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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgattcctgttctataactttatatatattcctggcaaaaaaatatagatgtatacgatgtgacttttaattgtcattgatataagcaaaagttcacttaaatgcatttactgctattgacgcagGCTTTCAAAACCAAGTATGCCACCATTGGTGTTG

Basic information

species Zea mays
transcript GRMZM2G073950_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G073950_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os02g33080.2 (Oryza sativa), 3'ss of exon 4
gtgattcctgttctataactttatatatattcctggcaaaaaaatatagatgtatacgatgtgacttttaattgtcattgatataagcaaaagttcact-----taaatgcatttactgctattgacgcagGCTTTCAAAACCAAGTATGCCACCATTGGTGTTG
                                   | ||| |    |  || | ||     |||    |  |||   ||| ||  || |||| ||||||     | ||||  |  | || || | | ||||||||||||||| |||||||| || ||||||||||
-----------------------------------gtaaacatggttttatatttatatcttgataggt--ttgcacttgttagtagtaaaaattcactaggtgttaatgtgta-attggtact-atgcagGCTTTCAAAACGAAGTATGCTACAATTGGTGTTG
















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|211141687|gb|FL053515.1|FL053515
EST:     GATACCAAGAGAAGTTTTATTTCAACCCCGGTGACACTGGCTTTAAG                         GCTTTCAAAACCAAGTATGCCACCATTGGTGTTG
genomic: GATATCAAGAGAAGTTTTATTTCAACCCCGGTGACACTGGCTTTAAGgtgattcctg ... attgacgcagGCTTTCAAAACCAAGTATGCCACCATTGGTGTTG
EST: gi|78077685|gb|DV506119.1|DV506119
EST:     GATATCAAGAGAAGTTTTATTTCAACCCCGGTGACACTGGCTTTAAG                         GCTTTCAAAACCAAGTATGCCACCATTGGTGTTG
genomic: GATATCAAGAGAAGTTTTATTTCAACCCCGGTGACACTGGCTTTAAGgtgattcctg ... attgacgcagGCTTTCAAAACCAAGTATGCCACCATTGGTGTTG
EST: gi|211141683|gb|FL053511.1|FL053511
EST:     GATACCAAGAGAAGTTTTATTTCAACCCCGGTGACACTGGCTTTAAG                         GCTTTCAAAACCAAGTATGCCACCATTGGTGTTG
genomic: GATATCAAGAGAAGTTTTATTTCAACCCCGGTGACACTGGCTTTAAGgtgattcctg ... attgacgcagGCTTTCAAAACCAAGTATGCCACCATTGGTGTTG
EST: gi|113702021|gb|EE679525.1|EE679525
EST:     GATATCAAGAGAAGTTTTATTTCAACCCCGGTGACACTGGCTTTAAG                         GCTTTCAAAACCAAGTATGCCACCATTGGTGTTG
genomic: GATATCAAGAGAAGTTTTATTTCAACCCCGGTGACACTGGCTTTAAGgtgattcctg ... attgacgcagGCTTTCAAAACCAAGTATGCCACCATTGGTGTTG
EST: gi|29130437|gb|CB381141.1|CB381141
EST:     GATATCAAGAGAAGTTTTATTTCAACCCCGGTGACACTGGCTTTAAG                         GCTTTCAAAACCAAGTATGCCACCATTGGTGTTG
genomic: GATATCAAGAGAAGTTTTATTTCAACCCCGGTGACACTGGCTTTAAGgtgattcctg ... attgacgcagGCTTTCAAAACCAAGTATGCCACCATTGGTGTTG
EST: gi|91056600|gb|EB167018.1|EB167018
EST:     GATATCAAGAGAAGTTTTATTTCAACCCCGGTGACACTGGCTTTAAG                         GCTTTCAAAACCAAGTATGCCACCATTGGTGTTG
genomic: GATATCAAGAGAAGTTTTATTTCAACCCCGGTGACACTGGCTTTAAGgtgattcctg ... attgacgcagGCTTTCAAAACCAAGTATGCCACCATTGGTGTTG
EST: gi|148953399|gb|EE152896.2|EE152896
EST:     GATATCAAGAGAAGTTTTATTTCAACCCCGGTGACACTGGCTTTAAG                         GCTTTCAAAACCAAGTATGCCACCATTGGTGTTG
genomic: GATATCAAGAGAAGTTTTATTTCAACCCCGGTGACACTGGCTTTAAGgtgattcctg ... attgacgcagGCTTTCAAAACCAAGTATGCCACCATTGGTGTTG
EST: gi|78081735|gb|DV510147.1|DV510147
EST:     GATATCAAGAGAAGTTTTATTTCAACCCCGGTGACACTGGCTTTAAG                         GCTTTCAAAACCAAGTATGCCACCATTGGTGTTG
genomic: GATATCAAGAGAAGTTTTATTTCAACCCCGGTGACACTGGCTTTAAGgtgattcctg ... attgacgcagGCTTTCAAAACCAAGTATGCCACCATTGGTGTTG
EST: gi|88758160|gb|DY542301.1|DY542301
EST:     GATATCAAGAGAAGTTTTATTTCAACCCCGGTGACACTGGCTTTAAG                         GCTTTCAAAACCAAGTATGCCACCATTGGTGTTG
genomic: GATATCAAGAGAAGTTTTATTTCAACCCCGGTGACACTGGCTTTAAGgtgattcctg ... attgacgcagGCTTTCAAAACCAAGTATGCCACCATTGGTGTTG
EST: gi|50324199|gb|CO519325.1|CO519325
EST:     GATATCAAGAGAAGTTTTATTTCAACCCCGGTGACACTGGCTTTAAG                         GCTTTCAAAACCAAGTATGCCACCATTGGTGTTG
genomic: GATATCAAGAGAAGTTTTATTTCAACCCCGGTGACACTGGCTTTAAGgtgattcctg ... attgacgcagGCTTTCAAAACCAAGTATGCCACCATTGGTGTTG
EST: gi|84908437|gb|DW404315.1|DW404315
EST:     GATACCAAGAGAAGTTTTATTTCAACCCCGGTGACACTGGCTTTAAG                         GCTTTCAAAACCAAGTATGCCACCATTGGTGTTG
genomic: GATATCAAGAGAAGTTTTATTTCAACCCCGGTGACACTGGCTTTAAGgtgattcctg ... attgacgcagGCTTTCAAAACCAAGTATGCCACCATTGGTGTTG
EST: gi|60346678|gb|DN213651.1|DN213651
EST:     GATATCAAGAGAAGTTTTATTTCAACCCCGGTGACACTGGCTTTAAG                         GCTTTCAAAACCAAGTATGCCACCATTGGTGTTG
genomic: GATATCAAGAGAAGTTTTATTTCAACCCCGGTGACACTGGCTTTAAGgtgattcctg ... attgacgcagGCTTTCAAAACCAAGTATGCCACCATTGGTGTTG
EST: gi|148939361|gb|EC883888.2|EC883888
EST:     GATATCAAGAGAAGTTTTATTTCAACCCCGGTGACACTGGCTTTAAG                         GCTTTCAAAACCAAGTATGCCACCATTGGTGTTG
genomic: GATATCAAGAGAAGTTTTATTTCAACCCCGGTGACACTGGCTTTAAGgtgattcctg ... attgacgcagGCTTTCAAAACCAAGTATGCCACCATTGGTGTTG
EST: gi|78078908|gb|DV507320.1|DV507320
EST:     GATATCAAGAGAAGTTTTATTTCAACCCCGGTGACACTGGCTTTAAG                         GCTTTCAAAACCAAGTATGCCACCATTGGTGTTG
genomic: GATATCAAGAGAAGTTTTATTTCAACCCCGGTGACACTGGCTTTAAGgtgattcctg ... attgacgcagGCTTTCAAAACCAAGTATGCCACCATTGGTGTTG
EST: gi|71417126|gb|DR803932.1|DR803932
EST:     GATATCAAGAGAAGTTTTATTTCAACCCCGGTGACACTGGCTTTAAG                         GCTTTCAAAACCAAGTATGCCACCATTGGTGTTG
genomic: GATATCAAGAGAAGTTTTATTTCAACCCCGGTGACACTGGCTTTAAGgtgattcctg ... attgacgcagGCTTTCAAAACCAAGTATGCCACCATTGGTGTTG
EST: gi|71417127|gb|DR803933.1|DR803933
EST:     GATATCAAGAGAAGTTTTATTTCAACCCCGGTGACACTGGCTTTAAG                         GCTTTCAAAACCAAGTATGCCACCATTGGTGTTG
genomic: GATATCAAGAGAAGTTTTATTTCAACCCCGGTGACACTGGCTTTAAGgtgattcctg ... attgacgcagGCTTTCAAAACCAAGTATGCCACCATTGGTGTTG
EST: gi|29544724|gb|CB605104.1|CB605104
EST:     CAGGATATCAAGAGAAGTTTTATTTCAACCCCGGTGACACTGGCTTTAAG                         GCTTTCAAAACCAAGTATGCCACCATTGGTGTTG
genomic: CAGGATATCAAGAGAAGTTTTATTTCAACCCCGGTGACACTGGCTTTAAGgtgattcctg ... attgacgcagGCTTTCAAAACCAAGTATGCCACCATTGGTGTTG
EST: gi|94478259|gb|EB707217.1|EB707217
EST:     GATATCAAGAGAAGTTTTATTTCAACCCCGGTGACACTGGCTTTAAG                         GCTTTCAAAACCAAGTATGCCACCATTGGTGTTG
genomic: GATATCAAGAGAAGTTTTATTTCAACCCCGGTGACACTGGCTTTAAGgtgattcctg ... attgacgcagGCTTTCAAAACCAAGTATGCCACCATTGGTGTTG
EST: gi|78077686|gb|DV506120.1|DV506120
EST:     GATATCAAGAGAAGTTTTATTTCAACCCCGGTGACACTGGCTTTAAG                         GCTTTCAAAACCAAGTATGCCACCATTGGTGTTG
genomic: GATATCAAGAGAAGTTTTATTTCAACCCCGGTGACACTGGCTTTAAGgtgattcctg ... attgacgcagGCTTTCAAAACCAAGTATGCCACCATTGGTGTTG

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: 47 (upstream exon), 34 (downstream exon)
Score: 188

GATATCAAGAGAAGTTTTATTTCAACCCCGGTGACACTGGCTTTAAGgtgattcctg ... attgacgcagGCTTTCAAAACCAAGTATGCCACCATTGGTGTTG


Block sizes: 47 (upstream exon), 34 (downstream exon)
Score: 294

GATATCAAGAGAAGTTTTATTTCAACCCCGGTGACACTGGCTTTAAGgtgattcctg ... attgacgcagGCTTTCAAAACCAAGTATGCCACCATTGGTGTTG


Block sizes: 47 (upstream exon), 34 (downstream exon)
Score: 331

GATATCAAGAGAAGTTTTATTTCAACCCCGGTGACACTGGCTTTAAGgtgattcctg ... attgacgcagGCTTTCAAAACCAAGTATGCCACCATTGGTGTTG


Block sizes: 47 (upstream exon), 34 (downstream exon)
Score: 330

GATATCAAGAGAAGTTTTATTTCAACCCCGGTGACACTGGCTTTAAGgtgattcctg ... attgacgcagGCTTTCAAAACCAAGTATGCCACCATTGGTGTTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtcattgatataagcaaaagttcacttaaatgcatttactgctattgacgcagGCTTTCAAAACCAAGTATGCCACCATTGGTGTTG
                                            tattgac  putative branch site (score: 330)
     attgatataa  TA-rich tract