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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatatattatattattactatttattatataatgaatttacccagagctcccttccctcacactgataatgcttatttgatcagTGGAAGCTTGCATTCATATCCATGAACCGGCCAGAGTACCTCCAGGACACTGACGTTGTATCAGCACGTTTTCAG

Basic information

species Zea mays
transcript GRMZM2G303655_T01
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G303655_T01 (Zea mays), 3'ss of exon 18
lower sequence: LOC_Os12g30540.1 (Oryza sativa), 3'ss of exon 29
----------------gtaatatattatattattactatttattatataatgaatttacccagagctcccttccctcacactgataatgcttatttgatcagTGGAAGCTTGCATTCATATCCATGAACCGGCCAGAGTACCTCCAGGACACTGACGTTGTATCAGCACGTTTTCAG
                 |  | | ||  ||  | |  || | || | || | | |||||    | |     || ||||  | | |||||||||||||| ||||||||||||||||||||||| ||||| ||||| || |||||||||||    ||||||||||| ||||||||||||
gatgttagtactttaactgctgtcttccatc-tgatcatcttttctcta-taattttacggccaacatggatctctcatgccggtaatgcttatttgaacagTGGAAGCTTGCATTCATATCTATGAATCGGCCTGAATACCTCCAGGATGTCGACGTTGTATCTGCACGTTTTCAG
















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|60357459|gb|DN224432.1|DN224432
EST:     TGGAGCGCATCCAGAGAAAACTTAGAGTTCCTGATGATGAGTTCTCCAAG                         TGGAAGCTTGCATTCATATCCATGAACCGGCCAGAGTACCTCCAGGACACT
genomic: TGGAGCGCATCCAGAGAAAACTTAGAGTTCCTGATGATGAGTTCTCCAAGgtaatatatt ... atttgatcagTGGAAGCTTGCATTCATATCCATGAACCGGCCAGAGTACCTCCAGGACACT
EST: gi|71767531|gb|DR965468.1|DR965468
EST:     TGGAGCGCATCCAGAGAAAACTTAGAGTTCCTGATGATGAGTTCTCCAAG                         TGGAAGCTTGCATTCATATCCATGAACCGGCCAGAGTACCTCCAGGACACT
genomic: TGGAGCGCATCCAGAGAAAACTTAGAGTTCCTGATGATGAGTTCTCCAAGgtaatatatt ... atttgatcagTGGAAGCTTGCATTCATATCCATGAACCGGCCAGAGTACCTCCAGGACACT
EST: gi|67032245|gb|CO460994.1|CO460994
EST:     TGGAGCGCATCCAGAGAAAACTTAGAGTTCCTGATGATGAGTTCTCCAAG                         TGGAAGCTTGCATTCATATCCATGAACCGGCCAGAGTACCCTCCAG-ACAC
genomic: TGGAGCGCATCCAGAGAAAACTTAGAGTTCCTGATGATGAGTTCTCCAAGgtaatatatt ... atttgatcagTGGAAGCTTGCATTCATATCCATGAACCGGCCAGAGTACC-TCCAGGACAC
EST: gi|47962024|gb|CN844733.1|CN844733
EST:     TGGAGCGCATCCAGAGAAAACTTAGAGTTCCTGATGATGAGTTCTCCAAG                         TGGAAGCTTGCATTCATATCCATGAACCGGCCAGAGTACCTCCAGGACACT
genomic: TGGAGCGCATCCAGAGAAAACTTAGAGTTCCTGATGATGAGTTCTCCAAGgtaatatatt ... atttgatcagTGGAAGCTTGCATTCATATCCATGAACCGGCCAGAGTACCTCCAGGACACT
EST: gi|60359281|gb|DN226254.1|DN226254
EST:     TGGAGCGCATCCAGAGAAAACTTAGAGTTCCTGATGATGAGTTCTCCAAG                         TGGAAGCTTGCATTCATATCCATGAACCGGCCAGAGTACCTC
genomic: TGGAGCGCATCCAGAGAAAACTTAGAGTTCCTGATGATGAGTTCTCCAAGgtaatatatt ... atttgatcagTGGAAGCTTGCATTCATATCCATGAACCGGCCAGAGTACCTC
EST: gi|60346259|gb|DN213232.1|DN213232
EST:     CATCCAGAGAAAACTTAGAGTTCCTGATGATGAGTTCTCCAAG                         TGGAAGCTTGCATTCATATCCATGAACCGGCCAGAGTACCTCCAGGACACT
genomic: CATCCAGAGAAAACTTAGAGTTCCTGATGATGAGTTCTCCAAGgtaatatatt ... atttgatcagTGGAAGCTTGCATTCATATCCATGAACCGGCCAGAGTACCTCCAGGACACT

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), 49 (downstream exon)
Score: 305

AGATCCTTTTTTGATGGTTATTCGGGAAGGTGAGACTGCTGCAGAGGTAATGGAGCGCATCCAGAGAAAACTTAGAGTTCCTGATGATGAGTTCTCCAAGgtaatatatt ... atttgatcagTGGAAGCTTGCATTCATATCCATGAACCGGCCAGAGTACCTCCAGGACACTGACGTTGTATCAGCACGTTTTCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 184

AGATCCTTTTTTGATGGTTATTCGGGAAGGTGAGACTGCTGCAGAGGTAATGGAGCGCATCCAGAGAAAACTTAGAGTTCCTGATGATGAGTTCTCCAAGgtaatatatt ... atttgatcagTGGAAGCTTGCATTCATATCCATGAACCGGCCAGAGTACCTCCAGGACACTGACGTTGTATCAGCACGTTTTCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 182

AGATCCTTTTTTGATGGTTATTCGGGAAGGTGAGACTGCTGCAGAGGTAATGGAGCGCATCCAGAGAAAACTTAGAGTTCCTGATGATGAGTTCTCCAAGgtaatatatt ... atttgatcagTGGAAGCTTGCATTCATATCCATGAACCGGCCAGAGTACCTCCAGGACACTGACGTTGTATCAGCACGTTTTCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 308

AGATCCTTTTTTGATGGTTATTCGGGAAGGTGAGACTGCTGCAGAGGTAATGGAGCGCATCCAGAGAAAACTTAGAGTTCCTGATGATGAGTTCTCCAAGgtaatatatt ... atttgatcagTGGAAGCTTGCATTCATATCCATGAACCGGCCAGAGTACCTCCAGGACACTGACGTTGTATCAGCACGTTTTCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taatgaatttacccagagctcccttccctcacactgataatgcttatttgatcagTGGAAGCTTGCATTCATATCCATGAACCGGCCAGAGTACCTCCAGGACACTGACGTTGTATCAGCACGTTTTCAG
                               cactgat  putative branch site (score: 308)
                                          cttattt  putative PPT
                                           ttatttgat  TA-rich tract