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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCCGGACATGCTGGAGGTGGGCAACGGGGGCATGACCAACAGCGAGTACGTCGTGCACTTCAGCCTCTGGGCGATCTCCAAGgtcagtgagactgcgtacacctgatgcctgcatcctggtagtggtacacagacagaacattttagtttctttttttgtctgaacttgtcctcgcccggccaatgaacgcgcag

Basic information

species Zea mays
transcript GRMZM2G095126_T03
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G095126_T03 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os10g35070.1 (Oryza sativa), 5'ss of exon 11
ATCCGGACATGCTGGAGGTGGGCAACGGGGGCATGACCAACAGCGAGTACGTCGTGCACTTCAGCCTCTGGGCGATCTCCAAGgt------cagtgagactgcgtacacctgatgcctgcatcctggtagtggtacacagacagaacattttagtttctttttttgtctgaacttgtcctcgcccggccaatgaacgcgcag
| ||||||||||||||||| ||||| || || |||||||||  ||||||| |||| || |||||||||||||| |||||||||||       | || ||| |    |   | |||   | || | | |  |  || | |    ||  |   |||| |             || || || |||                    
ACCCGGACATGCTGGAGGTTGGCAATGGCGGGATGACCAACGACGAGTACATCGTCCATTTCAGCCTCTGGGCCATCTCCAAGgtactaccaaatgtgacggatgtcggataatgatggtattc-gtttctactaaagatgacgatgaaaatagtgtaaagaaaaaaagaaagttatcatcggt------------------
















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|71323535|gb|DR798428.1|DR798428
EST:     TGACCAACAGCGAGTACGTCGTGCACTTCAGCCTCTGGGCGATCTCCAAG                         GCGCCTCTCATCATCGGCTGCGACGTCAGGCACATGTCGCGGGAGACGTAC
genomic: TGACCAACAGCGAGTACGTCGTGCACTTCAGCCTCTGGGCGATCTCCAAGgtcagtgaga ... gaacgcgcagGCGCCTCTCATCATCGGCTGCGACGTCAGGCACATGTCGCGGGAGACGTAC
EST: gi|88753305|gb|DY537446.1|DY537446
EST:     GGCCCAACAGCGAGTACGTCGTGCACTTCAGCCTCTGGGCGATCTCCAAG                         GCGCCTCTCATCATCGGCTGCGACGTCAGGCACATGTCGCGGGAGACGTAC
genomic: TGACCAACAGCGAGTACGTCGTGCACTTCAGCCTCTGGGCGATCTCCAAGgtcagtgaga ... gaacgcgcagGCGCCTCTCATCATCGGCTGCGACGTCAGGCACATGTCGCGGGAGACGTAC
EST: gi|94473544|gb|EB702502.1|EB702502
EST:     TGACCAACAGCGAGTACGTCGTGCACTTCAGCCTCTGGGCGATCTCCAAG                         GCGCCTCTCATCATCGGCTGGGACGTCAGGCACATGTCGCGGGAGACGTAC
genomic: TGACCAACAGCGAGTACGTCGTGCACTTCAGCCTCTGGGCGATCTCCAAGgtcagtgaga ... gaacgcgcagGCGCCTCTCATCATCGGCTGCGACGTCAGGCACATGTCGCGGGAGACGTAC
EST: gi|148929477|gb|EC875592.2|EC875592
EST:     TGACCAACAGCGAGTACGTCGTGCACTTCAGCCTCTGGGCGATCTCCAAG                         GCGCCTCTCATCATCGGTTGCGACGTCAGGCACATGTCGCGGGAGAGGTAC
genomic: TGACCAACAGCGAGTACGTCGTGCACTTCAGCCTCTGGGCGATCTCCAAGgtcagtgaga ... gaacgcgcagGCGCCTCTCATCATCGGCTGCGACGTCAGGCACATGTCGCGGGAGACGTAC
EST: gi|5740192|gb|AI947882.1|AI947882
EST:     TGACCAACAGCGAGTCCTTCGTGCACTTCAGCCTCTGGGCGATCTCCAAG                         GCGCCTCTCATCATCGGCTGCGACGTCAGGCACATGTCCCGGGAGACGTAC
genomic: TGACCAACAGCGAGTACGTCGTGCACTTCAGCCTCTGGGCGATCTCCAAGgtcagtgaga ... gaacgcgcagGCGCCTCTCATCATCGGCTGCGACGTCAGGCACATGTCGCGGGAGACGTAC
EST: gi|149080680|gb|EE169738.2|EE169738
EST:     TGACCAACAGCGAGTACGTCGTGCACTTCAGCCTCTGGGCGATCTCCAAG                         GCGCCTCTCATCATCGGCTGCGACGTCAGGCACATGTCGCGGGAGACGTAC
genomic: TGACCAACAGCGAGTACGTCGTGCACTTCAGCCTCTGGGCGATCTCCAAGgtcagtgaga ... gaacgcgcagGCGCCTCTCATCATCGGCTGCGACGTCAGGCACATGTCGCGGGAGACGTAC
EST: gi|71767715|gb|DR965652.1|DR965652
EST:     TGACCAACAGCGAGTACGTCGTGCACTTCAGCCTCTGGGCGATCTCCAAG                         GCGCCTCTCATCATCGGCTGCGACGTCAGGCACATGTCGCGGGAGACGTAC
genomic: TGACCAACAGCGAGTACGTCGTGCACTTCAGCCTCTGGGCGATCTCCAAGgtcagtgaga ... gaacgcgcagGCGCCTCTCATCATCGGCTGCGACGTCAGGCACATGTCGCGGGAGACGTAC

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: 35 (upstream exon), 48 (downstream exon)
Score: 7

ATCCGGACATGCTGGAGGTGGGCAACGGGGGCATGACCAACAGCGAGTACGTCGTGCACTTCAGCCTCTGGGCGATCTCCAAGgtcagtgaga ... gaacgcgcagGCGCCTCTCATCATCGGCTGCGACGTCAGGCACATGTCGCGGGAGACGTACGCCATCCTGGCCAACAAGGAGGTGATCGCCGTCAACCAAG


Block sizes: 35 (upstream exon), 47 (downstream exon)
Score: 27

ATCCGGACATGCTGGAGGTGGGCAACGGGGGCATGACCAACAGCGAGTACGTCGTGCACTTCAGCCTCTGGGCGATCTCCAAGgtcagtgaga ... gaacgcgcagGCGCCTCTCATCATCGGCTGCGACGTCAGGCACATGTCGCGGGAGACGTACGCCATCCTGGCCAACAAGGAGGTGATCGCCGTCAACCAAG


Block sizes: 42 (upstream exon), 49 (downstream exon)
Score: 58

ATCCGGACATGCTGGAGGTGGGCAACGGGGGCATGACCAACAGCGAGTACGTCGTGCACTTCAGCCTCTGGGCGATCTCCAAGgtcagtgaga ... gaacgcgcagGCGCCTCTCATCATCGGCTGCGACGTCAGGCACATGTCGCGGGAGACGTACGCCATCCTGGCCAACAAGGAGGTGATCGCCGTCAACCAAG


Block sizes: 35 (upstream exon), 49 (downstream exon)
Score: 17

ATCCGGACATGCTGGAGGTGGGCAACGGGGGCATGACCAACAGCGAGTACGTCGTGCACTTCAGCCTCTGGGCGATCTCCAAGgtcagtgaga ... gaacgcgcagGCGCCTCTCATCATCGGCTGCGACGTCAGGCACATGTCGCGGGAGACGTACGCCATCCTGGCCAACAAGGAGGTGATCGCCGTCAACCAAG