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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaagcttgctcgactgccttgccttgtgtactgttatgttaatagcttctcagccgctccgctgggtttttttgaatctgatgaatcgacgggcagCGCTGGTCCCGCTGGAGGAGCTCATGGAGCCGCCCGTGAGGCAGCGCTACGACGTGCCGTATGACGCGGAGGTGTTCGACATGCTCAACGCCGCGGCCCG

Basic information

species Zea mays
transcript GRMZM2G045278_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G045278_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g63010.1 (Oryza sativa), 3'ss of exon 1
---------------------gtaaaagcttgctcgact---gccttgccttgtgtactgt---tatgttaatagcttctc---agccgctccgctgggtttttttgaatctg-atgaatcgacgggcagCGCTGGTCCCGCTGGAGGAGCTCATGGAGCCGCCCGTGAGGCAGCGCTACGACGTGCCGTATGACGCGGAGGTGTTCGACATGCTCAACGCCGCGGCCCG
                       | || |   |     |     ||||| || |  | | |   |   || ||  |   ||   |   |    |    ||    | |  |||| |   |||| |  ||||||||| ||||||| ||||||||||||||| || | |||||||||||||| ||  | || |  ||||  ||||||||||||||||||||||||| | ||||
gtacgtaatagtaatactaagagagaaacgcaccgagtttacctcttgcattctaaattttgaatgccttgatctcccatcgaaaattgtcatgtcatgtcgcgtcgtctctgtactgatcg-cacgcagCGCTGATCCCGCTCGAGGAGCTCATGGAGACGGCGGTGAGGCAGCGCTATGATATACCTTCGGACGAAGAGGTGTTCGACATGCTCAACGCCGTGTCCCG
















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|7216551|gb|AW562673.1|AW562673
EST:     CCACGGCCGTGAGGAGGGCAAGAACGTCCTCTGGTCCCGCACCGGATCGC                         CGCTGGTCCCGCTGGAGGAGCTCATGGAGCCGCCCGTGAGGCAGCGCTACG
genomic: CCACGGCCGTGAGGAGGGCAAGAACGTCCTCTGGTCCCGCACCGGATCGCgtaaaagctt ... cgacgggcagCGCTGGTCCCGCTGGAGGAGCTCATGGAGCCGCCCGTGAGGCAGCGCTACG
EST: gi|50337518|gb|CO532644.1|CO532644
EST:     CCACGGCCGTGAGGAGGGCAAGAACGTCCTCTGGTCCCGCACCGGATCGC                         CGCTGGTCCCGCTGGAGGAGCTCATGGAGCCGCCCGTGAGGCAGCGCTACG
genomic: CCACGGCCGTGAGGAGGGCAAGAACGTCCTCTGGTCCCGCACCGGATCGCgtaaaagctt ... cgacgggcagCGCTGGTCCCGCTGGAGGAGCTCATGGAGCCGCCCGTGAGGCAGCGCTACG
EST: gi|32869247|gb|CF008929.1|CF008929
EST:     CCACGGCCGTGAGGAGGGCAAGAACGTCCTTTGTTTCCGCACCGGATCGC                         CGCTGGNCCCGCTGGAGGAGCTCATGGAGCCGCCCGTGAGGCAGCGCTACG
genomic: CCACGGCCGTGAGGAGGGCAAGAACGTCCTCTGGTCCCGCACCGGATCGCgtaaaagctt ... cgacgggcagCGCTGGTCCCGCTGGAGGAGCTCATGGAGCCGCCCGTGAGGCAGCGCTACG
EST: gi|21481556|gb|BQ578239.1|BQ578239
EST:     CCACGGCCGTGAGGAGGGCAAGAACGTCCTCTGGTCCCGCACCGGATCGC                         CGCTGGTCCCGCTGGAGGAGCTCATGGAGCCGCCCGTGAGGCAGCGCTACG
genomic: CCACGGCCGTGAGGAGGGCAAGAACGTCCTCTGGTCCCGCACCGGATCGCgtaaaagctt ... cgacgggcagCGCTGGTCCCGCTGGAGGAGCTCATGGAGCCGCCCGTGAGGCAGCGCTACG
EST: gi|101383316|gb|EB813714.1|EB813714
EST:     CCACGGCCGTGAGGAGGGCAAGAACGTCCTCTGGTCCCGCACCGGATCGC                         CGCTGGTCCCGCTGGAGGAGCTCATGGAGCCGCCCGTGAGGCAGCGCTACG
genomic: CCACGGCCGTGAGGAGGGCAAGAACGTCCTCTGGTCCCGCACCGGATCGCgtaaaagctt ... cgacgggcagCGCTGGTCCCGCTGGAGGAGCTCATGGAGCCGCCCGTGAGGCAGCGCTACG
EST: gi|87154532|gb|DY399321.1|DY399321
EST:     CCACGGCCGTGAGGAGGGCAAGAACGTCCTCTGGTCCCGCACCGGATCGC                         CGCTGGTCCCGCTGGAGGAGCTCATGGAGCCGCCCGTGAGGCAGCGCTACG
genomic: CCACGGCCGTGAGGAGGGCAAGAACGTCCTCTGGTCCCGCACCGGATCGCgtaaaagctt ... cgacgggcagCGCTGGTCCCGCTGGAGGAGCTCATGGAGCCGCCCGTGAGGCAGCGCTACG
EST: gi|26454905|gb|CA826488.1|CA826488
EST:     CCACGGCCGTGAGGAGGGCAAGAACGTCCTCTGGTCCCGCACCGGATCGC                         CGCTGGTCCCGCTGGAGGAGCTCATGGAGCCGCCCGTGAGGCAGCGCTACG
genomic: CCACGGCCGTGAGGAGGGCAAGAACGTCCTCTGGTCCCGCACCGGATCGCgtaaaagctt ... cgacgggcagCGCTGGTCCCGCTGGAGGAGCTCATGGAGCCGCCCGTGAGGCAGCGCTACG
EST: gi|21329933|gb|BQ485314.1|BQ485314
EST:     CCACGGCCGTGAGGAGGGCAAGAACGTCCTCTGGTCCCGCACCGGATCGC                         CGCTGGTCCCGCTGGAGGAGCTCATGGAGCCGCCCGTGAGGCAGCGCTACG
genomic: CCACGGCCGTGAGGAGGGCAAGAACGTCCTCTGGTCCCGCACCGGATCGCgtaaaagctt ... cgacgggcagCGCTGGTCCCGCTGGAGGAGCTCATGGAGCCGCCCGTGAGGCAGCGCTACG
EST: gi|87154904|gb|DY399693.1|DY399693
EST:     CCACGGCCGTGAGGAGGGCAAGAACGTCCTCTGGTCCCGCACCGGATCGC                         CGCTGGTCCCGCTGGAGGAGCTCATGGAGCCGCCCGTGAGGCAGCGCTACG
genomic: CCACGGCCGTGAGGAGGGCAAGAACGTCCTCTGGTCCCGCACCGGATCGCgtaaaagctt ... cgacgggcagCGCTGGTCCCGCTGGAGGAGCTCATGGAGCCGCCCGTGAGGCAGCGCTACG

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: 49 (upstream exon), 47 (downstream exon)
Score: 30

GACAACCTGGTCCGCAGGGGCGACACCCTCGTGCTCCTCCACGTCCGGCACCACGGCCGTGAGGAGGGCAAGAACGTCCTCTGGTCCCGCACCGGATCGCgtaaaagctt ... cgacgggcagCGCTGGTCCCGCTGGAGGAGCTCATGGAGCCGCCCGTGAGGCAGCGCTACGACGTGCCGTATGACGCGGAGGTGTTCGACATGCTCAACGCCGCGGCCCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atagcttctcagccgctccgctgggtttttttgaatctgatgaatcgacgggcagCGCTGGTCCCGCTGGAGGAGCTCATGGAGCCGCCCGTGAGGCAGCGCTACGACGTGCCGTATGACGCGGAGGTGTTCGACATGCTCAACGCCGCGGCCCG
                         tttttttgaat  TA-rich tract