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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAGCCATCAAAGTACATTAAACACTGGACGGGCACCAAACCGAAGACTGGTGCAAAATACACATGTGACATTGGATATGAGCGATTCCTAGGGCCTGAGgtatttggttttactaaacagagcatacagatatgtagtaacttctatttcaccattcgtgtcagacttgcagtaattggttgtagcttgtaggtagaca...

Basic information

species Zea mays
transcript AC205703.4_FGT002
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC205703.4_FGT002 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os02g38340.1 (Oryza sativa), 5'ss of exon 6
GGAGCCATCAAAGTACATTAAACACTGGACGGGCACCAAACCGAAGACTGGTGCAAAATACACATGTGACATTGGATATGAGCGATTCCTAGGGCCTGAGgtatttggttttactaaacagagcatacagatatgtagtaacttctat--ttcaccattcgtgtcagacttgcagtaattggttgtagcttgtaggtagaca--
 |||||    |||||||| || |||||||  |||| |||||| || |||||||| |||||||| || |||||||||||||| || |||||||||||||||||| ||| |||| |   |  | |   ||   ||  | ||  ||||||   |  | |||| |  | ||  |  ||  | ||   ||    |  ||  |  ||   
AGAGCCCAATAAGTACATAAAGCACTGGAGTGGCATCAAACCAAAAACTGGTGCCAAATACACCTGCGACATTGGATATGAACGCTTCCTAGGGCCTGAGgtaattgattttgcattaatgtgttcaccattaact-gtggcttctacaatgtaacatttgatttaggtt--caaaacttaactgcga-tcataatttaactcc
















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|8318635|gb|BE025380.1|BE025380
EST:     GTGCAAAATACACATGTGACATTGGATATGAGCGATTCCTAGGGCCTGAG                         ATCTTCTTCAACCCAGAGATATATAACAACGACTTCACCACTCCTTTGCAA
genomic: GTGCAAAATACACATGTGACATTGGATATGAGCGATTCCTAGGGCCTGAGgtatttggtt ... atctgcgcagATCTTCTTCAACCCAGAGATATATAACAACGACTTCACCACTCCTTTGCAA
EST: gi|32920418|gb|CF025230.1|CF025230
EST:     GTGCAAAATACACATGTGACATTGGATATGAGCGATTCCTAGGGCCTGAG                         ATCTTCTTCAACCCAGAGATATATAACAACGACTTCACCACTCCTTTGCAA
genomic: GTGCAAAATACACATGTGACATTGGATATGAGCGATTCCTAGGGCCTGAGgtatttggtt ... atctgcgcagATCTTCTTCAACCCAGAGATATATAACAACGACTTCACCACTCCTTTGCAA
EST: gi|32921953|gb|CF026765.1|CF026765
EST:     GTGCAAAATACACATGTGACATTGGATATGAGCGATTCCTAGGGCCTGAG                         ATCTTCTTCAACCCAGAGATATATAACAGCGACTTCACCACTCCTTTGCAA
genomic: GTGCAAAATACACATGTGACATTGGATATGAGCGATTCCTAGGGCCTGAGgtatttggtt ... atctgcgcagATCTTCTTCAACCCAGAGATATATAACAACGACTTCACCACTCCTTTGCAA
EST: gi|67032896|gb|CO461645.1|CO461645
EST:     GTGCAAAATACACATGTGACATTGGATATGAGCGATTCCTAGGGCCTGAG                         ATCTTCTTCAACCCAGAGATATATAACAACGACTTCACCACTCCTTTGCAA
genomic: GTGCAAAATACACATGTGACATTGGATATGAGCGATTCCTAGGGCCTGAGgtatttggtt ... atctgcgcagATCTTCTTCAACCCAGAGATATATAACAACGACTTCACCACTCCTTTGCAA
EST: gi|32920457|gb|CF025269.1|CF025269
EST:     GTGCAAAATACACATGTGACATTGGATATGAGCGATTCCTAGGGCCTGAG                         ATCTTCTTCAACCCAGAGATATATAACAACGACTTCACCACTCCTTTGCAA
genomic: GTGCAAAATACACATGTGACATTGGATATGAGCGATTCCTAGGGCCTGAGgtatttggtt ... atctgcgcagATCTTCTTCAACCCAGAGATATATAACAACGACTTCACCACTCCTTTGCAA
EST: gi|32922282|gb|CF027094.1|CF027094
EST:     GTGCAAAATACACATGTGACATTGGATATGAGCGATTCCTAGGGCCTGAG                         ATCTTCTTCAACCCAGAGATATATAACAACGACTTCACCACTCCTTTGCAA
genomic: GTGCAAAATACACATGTGACATTGGATATGAGCGATTCCTAGGGCCTGAGgtatttggtt ... atctgcgcagATCTTCTTCAACCCAGAGATATATAACAACGACTTCACCACTCCTTTGCAA
EST: gi|211162839|gb|FL160696.1|FL160696
EST:     GTGCAAAATACACATGTGACATTGGATATGAGCGATTCCTAGGGCCTGAG                         ATCTTCTTCAACCCAGAGATATATAACAACCGACTTCACCACTCCCTTTGC
genomic: GTGCAAAATACACATGTGACATTGGATATGAGCGATTCCTAGGGCCTGAGgtatttggtt ... atctgcgcagATCTTCTTCAACCCAGAGATATATAACAAC-GACTTCACCACTCC-TTTGC
EST: gi|32846117|gb|CD985798.1|CD985798
EST:     GTGCAAAATACACATGTGACATTGGATATGAGCGATTCCTAGGGCCTGAG                         ATCTTCTTCAACCCAGAGATATATAACAACGACTTCACCACTCCTTTGCAA
genomic: GTGCAAAATACACATGTGACATTGGATATGAGCGATTCCTAGGGCCTGAGgtatttggtt ... atctgcgcagATCTTCTTCAACCCAGAGATATATAACAACGACTTCACCACTCCTTTGCAA
EST: gi|67042751|gb|CO469006.1|CO469006
EST:     CTAGGGCTTGCG                         ATCTTCTTCAACCCAGAGATATATAACAACGACTTCACCACTCCTTTGCAT
genomic: CTAGGGCCTGAGgtatttggtt ... atctgcgcagATCTTCTTCAACCCAGAGATATATAACAACGACTTCACCACTCCTTTGCAA
EST: gi|148957989|gb|EC904154.2|EC904154
EST:     GACATTGGATATGAGGGATTCCTAGGGCCGGAG                         ANNNNNNNCAACCCAGAGATATATAACAACGACTTCACCACTCCTTTGCAA
genomic: GACATTGGATATGAGCGATTCCTAGGGCCTGAGgtatttggtt ... atctgcgcagATCTTCTTCAACCCAGAGATATATAACAACGACTTCACCACTCCTTTGCAA
EST: gi|109637254|gb|EC590799.1|EC590799
EST:     GACATTGGATATGAGCGATTCCTAGGGCCTGAG                         ATCTTCTTCAACCCAGAGATATATAACAACGACTTCACCACTCCTTTGCAA
genomic: GACATTGGATATGAGCGATTCCTAGGGCCTGAGgtatttggtt ... atctgcgcagATCTTCTTCAACCCAGAGATATATAACAACGACTTCACCACTCCTTTGCAA

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), 47 (downstream exon)
Score: 105

GGAGCCATCAAAGTACATTAAACACTGGACGGGCACCAAACCGAAGACTGGTGCAAAATACACATGTGACATTGGATATGAGCGATTCCTAGGGCCTGAGgtatttggtt ... atctgcgcagATCTTCTTCAACCCAGAGATATATAACAACGACTTCACCACTCCTTTGCAAGTTGTTATTGACAAGTGCATCCAATCATCTCCAATCGACACAAGGAGGG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 117

GGAGCCATCAAAGTACATTAAACACTGGACGGGCACCAAACCGAAGACTGGTGCAAAATACACATGTGACATTGGATATGAGCGATTCCTAGGGCCTGAGgtatttggtt ... atctgcgcagATCTTCTTCAACCCAGAGATATATAACAACGACTTCACCACTCCTTTGCAAGTTGTTATTGACAAGTGCATCCAATCATCTCCAATCGACACAAGGAGGG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 186

GGAGCCATCAAAGTACATTAAACACTGGACGGGCACCAAACCGAAGACTGGTGCAAAATACACATGTGACATTGGATATGAGCGATTCCTAGGGCCTGAGgtatttggtt ... atctgcgcagATCTTCTTCAACCCAGAGATATATAACAACGACTTCACCACTCCTTTGCAAGTTGTTATTGACAAGTGCATCCAATCATCTCCAATCGACACAAGGAGGG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 159

GGAGCCATCAAAGTACATTAAACACTGGACGGGCACCAAACCGAAGACTGGTGCAAAATACACATGTGACATTGGATATGAGCGATTCCTAGGGCCTGAGgtatttggtt ... atctgcgcagATCTTCTTCAACCCAGAGATATATAACAACGACTTCACCACTCCTTTGCAAGTTGTTATTGACAAGTGCATCCAATCATCTCCAATCGACACAAGGAGGG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAGCCATCAAAGTACATTAAACACTGGACGGGCACCAAACCGAAGACTGGTGCAAAATACACATGTGACATTGGATATGAGCGATTCCTAGGGCCTGAGgtatttggttttactaaacagagcatacagatatgtagtaacttctatttcaccattcgtgtcagacttgcagtaattggttgtagcttgtaggtagaca

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaacagag