 12
lower sequence: PP1S28_182V6.1 (Physcomitrella patens), 5'ss of exon 12
AACTGATTTGGGATTGATATCACAATGTTGCTTAACCAAGCATGTTTTTAAGATCAGCAAACAGTACTTGGCAAATGTCTCACTGAAAATTAATGTTAAGgtacttaccaccttggttatacatcaaatacagttcagaacagcaact-ttataagagaaatggctcgatattgactaatgataccat----caaattcag----------------------------------------------------
 ||||   ||||  || | || || ||||| || |||||||||||||| ||||| ||||| |||||| ||||||| ||  | || ||||||||||| |||||| |  |||  |    | | ||     |          |||  || |  || ||    | | | |  ||  |  |  ||| ||  ||    |||||   |                                                    
GACTGTACTGGGTGTGGTTTCTCAGTGTTGTTTGACCAAGCATGTTTTCAAGATGAGCAAGCAGTACCTGGCAAACGTGGCTCTCAAAATTAATGTCAAGgtagtgtccaaatgacatgtccaggctctgtgtacttctacactaattgctaaaactttacttgttgcatcattgcatatgttatgattgcgcaaatgtgggtttaccaaaaatagatttttacttatttttgtgcgactgttcgctgtacag

upper sequence: AC189879.3_FGT003 (Zea mays), 5'ss of exon 12
lower sequence: PP1S173_134V6.1 (Physcomitrella patens), 5'ss of exon 12
AACTGATTTGGGATTGATATCACAATGTTGCTTAACCAAGCATGTTTTTAAGATCAGCAAACAGTACTTGGCAAATGTCTCACTGAAAATTAATGTTAAGgta------cttaccaccttggttatacatcaaata---cagttcagaacagcaactttata-agagaaatggctcgatattgactaatgataccatcaaattcag-----------------------------------------------------------------
 ||||   ||||  |  | || |||||||| || || || ||||| |||||||| |||||||||||||||||||||||  | |||||||| ||||| |||||        | |  || |   ||   | | | ||       || |   ||  ||  || || | |||  |  || |    ||| | |  |       ||| |  |                                                                 
GACTGTCCTGGGGGTCGTGTCTCAATGTTGTTTGACGAAACATGTATTTAAGATGAGCAAACAGTACTTGGCAAATGTTGCCCTGAAAATCAATGTCAAGgtcatgctcttgaatacttccatttctcctgatatggcttgattgatctcaagaatgttctagaaagagtttcctaggagctgatttaaaactgttcaaaacttggaatagatgattgttcaagtgcagatgactatttctttttctttacgttcactctgtatttgacag

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|91877156|gb|EB407113.1|EB407113
EST:     AGATCAGCAAACAGTACTTGGCAAATGTCTCACTGAAAATTAATGTTAAG                         ATGGGAGGAAGAAACACTGTGCTCCTGGACGCAATAAGTTGGAGCATTCCT
genomic: AGATCAGCAAACAGTACTTGGCAAATGTCTCACTGAAAATTAATGTTAAGgtacttacca ... tcaaattcagATGGGAGGAAGAAACACTGTGCTCCTGGACGCAATAAGTTGGAGCATTCCT
EST: gi|21088909|gb|BQ401222.1|BQ401222
EST:     AGATCAGCAAACAGTACTTGGCAAATGTCTCACTGAAAATTAATGTTAAG                         ATGGGAGGAAGAAACACTGTGCTCCTGGACGCAATAAGTTGGAGCATTCCT
genomic: AGATCAGCAAACAGTACTTGGCAAATGTCTCACTGAAAATTAATGTTAAGgtacttacca ... tcaaattcagATGGGAGGAAGAAACACTGTGCTCCTGGACGCAATAAGTTGGAGCATTCCT

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: 49 (upstream exon), 49 (downstream exon)
Score: 377

AACTGATTTGGGATTGATATCACAATGTTGCTTAACCAAGCATGTTTTTAAGATCAGCAAACAGTACTTGGCAAATGTCTCACTGAAAATTAATGTTAAGgtacttacca ... tcaaattcagATGGGAGGAAGAAACACTGTGCTCCTGGACGCAATAAGTTGGAGCATTCCTTTGGTCAGTGACATCCCAACTATTATATTTGGTGCAGATGTAACACACC


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 55

AACTGATTTGGGATTGATATCACAATGTTGCTTAACCAAGCATGTTTTTAAGATCAGCAAACAGTACTTGGCAAATGTCTCACTGAAAATTAATGTTAAGgtacttacca ... tcaaattcagATGGGAGGAAGAAACACTGTGCTCCTGGACGCAATAAGTTGGAGCATTCCTTTGGTCAGTGACATCCCAACTATTATATTTGGTGCAGATGTAACACACC


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

AACTGATTTGGGATTGATATCACAATGTTGCTTAACCAAGCATGTTTTTAAGATCAGCAAACAGTACTTGGCAAATGTCTCACTGAAAATTAATGTTAAGgtacttacca ... tcaaattcagATGGGAGGAAGAAACACTGTGCTCCTGGACGCAATAAGTTGGAGCATTCCTTTGGTCAGTGACATCCCAACTATTATATTTGGTGCAGATGTAACACACC


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 62

AACTGATTTGGGATTGATATCACAATGTTGCTTAACCAAGCATGTTTTTAAGATCAGCAAACAGTACTTGGCAAATGTCTCACTGAAAATTAATGTTAAGgtacttacca ... tcaaattcagATGGGAGGAAGAAACACTGTGCTCCTGGACGCAATAAGTTGGAGCATTCCTTTGGTCAGTGACATCCCAACTATTATATTTGGTGCAGATGTAACACACC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AACTGATTTGGGATTGATATCACAATGTTGCTTAACCAAGCATGTTTTTAAGATCAGCAAACAGTACTTGGCAAATGTCTCACTGAAAATTAATGTTAAGgtacttaccaccttggttatacatcaaatacagttcagaacagcaactttataagagaaatggctcgatattgactaatgataccatcaaattcag

- - - - - - - - - - - - - - - - - - - - - - - - - AGATCA