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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacaatccatgacattttttactgagtacttgcaaatgatttgtgtatactgtataaggtgcaatacttatttctcttcctttttttgtccagTCTCTGATGTTAGTGACATCTTTGAACCCT

Basic information

species Zea mays
transcript GRMZM2G010823_T01
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G010823_T01 (Zea mays), 3'ss of exon 14
lower sequence: LOC_Os03g21950.1 (Oryza sativa), 3'ss of exon 14
gtaacaatccatgacattttttactgag-tacttgcaaatgatttgtgtatactgtat-----aaggtgcaatacttatttctcttcctttttttgtccagTCTCTGATGTTAGTGACATCTTTGAACCCT
          |    || | | |||||  |    | |||  ||   | || | | | |     ||  |||   | | |||| | |  | |||||| |||||||| ||||||| ||||||||||||||||||
--------gtaaagtatctgtgactgaactgtaggaaaaaaatgcatatacaatttttcaacaaatttgcttgattaatttgtgtatccttttttttccagTCTTTGATGTTGGTGACATCTTTGAACCCT
















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|60342181|gb|DN209154.1|DN209154
EST:     TCAGGGGAATTCAAGCAAACCACAAGAGAATTTCACAACTTTTGCATGAG                         TCTCTGATGTTAGTGACATCTTTGAACCCT
genomic: TCAGGGGAATTCAAGCAAACCACAAGAGAATTTCACAACTTTTGCATGAGgtaacaatcc ... ttttgtccagTCTCTGATGTTAGTGACATCTTTGAACCCT
EST: gi|60357469|gb|DN224442.1|DN224442
EST:     TCAGGGGAATTCAAGCAAACCACAAGAGAATTTCACAACTTTTGCATGAG                         TCTCTGATGTTAGTGACATCTTTGAACCCT
genomic: TCAGGGGAATTCAAGCAAACCACAAGAGAATTTCACAACTTTTGCATGAGgtaacaatcc ... ttttgtccagTCTCTGATGTTAGTGACATCTTTGAACCCT
EST: gi|149081506|gb|EE170642.2|EE170642
EST:     CAGGGGAATTCAAGCAAACCACAAGAGAATTTCACAACTTTTGCATGAG                         TCTCTGATGTTAGTGACATCTTTGAACCCT
genomic: CAGGGGAATTCAAGCAAACCACAAGAGAATTTCACAACTTTTGCATGAGgtaacaatcc ... ttttgtccagTCTCTGATGTTAGTGACATCTTTGAACCCT
EST: gi|149089383|gb|EE178622.2|EE178622
EST:     TCAGGGGAATTCAAGCAAACCACAAGAGAATTTCACAACTTTTGCATGAG                         TCTCTGATGTTAGTGACATCTTTGAACCCT
genomic: TCAGGGGAATTCAAGCAAACCACAAGAGAATTTCACAACTTTTGCATGAGgtaacaatcc ... ttttgtccagTCTCTGATGTTAGTGACATCTTTGAACCCT
EST: gi|6022572|gb|AW067384.1|AW067384
EST:     TCAGGGGAATTCAAGCAAACCACAAGAGAATTTCACAACTTTTGCATGAG                         TCTCTGATGTTAGTGACATCTTTGAACCCT
genomic: TCAGGGGAATTCAAGCAAACCACAAGAGAATTTCACAACTTTTGCATGAGgtaacaatcc ... ttttgtccagTCTCTGATGTTAGTGACATCTTTGAACCCT
EST: gi|5901092|gb|AW042192.1|AW042192
EST:     TCAGGGGAATTCAAGCAAACCACAAGAGAATTTCACAACTTTTGCATGAG                         TCTCTGATGTTAGTGACATCTTTGAACCCT
genomic: TCAGGGGAATTCAAGCAAACCACAAGAGAATTTCACAACTTTTGCATGAGgtaacaatcc ... ttttgtccagTCTCTGATGTTAGTGACATCTTTGAACCCT
EST: gi|78022604|gb|DV490991.1|DV490991
EST:     TCAGGGGAATTCAAGCAAACCACAAGAGAATTTCACAACTTTTGCATGAG                         TCTCTGATGTTAGTGACATCTTTGAACCCT
genomic: TCAGGGGAATTCAAGCAAACCACAAGAGAATTTCACAACTTTTGCATGAGgtaacaatcc ... ttttgtccagTCTCTGATGTTAGTGACATCTTTGAACCCT
EST: gi|211208053|gb|FL436834.1|FL436834
EST:     TCAGGGGATTTCAAGCAACCCACAAGAGAATTTCACAATTTTTGCATGAG                         TTTCTGATGTTAGTGACATCTTTGAACCCT
genomic: TCAGGGGAATTCAAGCAAACCACAAGAGAATTTCACAACTTTTGCATGAGgtaacaatcc ... ttttgtccagTCTCTGATGTTAGTGACATCTTTGAACCCT
EST: gi|8930245|gb|BE225009.1|BE225009
EST:     AATTTCACAACTTTTGCATGAG                         TCTCTGATGTTAGTGACATCTTTGAACCCT
genomic: AATTTCACAACTTTTGCATGAGgtaacaatcc ... ttttgtccagTCTCTGATGTTAGTGACATCTTTGAACCCT

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), 30 (downstream exon)
Score: 266

TCATTGAGGTTGTTAGGGGATGCATCCGTGTCCTTTGAGAAAAATTGTGTCAGGGGAATTCAAGCAAACCACAAGAGAATTTCACAACTTTTGCATGAGgtaacaatcc ... ttttgtccagTCTCTGATGTTAGTGACATCTTTGAACCCT


Block sizes: 49 (upstream exon), 30 (downstream exon)
Score: 407

TCATTGAGGTTGTTAGGGGATGCATCCGTGTCCTTTGAGAAAAATTGTGTCAGGGGAATTCAAGCAAACCACAAGAGAATTTCACAACTTTTGCATGAGgtaacaatcc ... ttttgtccagTCTCTGATGTTAGTGACATCTTTGAACCCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 442

TCATTGAGGTTGTTAGGGGATGCATCCGTGTCCTTTGAGAAAAATTGTGTCAGGGGAATTCAAGCAAACCACAAGAGAATTTCACAACTTTTGCATGAGgtaacaatcc ... ttttgtccagTCTCTGATGTTAGTGACATCTTTGAACCCT


Block sizes: 49 (upstream exon), 30 (downstream exon)
Score: 544

TCATTGAGGTTGTTAGGGGATGCATCCGTGTCCTTTGAGAAAAATTGTGTCAGGGGAATTCAAGCAAACCACAAGAGAATTTCACAACTTTTGCATGAGgtaacaatcc ... ttttgtccagTCTCTGATGTTAGTGACATCTTTGAACCCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttgtgtatactgtataaggtgcaatacttatttctcttcctttttttgtccagTCTCTGATGTTAGTGACATCTTTGAACCCT
                          tacttatttctcttcc  CT-rich tract
                        aatacttattt  TA-rich tract