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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGAAGGGTTGGAATTTGGGAACAGTGTTTACTGGATTAGCTTTGGCAATGAGTACGCTGAAAAGgtgaaatttggtaagatatttgtgatatttatcctttttctggtatagtaactgttccatttgtttcttttgataatggtgtag

Basic information

species Zea mays
transcript GRMZM2G042398_T01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G042398_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os08g08200.2 (Oryza sativa), 5'ss of exon 8
CTGAAGGGTTGGAATTTGGGAACAGTGTTTACTGGATTAGCTTTGGCAATGAGTACGCTGAAAAGgtgaaatttggtaagatatttgtgatatttatcctttttctggt----atagtaactgttccatttgtttcttttgat------aatggtgtag
|||| ||  |||||||||||||  |||||||||||||||| |||||| | ||||| ||||||||||| || | || | | || ||  | |||   |   | | |  |||    ||| |||||   |  |||  |  ||||| |      ||||||||||
CTGATGGCATGGAATTTGGGAATGGTGTTTACTGGATTAGTTTTGGCGAAGAGTATGCTGAAAAGgt-aattgtgttcatatgttcataataaccactttctgttgggtcttgatactaactagcctgttttctatttttggttttcacaatggtgtag
















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|16925826|gb|BM078894.1|BM078894
EST:     TTGGGAACAGTGTTTACTGGATTAGCTTTGGCAATGAGTACGCTGAAAAG                         AAATTCCCTGCATCCAGACCGTTTGGTATCAAGTACAAGTTTCACTTAGAG
genomic: TTGGGAACAGTGTTTACTGGATTAGCTTTGGCAATGAGTACGCTGAAAAGgtgaaatttg ... aatggtgtagAAATTCCCTGCATCCAGACCGTTTGGTATCAAGTACAAGTTTCACTTAGAG
EST: gi|32937233|gb|CF042052.1|CF042052
EST:     GGGAACAGTGTTTACTGGATTAGCTTTGGCAATGAGTACGTTGAAAAG                         AAATTCCCTGCATCCAGACCGTTTGGTATCAAGTACAAGTTTCACTTAGAG
genomic: GGGAACAGTGTTTACTGGATTAGCTTTGGCAATGAGTACGCTGAAAAGgtgaaatttg ... aatggtgtagAAATTCCCTGCATCCAGACCGTTTGGTATCAAGTACAAGTTTCACTTAGAG
EST: gi|211031439|gb|FL127271.1|FL127271
EST:     TTGGGAACAGTGTTTACTGGATTAGCTTTGGCAATGAGTACGCTGAAAAG                         AAATTCCCTGCTTCCAGACCGTTTGGTATCAAGTACAAGTTTCACTTAGAG
genomic: TTGGGAACAGTGTTTACTGGATTAGCTTTGGCAATGAGTACGCTGAAAAGgtgaaatttg ... aatggtgtagAAATTCCCTGCATCCAGACCGTTTGGTATCAAGTACAAGTTTCACTTAGAG
EST: gi|60395442|gb|DN228312.1|DN228312
EST:     TTGGGAACAGTGTTTACTGGATTAGCTTTGGCAATGAGTACGCTGAAAAG                         AAATTCCCTGCATCCAGACCGTTTGGTATCAAGTACAAGTTTCACTTAGAG
genomic: TTGGGAACAGTGTTTACTGGATTAGCTTTGGCAATGAGTACGCTGAAAAGgtgaaatttg ... aatggtgtagAAATTCCCTGCATCCAGACCGTTTGGTATCAAGTACAAGTTTCACTTAGAG
EST: gi|211475864|gb|FL467329.1|FL467329
EST:     GAACAGTGTTTACTGCATTAGCTTTGGCAATGAGTACGCTGAAAAG                         AAATTCCCTGCATCCAGACCGTTTGGTATCAAGTACAAGTTTCACTTAGAG
genomic: GAACAGTGTTTACTGGATTAGCTTTGGCAATGAGTACGCTGAAAAGgtgaaatttg ... aatggtgtagAAATTCCCTGCATCCAGACCGTTTGGTATCAAGTACAAGTTTCACTTAGAG

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), 49 (downstream exon)
Score: 101

CTGAAGGGTTGGAATTTGGGAACAGTGTTTACTGGATTAGCTTTGGCAATGAGTACGCTGAAAAGgtgaaatttg ... aatggtgtagAAATTCCCTGCATCCAGACCGTTTGGTATCAAGTACAAGTTTCACTTAGAG


Block sizes: 47 (upstream exon), 45 (downstream exon)
Score: 129

CTGAAGGGTTGGAATTTGGGAACAGTGTTTACTGGATTAGCTTTGGCAATGAGTACGCTGAAAAGgtgaaatttg ... aatggtgtagAAATTCCCTGCATCCAGACCGTTTGGTATCAAGTACAAGTTTCACTTAGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 176

CTGAAGGGTTGGAATTTGGGAACAGTGTTTACTGGATTAGCTTTGGCAATGAGTACGCTGAAAAGgtgaaatttg ... aatggtgtagAAATTCCCTGCATCCAGACCGTTTGGTATCAAGTACAAGTTTCACTTAGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 186

CTGAAGGGTTGGAATTTGGGAACAGTGTTTACTGGATTAGCTTTGGCAATGAGTACGCTGAAAAGgtgaaatttg ... aatggtgtagAAATTCCCTGCATCCAGACCGTTTGGTATCAAGTACAAGTTTCACTTAGAG