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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgtttgatttgggcttactcgttcctctcaggtatccagtgtcttaatgacatttatttatttatttttttaaaaaatcctgcagGTCTTTCAGCTTCACTAAATGTTAGGATAGTTTATCTGGACATCATGAGGCCATTTGCTGAATCAACTTTGTTAGG

Basic information

species Zea mays
transcript GRMZM2G140917_T01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G140917_T01 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os06g48770.1 (Oryza sativa), 3'ss of exon 12
gtatgtgtttgatttgggcttactcgttcctctcaggtatccagtgtcttaatgacatttatttatttatttttttaaaaaatcctgcagGTCTTTCAGCTTCACTAAATGTTAGGATAGTTTATCTGGACATCATGAGGCCATTTGCTGAATCAACTTTGTTAGG
      || || |||    | | || ||||| | |  |||||||| || |  | ||||    |   |||| |        | |  |||||| || ||||| |||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||| ||||
------gtatgtttt----tcattctttcctttgaaatatccagtatcatggtaacatgctctctattatctgc------acttatgcagGGCTATCAGCATCACTAAATGTTAGGATAGTTTATCTAGACATCATGAGGCCATTTGCTGAATCAACTTTGCTAGG

upper sequence: GRMZM2G140917_T01 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os06g48770.2 (Oryza sativa), 3'ss of exon 11
------------gtatgtgttt---gatttgggctt-actcgttcctctcaggtatccagtgtcttaatgacatttatttatttatttttttaaaaaatcctgcagGTCTTTCAGCTTCACTAAATGTTAGGATAGTTTATCTGGACATCATGAGGCCATTTGCTGAATCAACTTTGTTAGG
            | || |  ||   | | ||   || | || ||||| | |  |||||||| || |  | ||||    |   |||| |        | |  |||||| || ||||| |||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||| ||||
catgagggttttgaatcttcttagaggtatgtttttcattctttcctttgaaatatccagtatcatggtaacatgctctctattatctgc------acttatgcagGGCTATCAGCATCACTAAATGTTAGGATAGTTTATCTAGACATCATGAGGCCATTTGCTGAATCAACTTTGCTAGG

upper sequence: GRMZM2G140917_T01 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA17G24420.1 (Glycine max), 3'ss of exon 11
gtatgtgtttgatttgggcttactcgttcctctcaggtatccagtgtcttaatgacatttatttatttatttttttaaaaaatcctgcagGTCTTTCAGCTTCACTAAATGTTAGGATAGTTTATCTGGACATCATGAGGCCATTTGCTGAATCAACTTTGTTAGG
|| ||| | |  | || | | |  |     |      |||   || ||  | |   ||||      ||| ||   | |       || ||| |||||  |  |  | |||||  | ||||| ||| ||||||| |||||||||||||||||||||  ||||   ||
gtctgt-tgtcttctgtggtgatgcaagtgtaatgcttattt-gtttcccagtcttattttacatattacttacctgatgtgga-tgtagGGCTTTCTTCCACCATGAATGTACGAATAGTATATATGGACATTATGAGGCCATTTGCTGAATCAGTTTTGAGTGG

upper sequence: GRMZM2G140917_T01 (Zea mays), 3'ss of exon 13
lower sequence: AT5G24810.2 (Arabidopsis thaliana), 3'ss of exon 12
-----gtatgtgtttgatttgggcttac-tcgttcctctcaggtatccagt--gtcttaatgacat-----ttatttatttatttttttaaaaaatcctgcagGTCTTTCAGCTTCACTAAATGTTAGGATAGTTTATCTGGACATCATGAGGCCATTTGCTGAATCAACTTTGTTAGG
      | | ||  | ||      |||| || ||      | | ||    |   || || |    |     || |||| |||||| |||     |   |  ||| |||||| || |  | |||||| |||| |||||||||||||||||||| |||||||| |||||   | |||||||
gtataatttatgaatcatactactttacctcattatgtcaaaggatttgctcaatcatagtactttactttttctttacttatttattttgtcgactatttagGACTTTCATCTACTATGAATGTTCGGATTGTTTATCTGGACATCATGAGACCATTTGCCGAATCTGTTCTGTTAGG

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|211142855|gb|FL032416.1|FL032416
EST:     TTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTCCTAAGAG                         GTCTTTCAGCTTCACTAAATGTTAGGATAGTTTATCTGGACATCATGAGGC
genomic: TTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTCCTCAGAGgtatgtgttt ... aatcctgcagGTCTTTCAGCTTCACTAAATGTTAGGATAGTTTATCTGGACATCATGAGGC
EST: gi|211402616|gb|FL252144.1|FL252144
EST:     TTTCCCCGGGGATGCCATAATATTTA--AGGGTCTTGAATCTCCTCAGAG                         GTCTTTCAGCTTCACTAAATGTTAGGATAGTTTATCTGGACATCATGAGGC
genomic: TTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTCCTCAGAGgtatgtgttt ... aatcctgcagGTCTTTCAGCTTCACTAAATGTTAGGATAGTTTATCTGGACATCATGAGGC
EST: gi|211145716|gb|FL032440.1|FL032440
EST:     TTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTCCTAAGAG                         GTCTTTCAGCTTCACTAAATGTTAGGATAGTTTATCTGGACATCATGAGGC
genomic: TTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTCCTCAGAGgtatgtgttt ... aatcctgcagGTCTTTCAGCTTCACTAAATGTTAGGATAGTTTATCTGGACATCATGAGGC
EST: gi|211144291|gb|FL032433.1|FL032433
EST:     TCCCCGGGGATGCCATAATGATTTGATGAGGGTCTTGAATCTCCTCAGAG                         GTCTTTCAGCTTCACTAAATGGTTAGGATAGTTTATCTGGACATCATGAGG
genomic: TCCCCGGGGATGCCATAAT-ATTT-ATGAGGGTCTTGAATCTCCTCAGAGgtatgtgttt ... aatcctgcagGTCTTTCAGCTTCACTAAATG-TTAGGATAGTTTATCTGGACATCATGAGG
EST: gi|89763775|gb|DY690831.1|DY690831
EST:     TTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTCCTCAGAG                         GTCTTTCAGCTTCACTAAATGTTAGGATAGTTTATCTGGACATCATGAGGC
genomic: TTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTCCTCAGAGgtatgtgttt ... aatcctgcagGTCTTTCAGCTTCACTAAATGTTAGGATAGTTTATCTGGACATCATGAGGC
EST: gi|211145718|gb|FL032442.1|FL032442
EST:     TTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTCCTCAGAG                         GTCTTTCAGCTTCACTAAATGTTAGGATAGTTTATCTGGACATCATGAGGC
genomic: TTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTCCTCAGAGgtatgtgttt ... aatcctgcagGTCTTTCAGCTTCACTAAATGTTAGGATAGTTTATCTGGACATCATGAGGC
EST: gi|148966697|gb|EE017760.2|EE017760
EST:     TTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTCCTCAGAG                         GTCTTTCAGCTTCACTAAATGTTAGGATAGTTTATCTGGACATCATGAGGC
genomic: TTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTCCTCAGAGgtatgtgttt ... aatcctgcagGTCTTTCAGCTTCACTAAATGTTAGGATAGTTTATCTGGACATCATGAGGC
EST: gi|211144288|gb|FL032430.1|FL032430
EST:     TTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTCCTCAGAG                         GTCTTTCAGCTTCACTAAATGTTAGGATAGTTTATCTGGACATCATGAGGC
genomic: TTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTCCTCAGAGgtatgtgttt ... aatcctgcagGTCTTTCAGCTTCACTAAATGTTAGGATAGTTTATCTGGACATCATGAGGC
EST: gi|211145719|gb|FL032443.1|FL032443
EST:     TTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTCCTCAGAG                         GTCTTTCAGCTTCACTAAATGTTAGGATAGTTTATCTGGACATCATGAGGC
genomic: TTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTCCTCAGAGgtatgtgttt ... aatcctgcagGTCTTTCAGCTTCACTAAATGTTAGGATAGTTTATCTGGACATCATGAGGC
EST: gi|211144285|gb|FL032427.1|FL032427
EST:     TTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTCCTCAGAG                         GTCTTTCAGCTTCACTAAATGTTAGGATAGTTTATCTGGACATCATGAGGC
genomic: TTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTCCTCAGAGgtatgtgttt ... aatcctgcagGTCTTTCAGCTTCACTAAATGTTAGGATAGTTTATCTGGACATCATGAGGC
EST: gi|211142858|gb|FL032419.1|FL032419
EST:     TTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTCCTCAGAG                         GTCTTTCAGCTTCACTAAATGTTAGGATAG
genomic: TTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTCCTCAGAGgtatgtgttt ... aatcctgcagGTCTTTCAGCTTCACTAAATGTTAGGATAG
EST: gi|211145714|gb|FL032438.1|FL032438
EST:     TTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTCCTCAGAG                         GTCTTTCAGCTTCACTAAATGTTAGGATAGTTTATCTGGACATCATGAGGC
genomic: TTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTCCTCAGAGgtatgtgttt ... aatcctgcagGTCTTTCAGCTTCACTAAATGTTAGGATAGTTTATCTGGACATCATGAGGC
EST: gi|211145713|gb|FL032437.1|FL032437
EST:     TTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTCCTCAGAG                         GTCTTTCAGCTTCACTAAATGTTAGGATAGTTTATCTGGACATCATGAGGC
genomic: TTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTCCTCAGAGgtatgtgttt ... aatcctgcagGTCTTTCAGCTTCACTAAATGTTAGGATAGTTTATCTGGACATCATGAGGC
EST: gi|211144284|gb|FL032426.1|FL032426
EST:     TTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTCCTCAGAG                         GTCTTTCAGCT
genomic: TTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTCCTCAGAGgtatgtgttt ... aatcctgcagGTCTTTCAGCT
EST: gi|211144294|gb|FL032436.1|FL032436
EST:     TTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTCCTCAGAG                         GTCTTTCAGCTTCACTAAATGTTAGGATAGTTTATCTGGACATCATGAGGC
genomic: TTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTCCTCAGAGgtatgtgttt ... aatcctgcagGTCTTTCAGCTTCACTAAATGTTAGGATAGTTTATCTGGACATCATGAGGC
EST: gi|211144287|gb|FL032429.1|FL032429
EST:     TTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTCCTCAGAG                         GTCTTTCAGCTTCACTAAATGTTAGGATAGTTTATCTGGACATCATGAGGC
genomic: TTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTCCTCAGAGgtatgtgttt ... aatcctgcagGTCTTTCAGCTTCACTAAATGTTAGGATAGTTTATCTGGACATCATGAGGC
EST: gi|211145717|gb|FL032441.1|FL032441
EST:     TTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTCCTCAGAG                         GTCTTTCAGCTTCACTAAATGTTAGGATAGTTTATCTGGACATCATGAGGC
genomic: TTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTCCTCAGAGgtatgtgttt ... aatcctgcagGTCTTTCAGCTTCACTAAATGTTAGGATAGTTTATCTGGACATCATGAGGC
EST: gi|211144283|gb|FL032425.1|FL032425
EST:     TTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTCCTCAGAG                         GTCTTTCAGCTTCACTAAATGTTAGGATAGTTTATCTGGACATCATGAGGC
genomic: TTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTCCTCAGAGgtatgtgttt ... aatcctgcagGTCTTTCAGCTTCACTAAATGTTAGGATAGTTTATCTGGACATCATGAGGC
EST: gi|211142856|gb|FL032417.1|FL032417
EST:     TTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTCCTCAGAG                         GTCTTTCAGCTTCACTAAATGTTAGGATAGTTTATCTGGACATCATGAGGC
genomic: TTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTCCTCAGAGgtatgtgttt ... aatcctgcagGTCTTTCAGCTTCACTAAATGTTAGGATAGTTTATCTGGACATCATGAGGC
EST: gi|211144292|gb|FL032434.1|FL032434
EST:     TTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTCCTCAGAG                         GTCTTTCAGCTTCACTAAATGTTAGGATAGTTTATCTGGACATCATGAGGC
genomic: TTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTCCTCAGAGgtatgtgttt ... aatcctgcagGTCTTTCAGCTTCACTAAATGTTAGGATAGTTTATCTGGACATCATGAGGC
EST: gi|211145720|gb|FL032444.1|FL032444
EST:     TTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTCCTCAGAG                         GTCTTTCAGCTTCACTAAATGTTAGGATAGTTTATCTGGACATCATGAGGC
genomic: TTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTCCTCAGAGgtatgtgttt ... aatcctgcagGTCTTTCAGCTTCACTAAATGTTAGGATAGTTTATCTGGACATCATGAGGC
EST: gi|211142860|gb|FL032421.1|FL032421
EST:     TTTCCCCGGNGATGCCATAATATTTATGAGGGTCTTGAATCTCCTCAGAG                         GTCTTTCAGCTTCACTAAATGTTAGGATAGTTTATCTGGACATCATGAGGC
genomic: TTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTCCTCAGAGgtatgtgttt ... aatcctgcagGTCTTTCAGCTTCACTAAATGTTAGGATAGTTTATCTGGACATCATGAGGC
EST: gi|211144290|gb|FL032432.1|FL032432
EST:     TTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTCCTCAGAG                         GTCTTTCAGCTTCACTAAATGTTAGGATAGTTTATCTGGACATCATGAGGC
genomic: TTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTCCTCAGAGgtatgtgttt ... aatcctgcagGTCTTTCAGCTTCACTAAATGTTAGGATAGTTTATCTGGACATCATGAGGC
EST: gi|67017334|gb|CO446083.1|CO446083
EST:     TCTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTCCTCAGAG                         GTCTTTCAGCTTCACTAAATGTTAGGATAGTTTATCTGGACATCATGAGGC
genomic: TTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTCCTCAGAGgtatgtgttt ... aatcctgcagGTCTTTCAGCTTCACTAAATGTTAGGATAGTTTATCTGGACATCATGAGGC
EST: gi|211142857|gb|FL032418.1|FL032418
EST:     TTTCCCCGGGGATGCCATAATATTTATGAGGGTCTAGAATCTCCTCAGAG                         GTCTTTCAGCTTCACTAAATGTTAGGATAGTTTATCTGGACATCATGAGGC
genomic: TTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTCCTCAGAGgtatgtgttt ... aatcctgcagGTCTTTCAGCTTCACTAAATGTTAGGATAGTTTATCTGGACATCATGAGGC
EST: gi|211142859|gb|FL032420.1|FL032420
EST:     TTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTCCTCAGAG                         GTCTTTCAGCTTCACTAAATGTTAGGATAGTTTATCTGGACATCATGAGGC
genomic: TTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTCCTCAGAGgtatgtgttt ... aatcctgcagGTCTTTCAGCTTCACTAAATGTTAGGATAGTTTATCTGGACATCATGAGGC
EST: gi|211144282|gb|FL032424.1|FL032424
EST:     TTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTCCTCAGAG                         GTCTTTCAGCTTCACTAAATGTTAGGATAGTTTATCTGGACATCATGAGGC
genomic: TTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTCCTCAGAGgtatgtgttt ... aatcctgcagGTCTTTCAGCTTCACTAAATGTTAGGATAGTTTATCTGGACATCATGAGGC

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), 43 (downstream exon)
Score: 105

GTTGATGCTTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTCCTCAGAGgtatgtgttt ... aatcctgcagGTCTTTCAGCTTCACTAAATGTTAGGATAGTTTATCTGGACATCATGAGGCCATTTGCTGAATCAACTTTGTTAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 615

GTTGATGCTTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTCCTCAGAGgtatgtgttt ... aatcctgcagGTCTTTCAGCTTCACTAAATGTTAGGATAGTTTATCTGGACATCATGAGGCCATTTGCTGAATCAACTTTGTTAGG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 678

GTTGATGCTTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTCCTCAGAGgtatgtgttt ... aatcctgcagGTCTTTCAGCTTCACTAAATGTTAGGATAGTTTATCTGGACATCATGAGGCCATTTGCTGAATCAACTTTGTTAGG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 790

GTTGATGCTTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTCCTCAGAGgtatgtgttt ... aatcctgcagGTCTTTCAGCTTCACTAAATGTTAGGATAGTTTATCTGGACATCATGAGGCCATTTGCTGAATCAACTTTGTTAGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtatccagtgtcttaatgacatttatttatttatttttttaaaaaatcctgcagGTCTTTCAGCTTCACTAAATGTTAGGATAGTTTATCTGGACATCATGAGGCCATTTGCTGAATCAACTTTGTTAGG
           tcttaat  putative branch site (score: 790)
         tgtcttaatgacattt  TA-rich tract