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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGATGGATGTTAACGAAAGCCCTGTTTATCTTCTATTAAATCCTACTATCAACCTCTCCCAGAAGGATCTCCCTGTGACTATTTATGAGAGTGgtaagtcaatatggatttaagtttggaattgttaatgtagtgcaacttgtttctcctgtgtttggttctaccctgaacctgtttatgcgactttagtgat...

Basic information

species Zea mays
transcript GRMZM2G028089_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G028089_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os08g39070.1 (Oryza sativa), 5'ss of exon 3
TTGATGGATGTTAACGAAAGCCCTGTTTATCTTCTATTAAATCCTACTATCAACCTCTCCCAGAAGGATCTCCCTGTGACTATTTATGAGAGTGgtaagtcaatatggatttaagtt-tggaattgttaa-tgtagtgcaacttgtttctcctgtgtttggttctaccctgaacctgtttatgcgactttagtgat--
 |||||||  |||||||||| || ||||||||||| || |||||| | ||||||||||||||||||||||||||||| || ||||||||||||||||||| ||| ||  || |  || |   ||| | || | || ||||| |  |||| |    ||||   | |    ||    | | | |     |||||   |  
CTGATGGACATTAACGAAAGTCCCGTTTATCTTCTTTTGAATCCTGCAATCAACCTCTCCCAGAAGGATCTCCCTGTAACAATTTATGAGAGTGgtaagtgaatctgacttcagcttgtatcattataaaatatattgcaattgatttcaca---gtttttatatggtttgggtttttgttt-tacttttaggtgtac

upper sequence: GRMZM2G028089_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA06G47850.1 (Glycine max), 5'ss of exon 3
TTGATGGATGTTAACGAAAGCCCTGTTTATCTTCTATTAAATCCTACTATCAACCTCTCCCAGAAGGATCTCCCTGTGACTATTTATGAGAGTGgtaagtcaatatggatttaagtttggaattgttaatgtagtgcaacttgtttctcctgtgtttggttctaccctgaacctgtttatgcga------ctttagtgat
||||||||| | || ||||| || |||||| ||||  | |||||| |||||||||  || ||||||||||| ||||| | ||||| ||| |||||||||| ||| |  ||      |||   |  ||| | | |||    || ||||  |     |||     |     ||    || ||  |       ||||||| | 
TTGATGGATATCAATGAAAGTCCAGTTTATGTTCTTCTCAATCCTTCTATCAACCATTCTCAGAAGGATCTACCTGTCAGTATTTTTGAAAGTGgtaagt-aatctccatc----attgtgttatttagtat-gtgactgttttttcaaccacagttgcaaaaatgaaaaaagcattaataaggaaagagctttagttac

upper sequence: GRMZM2G028089_T01 (Zea mays), 5'ss of exon 3
lower sequence: AT5G56280.1 (Arabidopsis thaliana), 5'ss of exon 3
TTGATGGATGTTAACGAAAGCCCTGTTTATCTTCTATTAAATCCTACTATCAACCTCTCCCAGAAGGATCTCCCTGTGACTATTTATGAGAGTGgtaagtca-----------atatggatttaag------tttggaattgttaatgtagtgcaacttgtttctcctgtgtttggttctaccctgaacctgtttatgc----gactttagtgat------------------------------------------------------------------------------
||||||||| | || |||   ||||||||| | || ||||| ||| ||||||| | | | ||||||||||| || |||||||||||||| ||||||| |              |||||| | |  |      ||  ||  |||||   |  |   |   || | | |   |||  |   | |     | ||    | |       ||||| |||                                                                               
TTGATGGATATCAATGAATCTCCTGTTTATGTGCTTTTAAACCCTGCTATCAATCACACACAGAAGGATCTTCCAGTGACTATTTATGAAAGTGgtatgcttcttataatgtcatatggttctgtgggtacattctgatatgttagcatgttagtataggtatatgcgtagttcagagtttctagatatcttcccaagtctttatctttattgacttccagatttaggtcagattgttttacaagatcctaacttttctctttgtttcattgattgatcttcattacttgaag

upper sequence: GRMZM2G028089_T01 (Zea mays), 5'ss of exon 3
lower sequence: Vv19s0015g01950.t01 (Vitis vinifera), 5'ss of exon 3
TTGATGGATGTTAACGAAAGCCCTGTTTATCTTCTATTAAATCCTACTATCAACCTCTCCCAGAAGGATCTCCCTGTGACTATTTATGAGAGTGgtaagtcaatatggatttaagtttggaattgttaa-tgtagtgcaacttgtttctcctgtgtttggttctaccc-tgaacctgtttatgcgactttagtgat
||||||||| |||| ||||||||||| ||| ||||  | |||||  | ||||| |   | || |||||||||||||||||||| ||||| ||||||| || |   |  ||||   | |       |||| |    |  || |  ||   |  || | |      |    |||  ||||  |   ||  |||     
TTGATGGATATTAATGAAAGCCCTGTCTATGTTCTTCTCAATCCGTCAATCAATCATGCACAAAAGGATCTCCCTGTGACTATCTATGAAAGTGgtatgtaacccttcatttttatcttcttcctttaactcccttataagtgattctgcaagtctataaaaaaaaaagtgattctgtaaagttgatcttatat--

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|5343228|gb|AI795413.1|AI795413
EST:     TACTATCAACCTCTCCCAGAAGGATCTCCCTGTGACTATTTATGAGAGTG                         AGTTGCATGTCATCGATGGGTGTCCTCAGCTTATCTTTGTCAGATCAAATT
genomic: TACTATCAACCTCTCCCAGAAGGATCTCCCTGTGACTATTTATGAGAGTGgtaagtcaat ... taattcgaagAGTTGCATGTCATCGATGGGTGTCCTCAGCTTATCTTTGTCAGATCAAATT
EST: gi|74245516|gb|DT653430.1|DT653430
EST:     TACTATCAACCTCTCCCAGAAGGATCTCCCTGTGACTATTTATGAGAGTG                         AGTTGCATGTCATCGATGGGTGTCCTCAGCTTATCTTTGTCAGATCAAATT
genomic: TACTATCAACCTCTCCCAGAAGGATCTCCCTGTGACTATTTATGAGAGTGgtaagtcaat ... taattcgaagAGTTGCATGTCATCGATGGGTGTCCTCAGCTTATCTTTGTCAGATCAAATT
EST: gi|148964739|gb|EC906002.2|EC906002
EST:     TACTATCAACCTCTCCCAGAAGGATCTCCCTGTGACTATTTATGAGAGTG                         AGTTGCATGTCATCGATGGGTGTCCTCAGCTTATCTTTGTCAGATCAAATT
genomic: TACTATCAACCTCTCCCAGAAGGATCTCCCTGTGACTATTTATGAGAGTGgtaagtcaat ... taattcgaagAGTTGCATGTCATCGATGGGTGTCCTCAGCTTATCTTTGTCAGATCAAATT
EST: gi|71427075|gb|DR808125.1|DR808125
EST:     TACTATCAACCTCTCCCAGAAGGATCTCCCTGTGACTATTTATGAGAGTG                         AGTTGCATGTCATCGATGGGTGTCCTCAGCTTATCTTTGTCAGATCAAATT
genomic: TACTATCAACCTCTCCCAGAAGGATCTCCCTGTGACTATTTATGAGAGTGgtaagtcaat ... taattcgaagAGTTGCATGTCATCGATGGGTGTCCTCAGCTTATCTTTGTCAGATCAAATT
EST: gi|78079914|gb|DV508326.1|DV508326
EST:     TACTATCAACCTCTCCCAGAAGGATCTCCCTGTGACTATTTATGAGAGTG                         AGTTGCATGTCATCGATGGGTGTCCTCAGCTTATCTTTGTCAGATCAAATT
genomic: TACTATCAACCTCTCCCAGAAGGATCTCCCTGTGACTATTTATGAGAGTGgtaagtcaat ... taattcgaagAGTTGCATGTCATCGATGGGTGTCCTCAGCTTATCTTTGTCAGATCAAATT
EST: gi|76020044|gb|DT947214.1|DT947214
EST:     TACTATCAACCTCTCCCAGAAGGATCTCCCTGTGACTATTTATGAGAGTG                         AGTTGCATGTCATCGATGGGTGTCCTCAGCTTATCTTTGTCAGATCAAATT
genomic: TACTATCAACCTCTCCCAGAAGGATCTCCCTGTGACTATTTATGAGAGTGgtaagtcaat ... taattcgaagAGTTGCATGTCATCGATGGGTGTCCTCAGCTTATCTTTGTCAGATCAAATT
EST: gi|71428767|gb|DR809817.1|DR809817
EST:     TACTATCAACCTCTCCCAGAAGGATCTCCCTGTGACTATTTATGAGAGTG                         AGTTGCATGTCATCGATGGGTGTCCTCAGCTTATCTTTGTCAGATCAAATT
genomic: TACTATCAACCTCTCCCAGAAGGATCTCCCTGTGACTATTTATGAGAGTGgtaagtcaat ... taattcgaagAGTTGCATGTCATCGATGGGTGTCCTCAGCTTATCTTTGTCAGATCAAATT
EST: gi|78079913|gb|DV508325.1|DV508325
EST:     GAAGGATCTCCCTGTGACTATTTATGAGAGTG                         AGTTGCATGTCATCGATGGGTGTCCTCAGCTTATCTTTGTCAGATCAAATT
genomic: GAAGGATCTCCCTGTGACTATTTATGAGAGTGgtaagtcaat ... taattcgaagAGTTGCATGTCATCGATGGGTGTCCTCAGCTTATCTTTGTCAGATCAAATT
EST: gi|78104235|gb|DV522653.1|DV522653
EST:     TACTATCAACCTCTCCCAGAAGGATCTCCCTGTGACTATTTATGAGAGTG                         AGTTGCATGTCATCGATGGGTGTCCTCAGCTTATCTTTGTCAGATCAAATT
genomic: TACTATCAACCTCTCCCAGAAGGATCTCCCTGTGACTATTTATGAGAGTGgtaagtcaat ... taattcgaagAGTTGCATGTCATCGATGGGTGTCCTCAGCTTATCTTTGTCAGATCAAATT
EST: gi|5650012|gb|AI920372.1|AI920372
EST:     ACCTCTCCCAGAAGGATCTCCCTGTGACTATTTATGAGAGTG                         AGTTGCATGTCATCGATGGGTGTCCTCAGCTTATCTTTGTCAGATCAAATT
genomic: ACCTCTCCCAGAAGGATCTCCCTGTGACTATTTATGAGAGTGgtaagtcaat ... taattcgaagAGTTGCATGTCATCGATGGGTGTCCTCAGCTTATCTTTGTCAGATCAAATT
EST: gi|76925807|gb|DV170603.1|DV170603
EST:     TACTATCAACCTCTCCCAGAAGGATCTCCCTGTGACTATTTATGAGAGTG                         AGTTGCATGTCATCGATGGGTGTCCTCAGCTTATCTTTGTCAGATCAAATT
genomic: TACTATCAACCTCTCCCAGAAGGATCTCCCTGTGACTATTTATGAGAGTGgtaagtcaat ... taattcgaagAGTTGCATGTCATCGATGGGTGTCCTCAGCTTATCTTTGTCAGATCAAATT
EST: gi|74245515|gb|DT653429.1|DT653429
EST:     TACTATCAACCTCTCCCAGAAGGATCTCCCTGTGACTATTTATGAGAGTG                         AGTTGCATGTCATCGATGGGTGTCCTCAGCTTATCTTTGTCAGATCAAATT
genomic: TACTATCAACCTCTCCCAGAAGGATCTCCCTGTGACTATTTATGAGAGTGgtaagtcaat ... taattcgaagAGTTGCATGTCATCGATGGGTGTCCTCAGCTTATCTTTGTCAGATCAAATT

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: 48 (upstream exon), 47 (downstream exon)
Score: 62

TTGATGGATGTTAACGAAAGCCCTGTTTATCTTCTATTAAATCCTACTATCAACCTCTCCCAGAAGGATCTCCCTGTGACTATTTATGAGAGTGgtaagtcaat ... taattcgaagAGTTGCATGTCATCGATGGGTGTCCTCAGCTTATCTTTGTCAGATCAAATTATACAATTGAG


Block sizes: 48 (upstream exon), 41 (downstream exon)
Score: 29

TTGATGGATGTTAACGAAAGCCCTGTTTATCTTCTATTAAATCCTACTATCAACCTCTCCCAGAAGGATCTCCCTGTGACTATTTATGAGAGTGgtaagtcaat ... taattcgaagAGTTGCATGTCATCGATGGGTGTCCTCAGCTTATCTTTGTCAGATCAAATTATACAATTGAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 15

TTGATGGATGTTAACGAAAGCCCTGTTTATCTTCTATTAAATCCTACTATCAACCTCTCCCAGAAGGATCTCCCTGTGACTATTTATGAGAGTGgtaagtcaat ... taattcgaagAGTTGCATGTCATCGATGGGTGTCCTCAGCTTATCTTTGTCAGATCAAATTATACAATTGAG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 36

TTGATGGATGTTAACGAAAGCCCTGTTTATCTTCTATTAAATCCTACTATCAACCTCTCCCAGAAGGATCTCCCTGTGACTATTTATGAGAGTGgtaagtcaat ... taattcgaagAGTTGCATGTCATCGATGGGTGTCCTCAGCTTATCTTTGTCAGATCAAATTATACAATTGAG