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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatgccctgtctttaactcacattggcaatgtcttagcatatatgttcattataatgctgtatttcataattcagcacaactcagtactttgtttgttcactggataacttttcatgttgaattttgaacatcagGCGAGTGCGGATATTATGTTTGGTGGAATTACTATAGTGTGTGGAATTGTTGGAACACTAGCAGGAGGTTTCATCCTTGACAAGATAGGGTCTACTATTC

Basic information

species Zea mays
transcript GRMZM2G164743_T01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G164743_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os04g44430.1 (Oryza sativa), 3'ss of exon 9
gtaaatgccctgtctttaactcacattggcaatgtcttagcatatatgttcattataatgctgtatttcataattcagcacaactc-agtactttgtttgttcactggataacttttcatgttgaattttga-acatcagGCGAGTGCGGATATTATGTTTGGTGGAATTACTATAGTGTGTGGAATTGTTGGAACACTAGCAGGAGGTTTCATCCTTGACAAGATAGGGTCTACTATTC
                                     |||  ||   ||  |  |||   ||   |      |||  | | | ||  | ||| || ||  |||| ||| |||| |||| ||||||| ||||  ||| ||||||||||| ||||| |||||||||||||| || || || ||||||||  |||| || ||  |||| |||||||| |||||||||||||  || || ||  
-------------------------------------tagtgta---gtgtagcatacatctaactgcagatatttggaatatctttaatacattcttgtttcattggttaacctttcttgttgaactttgtcacaccagGCGAGTGCAGATATAATGTTTGGTGGAATAACAATTGTCTGTGGAATATTTGGGACTCTTTCAGGGGGTTTCATTCTTGACAAGATAGACTCAACAATAT
















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|211351534|gb|FL310930.1|FL310930
EST:     GTGCTTATTCCTACTGGGGCCCAAAGGCAGGTCAAGAGATCTACAATATG                         GCGAGTGCGGATATTATGTTTGGTGGAATTACTATAGTGTGTGGAATTGTT
genomic: GTGCTTATTCCTACTGGGGCCCAAAGGCAGGTCAAGAGATCTACAATATGgtaaatgccc ... tgaacatcagGCGAGTGCGGATATTATGTTTGGTGGAATTACTATAGTGTGTGGAATTGTT
EST: gi|5325067|gb|AI783258.1|AI783258
EST:     GTGCTTATTCCTACTGGGGCCCAAAGGCAGGTCAAGAGATCTACAATATG                         GCGAGTGCGGATCTTATGTTTGGTGGAATTACTATAGTGTGTGGAATTGTT
genomic: GTGCTTATTCCTACTGGGGCCCAAAGGCAGGTCAAGAGATCTACAATATGgtaaatgccc ... tgaacatcagGCGAGTGCGGATATTATGTTTGGTGGAATTACTATAGTGTGTGGAATTGTT
EST: gi|211002558|gb|FL365524.1|FL365524
EST:     GTTCTTATTCCTACTGGGTCCCAAAGGCAGGTCAAGAGATCTACAATATG                         GCGAGTGCGGATATTATGTTTGGTGGAATTACTATAGTGTGTGGAATTGTT
genomic: GTGCTTATTCCTACTGGGGCCCAAAGGCAGGTCAAGAGATCTACAATATGgtaaatgccc ... tgaacatcagGCGAGTGCGGATATTATGTTTGGTGGAATTACTATAGTGTGTGGAATTGTT
EST: gi|71429290|gb|DR810340.1|DR810340
EST:     CAAAGGCAGGTCAAGAGATCTACAATATG                         GCGAGTGCGGATATTATGTTTGGTGGAATTACTATAGTGTGTGGAATTGTT
genomic: CAAAGGCAGGTCAAGAGATCTACAATATGgtaaatgccc ... tgaacatcagGCGAGTGCGGATATTATGTTTGGTGGAATTACTATAGTGTGTGGAATTGTT
EST: gi|6056590|gb|AW090995.1|AW090995
EST:     GTGCTTATTCCTACTGGGGCCCAAAGGCAGGTCAAGAGATCTACAATATG                         GCGAGTGCGGATCTTATGTTTGGTTTTATTACTATAGTGTGTGGAATTGTT
genomic: GTGCTTATTCCTACTGGGGCCCAAAGGCAGGTCAAGAGATCTACAATATGgtaaatgccc ... tgaacatcagGCGAGTGCGGATATTATGTTTGGTGGAATTACTATAGTGTGTGGAATTGTT
EST: gi|5846879|gb|AI999962.1|AI999962
EST:     GTGCTTATTCCTACTGGGGCCCAAAGGCAGGTCAAGAGATCTACAATATG                         GCGAGTGCGGATCTTATGTTTGGTGGAATTACTATAGTGTGTGGAATTGTT
genomic: GTGCTTATTCCTACTGGGGCCCAAAGGCAGGTCAAGAGATCTACAATATGgtaaatgccc ... tgaacatcagGCGAGTGCGGATATTATGTTTGGTGGAATTACTATAGTGTGTGGAATTGTT

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: 136

GTTATATCTCCTACAACTTCGTCATTGGTGCTTATTCCTACTGGGGCCCAAAGGCAGGTCAAGAGATCTACAATATGgtaaatgccc ... tgaacatcagGCGAGTGCGGATATTATGTTTGGTGGAATTACTATAGTGTGTGGAATTGTTGGAACACTAGCAGGAGGTTTCATCCTTGACAAGATAGGGTCTACTATTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 174

GTTATATCTCCTACAACTTCGTCATTGGTGCTTATTCCTACTGGGGCCCAAAGGCAGGTCAAGAGATCTACAATATGgtaaatgccc ... tgaacatcagGCGAGTGCGGATATTATGTTTGGTGGAATTACTATAGTGTGTGGAATTGTTGGAACACTAGCAGGAGGTTTCATCCTTGACAAGATAGGGTCTACTATTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 170

GTTATATCTCCTACAACTTCGTCATTGGTGCTTATTCCTACTGGGGCCCAAAGGCAGGTCAAGAGATCTACAATATGgtaaatgccc ... tgaacatcagGCGAGTGCGGATATTATGTTTGGTGGAATTACTATAGTGTGTGGAATTGTTGGAACACTAGCAGGAGGTTTCATCCTTGACAAGATAGGGTCTACTATTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 101

GTTATATCTCCTACAACTTCGTCATTGGTGCTTATTCCTACTGGGGCCCAAAGGCAGGTCAAGAGATCTACAATATGgtaaatgccc ... tgaacatcagGCGAGTGCGGATATTATGTTTGGTGGAATTACTATAGTGTGTGGAATTGTTGGAACACTAGCAGGAGGTTTCATCCTTGACAAGATAGGGTCTACTATTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcagtactttgtttgttcactggataacttttcatgttgaattttgaacatcagGCGAGTGCGGATATTATGTTTGGTGGAATTACTATAGTGTGTGGAATTGTTGGAACACTAGCAGGAGGTTTCATCCTTGACAAGATAGGGTCTACTATTC
                      ggataac  putative branch site (score: 101)
                        ataactttt  TA-rich tract