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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcgttgtaattcactatttgtttcaagtgtagcatcagtcaaagtgttggttgaaaacaattatgtgatgatgctcctcgtttctttgacagTTCGGCAAAGGCCTCTACTTTGCAGATCTAGTAAGCAAGAGCGCACAATACTGTTATGTGGATAGGAATAATCCTGTAGGTTTGATGCTTCTTTCTGAGG

Basic information

species Zea mays
transcript GRMZM5G831712_T02
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G831712_T02 (Zea mays), 3'ss of exon 17
lower sequence: LOC_Os07g23110.1 (Oryza sativa), 3'ss of exon 17
----gttcgttgta-attcactatttgtttcaagtgtagcatcagtcaaagtgttggttgaaaacaattatgtgatgatgctcctcgtttctttgacagTTCGGCAAAGGCCTCTACTTTGCAGATCTAGTAAGCAAGAGCGCACAATACTGTTATGTGGATAGGAATAATCCTGTAGGTTTGATGCTTCTTTCTGAGG
    | || ||||  | |   ||  || ||||| |||||||   |  ||||  |||||||||    |||| |  ||     |   | ||   |  |||||| || ||||||||||||||||||||| ||||||||||||| |||||||| ||||| ||||||||||| ||||| || ||||||||||||||||| ||||
gtttgctctttgttcacttcataaatggttcaactgtagcactggcaaaag-attggttgaatttgattaagctat-----tttcctttcaatcaacagTTTGGGAAAGGCCTCTACTTTGCAGATTTAGTAAGCAAGAGTGCACAATATTGTTACGTGGATAGGAAGAATCCAGTTGGTTTGATGCTTCTTTCCGAGG
















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|61119038|gb|DN559999.1|DN559999
EST:     GTCAAGGGCTAAGAATTGCACCTCCTGAGGCACCTGTTACTGGCTATATG                         TTCGGCAAAGGCCTCTACTTTGCAGATCTAGTAAGCAAGAGCGCACAATAC
genomic: GTCAAGGGCTAAGAATTGCACCTCCTGAGGCACCTGTTACTGGCTATATGgttcgttgta ... tctttgacagTTCGGCAAAGGCCTCTACTTTGCAGATCTAGTAAGCAAGAGCGCACAATAC
EST: gi|60351643|gb|DN218616.1|DN218616
EST:     GTCAAGGGCTAAGAATTGCACCTCCTGAGGCACCTGTTACTGGCTATATG                         TTCGGCAAAGGCCTCTACTTTGCAGATCTAGTAAGCAAGAGCGCACAATAC
genomic: GTCAAGGGCTAAGAATTGCACCTCCTGAGGCACCTGTTACTGGCTATATGgttcgttgta ... tctttgacagTTCGGCAAAGGCCTCTACTTTGCAGATCTAGTAAGCAAGAGCGCACAATAC
EST: gi|60394841|gb|DN227710.1|DN227710
EST:     GTCAAGGGCTAAGAATTGCACCTCCTGAGGCACCTGTTACTGGCTATATG                         TTCGGCAAAGGCCTCTACTTTGCAGATCTAGTAAGCAAGAGCGCACAATAC
genomic: GTCAAGGGCTAAGAATTGCACCTCCTGAGGCACCTGTTACTGGCTATATGgttcgttgta ... tctttgacagTTCGGCAAAGGCCTCTACTTTGCAGATCTAGTAAGCAAGAGCGCACAATAC
EST: gi|94475980|gb|EB704938.1|EB704938
EST:     GTCAAGGGCTAAGAATTGCACCTCCTGAGGCACCTGTTACTGGCTATATG                         TTCGGCAAAGGCCTCTACTTTGCAGATCTAGTAAGCAAGAGCGCACAATAC
genomic: GTCAAGGGCTAAGAATTGCACCTCCTGAGGCACCTGTTACTGGCTATATGgttcgttgta ... tctttgacagTTCGGCAAAGGCCTCTACTTTGCAGATCTAGTAAGCAAGAGCGCACAATAC
EST: gi|60345790|gb|DN212763.1|DN212763
EST:     GTCAAGGGCTAAGAATTGCACCTCCTGAGGCACCTGTTACTGGCTATATG                         TTCGGCAAAGGCCTCTACTTTGCAGATCTAGTAAGCAAGAGCGCACAATAC
genomic: GTCAAGGGCTAAGAATTGCACCTCCTGAGGCACCTGTTACTGGCTATATGgttcgttgta ... tctttgacagTTCGGCAAAGGCCTCTACTTTGCAGATCTAGTAAGCAAGAGCGCACAATAC
EST: gi|211088584|gb|FL093443.1|FL093443
EST:     GTCAAGGGCTAAGAATTGCACCTCCTGAGGCACCTGTTACTGGCTATATG                         TTCGGCAAAGGCCTCTACTTTGCAGATCTAGTAAGCAAGAGCGCACAATAC
genomic: GTCAAGGGCTAAGAATTGCACCTCCTGAGGCACCTGTTACTGGCTATATGgttcgttgta ... tctttgacagTTCGGCAAAGGCCTCTACTTTGCAGATCTAGTAAGCAAGAGCGCACAATAC
EST: gi|60350335|gb|DN217308.1|DN217308
EST:     GTCAAGGGCTAAGAATTGCACCTCCTGAGGCACCTGTTACTGGCTATATG                         TTCGGCAAAGGCCTCTACTTTGCAGATCTAGTAAGCAAGAGCGCACAATAC
genomic: GTCAAGGGCTAAGAATTGCACCTCCTGAGGCACCTGTTACTGGCTATATGgttcgttgta ... tctttgacagTTCGGCAAAGGCCTCTACTTTGCAGATCTAGTAAGCAAGAGCGCACAATAC
EST: gi|94475979|gb|EB704937.1|EB704937
EST:     AAGAATTGCACCTCCTGAGGCACCTGTTACTGGCTATATG                         TTCGGCAAAGGCCTCTACTTTGCAGATCTAGTAAGCAAGAGCGCACAATAC
genomic: AAGAATTGCACCTCCTGAGGCACCTGTTACTGGCTATATGgttcgttgta ... tctttgacagTTCGGCAAAGGCCTCTACTTTGCAGATCTAGTAAGCAAGAGCGCACAATAC

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: 47 (upstream exon), 49 (downstream exon)
Score: 168

GTTCAAGGTTGACGAATTTTGTGGGAATTCTTAGTCAAGGGCTAAGAATTGCACCTCCTGAGGCACCTGTTACTGGCTATATGgttcgttgta ... tctttgacagTTCGGCAAAGGCCTCTACTTTGCAGATCTAGTAAGCAAGAGCGCACAATACTGTTATGTGGATAGGAATAATCCTGTAGGTTTGATGCTTCTTTCTGAGG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 38

GTTCAAGGTTGACGAATTTTGTGGGAATTCTTAGTCAAGGGCTAAGAATTGCACCTCCTGAGGCACCTGTTACTGGCTATATGgttcgttgta ... tctttgacagTTCGGCAAAGGCCTCTACTTTGCAGATCTAGTAAGCAAGAGCGCACAATACTGTTATGTGGATAGGAATAATCCTGTAGGTTTGATGCTTCTTTCTGAGG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 32

GTTCAAGGTTGACGAATTTTGTGGGAATTCTTAGTCAAGGGCTAAGAATTGCACCTCCTGAGGCACCTGTTACTGGCTATATGgttcgttgta ... tctttgacagTTCGGCAAAGGCCTCTACTTTGCAGATCTAGTAAGCAAGAGCGCACAATACTGTTATGTGGATAGGAATAATCCTGTAGGTTTGATGCTTCTTTCTGAGG


Block sizes: 46 (upstream exon), 47 (downstream exon)
Score: 25

GTTCAAGGTTGACGAATTTTGTGGGAATTCTTAGTCAAGGGCTAAGAATTGCACCTCCTGAGGCACCTGTTACTGGCTATATGgttcgttgta ... tctttgacagTTCGGCAAAGGCCTCTACTTTGCAGATCTAGTAAGCAAGAGCGCACAATACTGTTATGTGGATAGGAATAATCCTGTAGGTTTGATGCTTCTTTCTGAGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtcaaagtgttggttgaaaacaattatgtgatgatgctcctcgtttctttgacagTTCGGCAAAGGCCTCTACTTTGCAGATCTAGTAAGCAAGAGCGCACAATACTGTTATGTGGATAGGAATAATCCTGTAGGTTTGATGCTTCTTTCTGAGG
                                  tgctcctcgtttcttt  CT-rich tract
             ttgaaaacaattat  TA-rich tract