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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATGGAGATGGGTGGGGGCAGTTGGGACAAAGATAAAGTCCAAAGGGCTCTCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCTgtatgtatttttctcattgccccattcttttgcatttttgcacttaatgatggaatccaattttctggtgctaatagattatttatgtcaaacattagggtattccag

Basic information

species Zea mays
transcript GRMZM2G143462_T05
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G143462_T05 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os02g08300.2 (Oryza sativa), 5'ss of exon 6
AATGGAGATGGGTGGGGGCAGTTGGGACAAAGATAAAGTCCAAAGGGCTCTCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCTgtatgtatt-tttctcattgccccattcttttgcatttttgcacttaatgatggaatccaattttctggtgctaatagattatttatgtcaaacattagggtattccag
 ||||| |||||||| ||||||||||||| ||||||||||||||| ||||| ||||| ||||| |||||||| || |||||||||||||| || || |||||||||  | ||||    ||      | | ||    ||||     ||| | |   |   ||| ||               | ||| |  ||||||||||          
GATGGAAATGGGTGGTGGCAGTTGGGACAGAGATAAAGTCCAAAGAGCTCTACGTGCAGCTTATAACAACCCAGAGCGTGCTGTTGAATATCTATATTCTgtatgttctgtttcctcctgtaaatgtttgttattcttttttttctaacgttaatagataatgtt---------------tgtttctcccaaacattag----------
















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|148999208|gb|EE036127.2|EE036127
EST:     TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCT                         G
genomic: TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCTgtatgtattt ... ggtattccag-
EST: gi|148999208|gb|EE036127.2|EE036127
EST:     TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCT                         G
genomic: TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCTgtatgtattt ... ggtattccag-
EST: gi|148999208|gb|EE036127.2|EE036127
EST:     TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCT                         G
genomic: TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCTgtatgtattt ... ggtattccag-
EST: gi|93280956|gb|EB673220.1|EB673220
EST:     TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCT                         G
genomic: TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCTgtatgtattt ... ggtattccag-
EST: gi|93280956|gb|EB673220.1|EB673220
EST:     TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCT                         G
genomic: TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCTgtatgtattt ... ggtattccag-
EST: gi|93280956|gb|EB673220.1|EB673220
EST:     TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCT                         G
genomic: TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCTgtatgtattt ... ggtattccag-
EST: gi|22489727|gb|BU049650.1|BU049650
EST:     TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCTGGTATT                    
genomic: TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTC------Tgtatgtattt ... ggtat
EST: gi|22489727|gb|BU049650.1|BU049650
EST:     TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCTGGTATT                    
genomic: TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTC------Tgtatgtattt ... ggtat
EST: gi|22489727|gb|BU049650.1|BU049650
EST:     TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCTGGTATT                    
genomic: TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTC------Tgtatgtattt ... ggtat
EST: gi|22489727|gb|BU049650.1|BU049650
EST:     TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCTGGTATT                    
genomic: TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTC------Tgtatgtattt ... ggtat
EST: gi|22489727|gb|BU049650.1|BU049650
EST:     TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCTGGTATT                    
genomic: TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTC------Tgtatgtattt ... ggtat
EST: gi|89759371|gb|DY688230.1|DY688230
EST:     TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCT                         G
genomic: TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCTgtatgtattt ... ggtattccag-
EST: gi|89759371|gb|DY688230.1|DY688230
EST:     TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCT                         G
genomic: TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCTgtatgtattt ... ggtattccag-
EST: gi|89759371|gb|DY688230.1|DY688230
EST:     TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCT                         G
genomic: TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCTgtatgtattt ... ggtattccag-
EST: gi|148947026|gb|EC892323.2|EC892323
EST:     TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCT                         G
genomic: TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCTgtatgtattt ... ggtattccag-
EST: gi|148947026|gb|EC892323.2|EC892323
EST:     TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCT                         G
genomic: TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCTgtatgtattt ... ggtattccag-
EST: gi|148947026|gb|EC892323.2|EC892323
EST:     TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCT                         G
genomic: TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCTgtatgtattt ... ggtattccag-
EST: gi|89758471|gb|DY687642.1|DY687642
EST:     TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCT                         G
genomic: TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCTgtatgtattt ... ggtattccag-
EST: gi|89758471|gb|DY687642.1|DY687642
EST:     TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCT                         G
genomic: TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCTgtatgtattt ... ggtattccag-
EST: gi|89758471|gb|DY687642.1|DY687642
EST:     TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCT                         G
genomic: TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCTgtatgtattt ... ggtattccag-
EST: gi|74242202|gb|DT650116.1|DT650116
EST:     TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCT                         G
genomic: TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCTgtatgtattt ... ggtattccag-
EST: gi|74242202|gb|DT650116.1|DT650116
EST:     TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCT                         G
genomic: TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCTgtatgtattt ... ggtattccag-
EST: gi|74242202|gb|DT650116.1|DT650116
EST:     TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCT                         G
genomic: TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCTgtatgtattt ... ggtattccag-
EST: gi|78111156|gb|DV529553.1|DV529553
EST:     TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCT                         TAACAGCTGAAATTGCTGTTCCAATTGGTGGTCAAGGGGCAAACANCA-CT
genomic: TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCTgtatgtattt ... ggtattccagTAACAGCTGAAATTGCTGTTCCAATTGGTGGTCAAGGGGCAAACA-CAACT
EST: gi|149095756|gb|EE181396.2|EE181396
EST:     TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCT                         G
genomic: TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCTgtatgtattt ... ggtattccag-
EST: gi|149095756|gb|EE181396.2|EE181396
EST:     TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCT                         G
genomic: TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCTgtatgtattt ... ggtattccag-
EST: gi|149095756|gb|EE181396.2|EE181396
EST:     TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCT                         G
genomic: TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCTgtatgtattt ... ggtattccag-

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 1 RNA-Seqlibrary.


Block sizes: 16 (upstream exon), 49 (downstream exon)
Score: 4

AATGGAGATGGGTGGGGGCAGTTGGGACAAAGATAAAGTCCAAAGGGCTCTCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCTgtatgtattt ... ggtattccagTAACAGCTGAAATTGCTGTTCCAATTGGTGGTCAAGGGGCAAACACAACTGATCGAGCTCCTACTGGGGAAGCTGGTCTCTCTGGGATTCCAAACACCGC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATGGAGATGGGTGGGGGCAGTTGGGACAAAGATAAAGTCCAAAGGGCTCTCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCTgtatgtatttttctcattgccccattcttttgcatttttgcacttaatgatggaatccaattttctggtgctaatagattatttatgtcaaacattagggtattccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT