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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTACGGGAAGCCCAGGTAGCTCAATTCAACTACATTCTTGTCGTAGGCGCACAGGAGGCCGAGACTGGAAATgtaagtcctctttacctcgtgccatttttttaatcttctacataccgtgtacttgtgtaccagtctcaccctcagtcctcagatattgatccacgcaaaatagatttgattccttgctgtttcacatggaccctttgtgtactgcag

Basic information

species Zea mays
transcript GRMZM2G137615_T01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G137615_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os08g19850.1 (Oryza sativa), 5'ss of exon 19
GTACGGGAAGCCCAGGTAGCTCAATTCAACTACATTCTTGTCGTAGGCGCACAGGAGGCCGAGACTGGAAATgtaagtcctctttacctcgtgccatttttttaatcttctacataccgtgtacttgtgtaccagtctcaccctcagtcctcagatattgatccacgcaaaatagatttgattccttgctgtttcacatggaccctttgtgtactgcag
|||||||| || ||  |||| ||||||||||||||||||||||| || ||||| || || ||||||||| | ||        ||||||   |||     | ||     |  | ||   |  || || | |     |  || ||  | |   ||| |   || | |  |||  || |||  |                                      
GTACGGGAGGCTCAATTAGCCCAATTCAACTACATTCTTGTCGTTGGTGCACAAGAAGCAGAGACTGGACAGgt-------ttttaccctttgcacccctgttttcactagagatgtggaataattatttctttctgccatccata-tgtacaggt---gaactagacaat-taaattcaagag-----------------------------------
















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|213172391|gb|FM188594.1|FM188594
EST:     AATTCAACTACATTCTTGTCGTA-GCGCACAGGAGGCCGAGACTGGAAAT                         GTCTGCGTTAGGGTAAGAGATAATGCCGACCTGGCCACAATGAGCGTTGAN
genomic: AATTCAACTACATTCTTGTCGTAGGCGCACAGGAGGCCGAGACTGGAAATgtaagtcctc ... tgtactgcagGTCTGCGTTAGGGTAAGAGATAATGCCGACCTGGCCACAATGAGCGTTGAT
EST: gi|32911351|gb|CF016163.1|CF016163
EST:     AATTCAACTACATTCTTGTCGTAGGCGCACAGGAGGCCGAGACTGGAAAT                         GTCTGCGTTAGGGTAAGAGATAATGCCGACCTGGCCACAATGAGCGTTGAT
genomic: AATTCAACTACATTCTTGTCGTAGGCGCACAGGAGGCCGAGACTGGAAATgtaagtcctc ... tgtactgcagGTCTGCGTTAGGGTAAGAGATAATGCCGACCTGGCCACAATGAGCGTTGAT
EST: gi|5791229|gb|AI978021.1|AI978021
EST:     AATTCAACTACATTCTTGTCGTAGGCGCACAGGAGGCCGAGACTGGAAAT                         GTCTGCGTTAGGGTAAGAGATAATGCCGACCTGGCCACAATGAGCGTTGAT
genomic: AATTCAACTACATTCTTGTCGTAGGCGCACAGGAGGCCGAGACTGGAAATgtaagtcctc ... tgtactgcagGTCTGCGTTAGGGTAAGAGATAATGCCGACCTGGCCACAATGAGCGTTGAT
EST: gi|60337159|gb|DN204132.1|DN204132
EST:     AATTCAACTACATTCTTGTCGTAGGCGCACAGGAGGCCGAGACTGGAAAT                         GTCTGCGTTAGGGTAAGAGATAATGCCGACCTGGCCACAATGAGCGTTGAT
genomic: AATTCAACTACATTCTTGTCGTAGGCGCACAGGAGGCCGAGACTGGAAATgtaagtcctc ... tgtactgcagGTCTGCGTTAGGGTAAGAGATAATGCCGACCTGGCCACAATGAGCGTTGAT
EST: gi|211513903|gb|FL285080.1|FL285080
EST:     AATTCAACTACATTCTTGTCGTAGGCGCACAGGAGGCCGAGACTGGAAAT                         GTCTGCGTTAGGGTAAGAGATAATGCCGACCTGGCCACAATGAGCGTTGAT
genomic: AATTCAACTACATTCTTGTCGTAGGCGCACAGGAGGCCGAGACTGGAAATgtaagtcctc ... tgtactgcagGTCTGCGTTAGGGTAAGAGATAATGCCGACCTGGCCACAATGAGCGTTGAT
EST: gi|30052636|gb|AI065926.2|AI065926
EST:     AATTCAACTACATTCTTGTCGTAGGCGCACAGGAGGCCGAGACTGGAAAT                         GTCTGCGTTAGGGTAAGAGATAATGCCGACCCGGCC
genomic: AATTCAACTACATTCTTGTCGTAGGCGCACAGGAGGCCGAGACTGGAAATgtaagtcctc ... tgtactgcagGTCTGCGTTAGGGTAAGAGATAATGCCGACCTGGCC
EST: gi|71770369|gb|DR968306.1|DR968306
EST:     AATTCAACTACATTCTTGTCGTAGGCGCACAGGAGGCCGAGACTGGAAAT                         GTCTGCGTTAGGGTAAGAGATAATGCCGACCTGGCCACAATGAGCGTTGAT
genomic: AATTCAACTACATTCTTGTCGTAGGCGCACAGGAGGCCGAGACTGGAAATgtaagtcctc ... tgtactgcagGTCTGCGTTAGGGTAAGAGATAATGCCGACCTGGCCACAATGAGCGTTGAT
EST: gi|9794315|gb|BE552623.1|BE552623
EST:     GTAGGCGCACAGGAGGCCGAGACTGGAAAT                         GTCTGCG-TAGGGTAAGAGATAATGCCGACCTGGCCACAATGAGCG-TGAT
genomic: GTAGGCGCACAGGAGGCCGAGACTGGAAATgtaagtcctc ... tgtactgcagGTCTGCGTTAGGGTAAGAGATAATGCCGACCTGGCCACAATGAGCGTTGAT

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), 48 (downstream exon)
Score: 165

GTACGGGAAGCCCAGGTAGCTCAATTCAACTACATTCTTGTCGTAGGCGCACAGGAGGCCGAGACTGGAAATgtaagtcctc ... tgtactgcagGTCTGCGTTAGGGTAAGAGATAATGCCGACCTGGCCACAATGAGCGTTGATGGCCTCATCACACGTTTGAGGGAGGAAATCGTAGCCTTCAAATGATTTT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 197

GTACGGGAAGCCCAGGTAGCTCAATTCAACTACATTCTTGTCGTAGGCGCACAGGAGGCCGAGACTGGAAATgtaagtcctc ... tgtactgcagGTCTGCGTTAGGGTAAGAGATAATGCCGACCTGGCCACAATGAGCGTTGATGGCCTCATCACACGTTTGAGGGAGGAAATCGTAGCCTTCAAATGATTTT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 190

GTACGGGAAGCCCAGGTAGCTCAATTCAACTACATTCTTGTCGTAGGCGCACAGGAGGCCGAGACTGGAAATgtaagtcctc ... tgtactgcagGTCTGCGTTAGGGTAAGAGATAATGCCGACCTGGCCACAATGAGCGTTGATGGCCTCATCACACGTTTGAGGGAGGAAATCGTAGCCTTCAAATGATTTT


Block sizes: 33 (upstream exon), 43 (downstream exon)
Score: 113

GTACGGGAAGCCCAGGTAGCTCAATTCAACTACATTCTTGTCGTAGGCGCACAGGAGGCCGAGACTGGAAATgtaagtcctc ... tgtactgcagGTCTGCGTTAGGGTAAGAGATAATGCCGACCTGGCCACAATGAGCGTTGATGGCCTCATCACACGTTTGAGGGAGGAAATCGTAGCCTTCAAATGATTTT