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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtaataattctttgcgtgccatctgtactgttggttcaatagcctttctgtatcgttacaaccttgtgatagctctctatgtattatggtaacaatttgtgtggtgcttatgttgaacttaatttagttttctccgatcattagGTATTGAATCAAATAGTTTGTGAACTTCCTTCTGAACACCCCTTGTCTGAGACAAGACCACTGCGAGAACTTTTAGGCCATACACCAACTCAG

Basic information

species Zea mays
transcript GRMZM2G091435_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G091435_T03 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g67560.1 (Oryza sativa), 3'ss of exon 3
----gtacgtaataattctttgcgtgccatctgtactgttggttcaatagcctttctgta------tcgttacaaccttgtgatagctctctatgtattatggtaaca-----------atttgtgtg-gtgcttatgttgaacttaatttagttttctccgatcattagGTATTGAATCAAATAGTTTGTGAACTTCCTTCTGAACACCCCTTGTCTGAGACAAGACCACTGCGAGAACTTTTAGGCCATACACCAACTCAG
    | |  || |  ||||||  |||  |     | | |        ||   |     |          |||  ||| |||  ||| | |   | |||| |  | |||           |||||| || |   ||||  ||||||  || |  |||    | ||  | |||| |||||||||||||| || ||||||||||||||||| ||||||||||| ||||||||| |||| ||||| ||||||||||| ||||| |||
gtatgcagttactgtttctttatgtgttaatatcaatatgaacatgctaatatcatcatgagacaccttttaacaccatgtattagatttgcctctattgtaatgacacaaagaaagatatttgtttgtgcagttatactgaactgtatctcatttctaactatattcagGTGTTGAATCAAATAGTCTGCGAACTTCCTTCTGAACATCCCTTGTCTGAAACAAGACCATTGCGTGAACTCTTAGGCCATACTCCAACCCAG

upper sequence: GRMZM2G091435_T03 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g67560.2 (Oryza sativa), 3'ss of exon 3
----gtacgtaataattctttgcgtgccatctgtactgttggttcaatagcctttctgta------tcgttacaaccttgtgatagctctctatgtattatggtaaca-----------atttgtgtg-gtgcttatgttgaacttaatttagttttctccgatcattagGTATTGAATCAAATAGTTTGTGAACTTCCTTCTGAACACCCCTTGTCTGAGACAAGACCACTGCGAGAACTTTTAGGCCATACACCAACTCAG-------
    | |  || |  ||||||  |||  |     | | |        ||   |     |          |||  ||| |||  ||| | |   | |||| |  | |||           |||||| || |   ||||  ||||||  || |  |||    | ||  | |||| |||||||||||||| || ||||||||||||||||| ||||||||||| ||||||||| |||| ||||| ||||||||||| ||||| |||       
gtatgcagttactgtttctttatgtgttaatatcaatatgaacatgctaatatcatcatgagacaccttttaacaccatgtattagatttgcctctattgtaatgacacaaagaaagatatttgtttgtgcagttatactgaactgtatctcatttctaactatattcagGTGTTGAATCAAATAGTCTGCGAACTTCCTTCTGAACATCCCTTGTCTGAAACAAGACCATTGCGTGAACTCTTAGGCCATACTCCAACCCAGGTTTGCT
















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|32923268|gb|CF028080.1|CF028080
EST:     TAATGTATGATGCTTCTGGTATCAGACTGCATGCTGGAAAGCAAGCAGAG                         GTATTGAATCAAATAGTTTGTGAACTTCCTTCTGAACACCCCTTGTCTGAG
genomic: TAATGTATGATGCTTCTGGTATCAGACTGCATGCTGGAAAGCAAGCAGAGgtacgtaata ... cgatcattagGTATTGAATCAAATAGTTTGTGAACTTCCTTCTGAACACCCCTTGTCTGAG
EST: gi|8401376|gb|BE057010.1|BE057010
EST:     TGGTATCAGACTGCATGCTGGAAAGCAAGCAGAG                         GTATTGAATCAAATAGTTTGTGAACTTCCTTCTGAACACCCCTTGTCTGAG
genomic: TGGTATCAGACTGCATGCTGGAAAGCAAGCAGAGgtacgtaata ... cgatcattagGTATTGAATCAAATAGTTTGTGAACTTCCTTCTGAACACCCCTTGTCTGAG
EST: gi|149074454|gb|EE162849.2|EE162849
EST:     TAATGTATGATGCTTCTGGTATCAGACTGCATGCTGGAAAGCAAGCAGAG                         GTATTGAATCAAATAGTTTGTGAACTTCCTTCTGAACACCCCTTGTTTGAG
genomic: TAATGTATGATGCTTCTGGTATCAGACTGCATGCTGGAAAGCAAGCAGAGgtacgtaata ... cgatcattagGTATTGAATCAAATAGTTTGTGAACTTCCTTCTGAACACCCCTTGTCTGAG
EST: gi|91871453|gb|EB401428.1|EB401428
EST:     TAATGTATGATGCTTTTGGTATCAGACTGCATGCTGGAAAGCAAGCAGAG                         GTATTGAATCAAATAGTTTGTGAACTTCCTTTTGAACACCCCTTGTTTGAG
genomic: TAATGTATGATGCTTCTGGTATCAGACTGCATGCTGGAAAGCAAGCAGAGgtacgtaata ... cgatcattagGTATTGAATCAAATAGTTTGTGAACTTCCTTCTGAACACCCCTTGTCTGAG

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), 30 (downstream exon)
Score: 11

GTAATGTATGATGCTTCTGGTATCAGACTGCATGCTGGAAAGCAAGCAGAGgtacgtaata ... cgatcattagGTATTGAATCAAATAGTTTGTGAACTTCCTTCTGAACACCCCTTGTCTGAGACAAGACCACTGCGAGAACTTTTAGGCCATACACCAACTCAG


Block sizes: 45 (upstream exon), 45 (downstream exon)
Score: 70

GTAATGTATGATGCTTCTGGTATCAGACTGCATGCTGGAAAGCAAGCAGAGgtacgtaata ... cgatcattagGTATTGAATCAAATAGTTTGTGAACTTCCTTCTGAACACCCCTTGTCTGAGACAAGACCACTGCGAGAACTTTTAGGCCATACACCAACTCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 93

GTAATGTATGATGCTTCTGGTATCAGACTGCATGCTGGAAAGCAAGCAGAGgtacgtaata ... cgatcattagGTATTGAATCAAATAGTTTGTGAACTTCCTTCTGAACACCCCTTGTCTGAGACAAGACCACTGCGAGAACTTTTAGGCCATACACCAACTCAG


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 61

GTAATGTATGATGCTTCTGGTATCAGACTGCATGCTGGAAAGCAAGCAGAGgtacgtaata ... cgatcattagGTATTGAATCAAATAGTTTGTGAACTTCCTTCTGAACACCCCTTGTCTGAGACAAGACCACTGCGAGAACTTTTAGGCCATACACCAACTCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taacaatttgtgtggtgcttatgttgaacttaatttagttttctccgatcattagGTATTGAATCAAATAGTTTGTGAACTTCCTTCTGAACACCCCTTGTCTGAGACAAGACCACTGCGAGAACTTTTAGGCCATACACCAACTCAG
                                      ttttctcc  CT-rich tract
                          aacttaatttagtttt  TA-rich tract