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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTTTGGCTCTTTGGGTTTGATGACATCAGTGTTGgtatgtagtttctgttttctggtttacttccttgactagatgtcataattactttttgttgaatcggtatcatacctgggaatgtaccttcagacataaatgttttaccttctcataaagatacaaaatgatgtcaatccgttctgtgtatag

Basic information

species Zea mays
transcript GRMZM2G033515_T01
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G033515_T01 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os01g46610.1 (Oryza sativa), 5'ss of exon 12
GTTTTGGCTCTTTGGGTTTGATGACATCAGTGTTGgtatgtagtt---tctgtt--ttctggtttact-tccttgactagatgtcataattactttttgttgaatcggtatcatacctgggaatgtaccttcagacataaatgttttaccttctcataaagatacaaaatgatgtcaatccgttctgtgtatag
| ||||| || |||||||||||||||||||| ||||||||||  |   | | ||  ||||  |||| | | | |||||| || | | |  || | |||   |     || |  |     |       |||| |    |    |||  ||| |  |  | | |||     |||    | |  |||   | | |||
GCTTTGGTTCATTGGGTTTGATGACATCAGTATTGgtatgtaactatgtatattacttctactttattgttcatgactaaatattaaatatattgttttagggtgttgtcttctgtacagtggaaagccttaa----ttttggttgaaccctgcctaatatata-----tgacactactttgtttaatatgtag
















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|78092176|gb|DV520550.1|DV520550
EST:     GTTTTGGCTCTTTGGGTTTGATGACATCAGTGTTG                         GTGTGCCCTGATGGGAAAACCATTGAAGCTGAAGCAGCCCATGGCACGGTT
genomic: GTTTTGGCTCTTTGGGTTTGATGACATCAGTGTTGgtatgtagtt ... ctgtgtatagGTGTGCCCTGATGGGAAAACCATTGAAGCTGAAGCAGCCCATGGCACGGTT
EST: gi|32850747|gb|CD990428.1|CD990428
EST:     GTTTTGGCTCTTTGGGTTTGATGACATCAGTGTTG                         GTGTGCCCTGATGGGAAAACCATTGAAGCTGAAGCAGCCCATGGCACGGTT
genomic: GTTTTGGCTCTTTGGGTTTGATGACATCAGTGTTGgtatgtagtt ... ctgtgtatagGTGTGCCCTGATGGGAAAACCATTGAAGCTGAAGCAGCCCATGGCACGGTT
EST: gi|32850346|gb|CD990027.1|CD990027
EST:     GTTT-GGCTCTTTGGGTTTGATGACATCAGTGTTG                         GTGTGCCCTGATGGGAAAACCATTTGA-GCTGAAG
genomic: GTTTTGGCTCTTTGGGTTTGATGACATCAGTGTTGgtatgtagtt ... ctgtgtatagGTGTGCCCTGATGGGAAAACCATT-GAAGCTGAAG
EST: gi|6742482|gb|AW313297.1|AW313297
EST:     CATCAGTGTTG                         GTGTGCCCTGATGGGAAAACCATTGAAGCTGAAGCAGCCCATGGCACGGTT
genomic: CATCAGTGTTGgtatgtagtt ... ctgtgtatagGTGTGCCCTGATGGGAAAACCATTGAAGCTGAAGCAGCCCATGGCACGGTT

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), 44 (downstream exon)
Score: 28

GTTTTGGCTCTTTGGGTTTGATGACATCAGTGTTGgtatgtagtt ... ctgtgtatagGTGTGCCCTGATGGGAAAACCATTGAAGCTGAAGCAGCCCATGGCACGGTTACCCGCCATTTCCGTGTTCACCAGAAAGGAGGTGAAACCAGTACGAACA


Block sizes: 45 (upstream exon), 46 (downstream exon)
Score: 30

GTTTTGGCTCTTTGGGTTTGATGACATCAGTGTTGgtatgtagtt ... ctgtgtatagGTGTGCCCTGATGGGAAAACCATTGAAGCTGAAGCAGCCCATGGCACGGTTACCCGCCATTTCCGTGTTCACCAGAAAGGAGGTGAAACCAGTACGAACA


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 46

GTTTTGGCTCTTTGGGTTTGATGACATCAGTGTTGgtatgtagtt ... ctgtgtatagGTGTGCCCTGATGGGAAAACCATTGAAGCTGAAGCAGCCCATGGCACGGTTACCCGCCATTTCCGTGTTCACCAGAAAGGAGGTGAAACCAGTACGAACA


Block sizes: 39 (upstream exon), 46 (downstream exon)
Score: 43

GTTTTGGCTCTTTGGGTTTGATGACATCAGTGTTGgtatgtagtt ... ctgtgtatagGTGTGCCCTGATGGGAAAACCATTGAAGCTGAAGCAGCCCATGGCACGGTTACCCGCCATTTCCGTGTTCACCAGAAAGGAGGTGAAACCAGTACGAACA