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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtaactgatttgattattatactatactcgtgtgatgaatttgttggaggtctttagtactaatggtttgaagcaatgtggtaccacagATAATACAACATGTGCTTCTGGATATGCCCGGGCTTGCATTCTTCACGACATATGCACTTTTAGTGCTCTTCTGGGCTGAGATTTATTATCAG

Basic information

species Zea mays
transcript GRMZM2G003076_T03
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G003076_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os10g39220.1 (Oryza sativa), 3'ss of exon 3
gtttgtaactgatttgattattatactatactcgtgtgatgaatttgttggaggtctttagtactaatggtttgaagcaatgtggtaccacagATAATACAACATGTGCTTCTGGATATGCCCGGGCTTGCATTCTTCACGACATATGCACTTTTAGTGCTCTTCTGGGCTGAGATTTATTATCAG
||||||    || ||| |  | ||   ||  ||    |||  ||      |     || |||  |  |||| | ||||||| |  |||| |||||| | |||||||||||||| |||||||||||||| |||||||||||||| ||||||||||| |||||||||||||| |||||||||||||||
gtttgt----gaattgttgctaatttgatgatca---gattgatgctgcagttcatttaagttatggtggtattaagcaatattctaccgcagATACTTCAACATGTGCTTCTAGATATGCCCGGGCTCGCATTCTTCACGACGTATGCACTTTTGGTGCTCTTCTGGGCCGAGATTTATTATCAG

upper sequence: GRMZM2G003076_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA07G28990.1 (Glycine max), 3'ss of exon 3
------------------------------------------gtttgtaactgatttgattattatactatactcgtgtgatgaatttgttggaggtctttagtactaatggtttgaagcaatgtggtaccacagATAATACAACATGTGCTTCTGGATATGCCCGGGCTTGCATTCTTCACGACATATGCACTTTTAGTGCTCTTCTGGGCTGAGATTTATTATCAG
                                           |||| | || || | | || | |  |||  ||   | |  |  |  || ||     ||| | || |   | || |      ||       ||||  | |||||  |  | || ||  ||||  | ||||| ||||| || |||||||||||||| || || ||||||||||||||||||||||||
gtattggagtatagggaatgtggcatttatttttgagttattttttgaacctaatattaataatttgttattttctaattagaatgtgattagactcacttaatgctcac--tctgcatttgcttgtgtttgtagATTGTTCAACACATCTTGCTTGACGTGCCGAGTCTTGCTTTCTTTACAACATATGCACTTTTGGTCCTGTTCTGGGCTGAGATTTATTATCAG

upper sequence: GRMZM2G003076_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA20G01360.1 (Glycine max), 3'ss of exon 3
-----------------------------------------------gtttgtaac-tgatttgattattatactatactcgtgtgat-gaatttgttggaggtctttagtactaatggtttgaagcaatgtggtaccacagATAATACAACATGTGCTTCTGGATATGCCCGGGCTTGCATTCTTCACGACATATGCACTTTTAGTGCTCTTCTGGGCTGAGATTTATTATCAG
                                                ||  |||| | |  | | |  | || |||  ||   | |  |||| || |     ||  |  |||| |     ||        |        ||||  | |||||  |  | || ||  ||||  | ||||| ||||| || |||||||||||||| || || |||||||||||||||||||| |||
gtattcgagtatagggaatggaatgtaacatttaatttgagtaattttttcttaacataagattagttgtttattattttctaattacagaatgtggttagactcacttatactcactcactgcgtttgcttatgtttgtagATTGTTCAACACATCTTGCTTGACGTGCCGAGTCTTGCTTTCTTTACAACATATGCACTTTTGGTCCTGTTCTGGGCTGAGATTTATTACCAG

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|149109085|gb|EE189999.2|EE189999
EST:     GGTCTGTCGTGTTTGTGCTGCGGCGAAATGTGCAACTTGTAGAGCCTGAG                         ATAATACAACATGTGCTTCTGGATATGCCCGGGCTTGCATTCTTCACGACA
genomic: GGTCTGTCGTGTTTGTGCTGCGGCGAAATGTGCAACTTGTAGAGCCTGAGgtttgtaact ... ggtaccacagATAATACAACATGTGCTTCTGGATATGCCCGGGCTTGCATTCTTCACGACA
EST: gi|211382284|gb|FL169263.1|FL169263
EST:     GGTCTGTCGTGTTTGTGCTGCGGCGAAATGTGCAACTTGTAGAGCCTGAG                         ATAATACAACATGTGCTTCTGGATATGCC
genomic: GGTCTGTCGTGTTTGTGCTGCGGCGAAATGTGCAACTTGTAGAGCCTGAGgtttgtaact ... ggtaccacagATAATACAACATGTGCTTCTGGATATGCC
EST: gi|148948893|gb|EC894307.2|EC894307
EST:     GGTCTGTCGTGTTTGTGCTGCGGCGAAATGTGCAACTTGTAGAGCCTGAG                         ATAATACAACATGTGCTTCTGGATATGCCCGGGCTTGCATTCTTCACGACA
genomic: GGTCTGTCGTGTTTGTGCTGCGGCGAAATGTGCAACTTGTAGAGCCTGAGgtttgtaact ... ggtaccacagATAATACAACATGTGCTTCTGGATATGCCCGGGCTTGCATTCTTCACGACA
EST: gi|149081139|gb|EE170248.2|EE170248
EST:     GGTCTGTCGTGTTTGTGCTGCGGCGAAATGTGCAACTTGTAGAGCCTGAG                         ATAATACAACATGTGCTTCTGGATATGCCCGGGCTTGCATTCTTCACGACA
genomic: GGTCTGTCGTGTTTGTGCTGCGGCGAAATGTGCAACTTGTAGAGCCTGAGgtttgtaact ... ggtaccacagATAATACAACATGTGCTTCTGGATATGCCCGGGCTTGCATTCTTCACGACA

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: 45 (upstream exon), 48 (downstream exon)
Score: 96

TGCGGTCTGTCGTGTTTGTGCTGCGGCGAAATGTGCAACTTGTAGAGCCTGAGgtttgtaact ... ggtaccacagATAATACAACATGTGCTTCTGGATATGCCCGGGCTTGCATTCTTCACGACATATGCACTTTTAGTGCTCTTCTGGGCTGAGATTTATTATCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 172

TGCGGTCTGTCGTGTTTGTGCTGCGGCGAAATGTGCAACTTGTAGAGCCTGAGgtttgtaact ... ggtaccacagATAATACAACATGTGCTTCTGGATATGCCCGGGCTTGCATTCTTCACGACATATGCACTTTTAGTGCTCTTCTGGGCTGAGATTTATTATCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 142

TGCGGTCTGTCGTGTTTGTGCTGCGGCGAAATGTGCAACTTGTAGAGCCTGAGgtttgtaact ... ggtaccacagATAATACAACATGTGCTTCTGGATATGCCCGGGCTTGCATTCTTCACGACATATGCACTTTTAGTGCTCTTCTGGGCTGAGATTTATTATCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 303

TGCGGTCTGTCGTGTTTGTGCTGCGGCGAAATGTGCAACTTGTAGAGCCTGAGgtttgtaact ... ggtaccacagATAATACAACATGTGCTTCTGGATATGCCCGGGCTTGCATTCTTCACGACATATGCACTTTTAGTGCTCTTCTGGGCTGAGATTTATTATCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgaatttgttggaggtctttagtactaatggtttgaagcaatgtggtaccacagATAATACAACATGTGCTTCTGGATATGCCCGGGCTTGCATTCTTCACGACATATGCACTTTTAGTGCTCTTCTGGGCTGAGATTTATTATCAG
                       tactaat  putative branch site (score: 303)
                  tttagta  TA-rich tract