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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatctgaacctgttccttaagcatcttcgttacttccgtgctttaatggcatgattaaccattccctaacttctccatatgctgaaatacagGTCATATCGTTTCTGCATCGTATGATCGAGATATTAGGTCTCTCAGTGCTTCCCTGTATTCCAATTGCACTGAGACTATTGCTTCTTGACAACGAG

Basic information

species Zea mays
transcript GRMZM2G096106_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G096106_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os07g42180.1 (Oryza sativa), 3'ss of exon 6
gtaaatctgaacctgttccttaagcatcttcgttacttccgtgctttaatggcatgattaaccattccctaacttctccatatgctgaaatacagGTCATATCGTTTCTGCATCGTATGATCGAGATATTAGGTCTCTCAGTGCTTCCCTGTATTCCAATTGCACTGAGACTATTGCTTCTTGACAACGAG
|||| |    | |||||     | ||||||    | ||   |||||     | ||||||||||| |   |||||| | || |||||||||||||| ||||||| ||||| || |||||| | |||||||||||  | || |||||||| |||||||||||||||||| |||  |||||  |||| || |||
gtaagt----aactgttatc--aacatcttttgcaatttactgctt-----ggatgattaaccaatttgtaacttatgca-atgctgaaatacagATCATATCATTTCTCCACCGTATGGTTGAGATATTAGGCATTTCGGTGCTTCCATGTATTCCAATTGCACTGCGACAGTTGCTCGTTGATAATGAG
















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|160481294|gb|EY254246.1|EY254246
EST:     TTTTGCAAGTCCTTGTTTCATTTCCTAGCGTGAGACCTCTGCGATCTAAG                         GTCATATCGTTTCTGCATCGTATGATCGAGATATTAGGTCTCTCAGTGCTT
genomic: TTTTGCAAGTCCTTGTTTCATTTCCTAGCGTGAGACCTCTGCGATCTAAGgtaaatctga ... tgaaatacagGTCATATCGTTTCTGCATCGTATGATCGAGATATTAGGTCTCTCAGTGCTT
EST: gi|89754581|gb|DY685311.1|DY685311
EST:     TTTTGCAAGTCCTTGTTTCATTTCCTAGCGTGAGACCTCTGCGATCTAAG                         GTCATATCGTTTCTGCATCGTATGATCGAGATATTAGGTCTCTCAGTGCTT
genomic: TTTTGCAAGTCCTTGTTTCATTTCCTAGCGTGAGACCTCTGCGATCTAAGgtaaatctga ... tgaaatacagGTCATATCGTTTCTGCATCGTATGATCGAGATATTAGGTCTCTCAGTGCTT

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: 46 (upstream exon), 38 (downstream exon)
Score: 20

ACCCTTGATGTAGTTTTGCAAGTCCTTGTTTCATTTCCTAGCGTGAGACCTCTGCGATCTAAGgtaaatctga ... tgaaatacagGTCATATCGTTTCTGCATCGTATGATCGAGATATTAGGTCTCTCAGTGCTTCCCTGTATTCCAATTGCACTGAGACTATTGCTTCTTGACAACGAG


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 30

ACCCTTGATGTAGTTTTGCAAGTCCTTGTTTCATTTCCTAGCGTGAGACCTCTGCGATCTAAGgtaaatctga ... tgaaatacagGTCATATCGTTTCTGCATCGTATGATCGAGATATTAGGTCTCTCAGTGCTTCCCTGTATTCCAATTGCACTGAGACTATTGCTTCTTGACAACGAG


Block sizes: 42 (upstream exon), 48 (downstream exon)
Score: 22

ACCCTTGATGTAGTTTTGCAAGTCCTTGTTTCATTTCCTAGCGTGAGACCTCTGCGATCTAAGgtaaatctga ... tgaaatacagGTCATATCGTTTCTGCATCGTATGATCGAGATATTAGGTCTCTCAGTGCTTCCCTGTATTCCAATTGCACTGAGACTATTGCTTCTTGACAACGAG


Block sizes: 47 (upstream exon), 45 (downstream exon)
Score: 49

ACCCTTGATGTAGTTTTGCAAGTCCTTGTTTCATTTCCTAGCGTGAGACCTCTGCGATCTAAGgtaaatctga ... tgaaatacagGTCATATCGTTTCTGCATCGTATGATCGAGATATTAGGTCTCTCAGTGCTTCCCTGTATTCCAATTGCACTGAGACTATTGCTTCTTGACAACGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgctttaatggcatgattaaccattccctaacttctccatatgctgaaatacagGTCATATCGTTTCTGCATCGTATGATCGAGATATTAGGTCTCTCAGTGCTTCCCTGTATTCCAATTGCACTGAGACTATTGCTTCTTGACAACGAG
                          ccctaac  putative branch site (score: 49)
             atgattaa  TA-rich tract