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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttgtgttcatattgtttgttctttgtttgtcatgtggctagcgcacatgaagttatttctaatatctctatgatatacagATATATTTGAGGTTGCCACAGAGGATGGTACAGTACTCGCCATGAAACTTCATAGGCTGGGAAGGACATCTTTTAGGGCTGTGAAATCTAAACGTGACTA

Basic information

species Zea mays
transcript GRMZM2G472991_T03
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G472991_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os01g66520.1 (Oryza sativa), 3'ss of exon 4
gtatgttgtgttcatattgtttgttc---tttgtttgtcatgtggctagcgcacatgaagt---------tatttctaatatctctatgatatacagATATATTTGAGGTTGCCACAGAGGATGGTACAGTACTCGCCATGAAACTTCATAGGCTGGGAAGGACATCTTTTAGGGCTGTGAAATCTAAACGTGACTA
|||  |  |||| ||  |||||  ||   |||   | | ||||  | | |||| || |  |         | | |||||| | ||  | |  | |||| || |||||||||||||||||||||||||| ||  | |||||||| ||||||||| |||| |||||||||||||||||||||||||| || ||||||||
gtacatgctgttgatgatgttttctcatgttttacttttatgtcacaatcgcatatcagatgttctaacatttgtctaatctttcctttacctgcagACATCTTTGAGGTTGCCACAGAGGATGGTACCGTTTTGGCCATGAAGCTTCATAGGTTGGGTAGGACATCTTTTAGGGCTGTGAAATCCAAGCGTGACTA

upper sequence: GRMZM2G472991_T01 (Zea mays), 3'ss of exon 6
lower sequence: Vv05s0094g01560.t01 (Vitis vinifera), 3'ss of exon 4
-------gtatgttgtgttcatattgtttgttctttg-----tttgtcatgtg-gctagcgcacatgaagttatttctaatatctctatgatatacagATATATTTGAGGTTGCCACAGAGGATGGTACAGTACTCGCCATGAAACTTCATAGGCTGGGAAGGACATCTTTTAGGGCTGTGAAATCTAAACGTGACTA
        | |  | | ||||| ||  ||     |       |||    |||| | |  | ||   ||   |  || |  ||| ||  |  |  | |||||||||||| |||||||  || ||||| |||||  | || ||||| || ||||||||||| || || ||||||||||| || |||||||| ||||| ||
gtaatttttcttatatattcattttaatttcctgtaaaaaaattttgtttgtgtgttttcacattagatactgattatggtatttcgtttcttca-agATATATTTGAAGTTGCCAAGGAAGATGGCACAGTCTTGGCAATGAAGCTGCATAGGCTGGGTAGAACTTCTTTTAGGGCCGTAAAATCTAAGCGTGATTA
















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|93016530|gb|EB642050.1|EB642050
EST:     GGGAGTTTTTGCTTCAGTTGGCCGTCAGATCGGTGTTGGAAAGGAGTCTG                         ATATATTTGAGGTTGCCACAGAGGATGGTACAGTACTCGCCATGAAACTTC
genomic: GGGAGTTTTTGCTTCAGTTGGCCGTCAGATCGGTGTTGGAAAGGAGTCTGgtatgttgtg ... tgatatacagATATATTTGAGGTTGCCACAGAGGATGGTACAGTACTCGCCATGAAACTTC
EST: gi|18384009|gb|BM417209.1|BM417209
EST:     GGGAGTTTTTGCTTCAGTTGGCCGTCAGATCGGTGTTGGAAAGGAGTCTG                         ATATATTTGAGGTTGCCACAGAGGATGGTACAGTACTCGCCATGAAACTTC
genomic: GGGAGTTTTTGCTTCAGTTGGCCGTCAGATCGGTGTTGGAAAGGAGTCTGgtatgttgtg ... tgatatacagATATATTTGAGGTTGCCACAGAGGATGGTACAGTACTCGCCATGAAACTTC
EST: gi|71429251|gb|DR810301.1|DR810301
EST:     GGGAGTTTTTGCTTCAGTTGGCCGTCAGATCGGTGTTGGAAAGGAGTCTG                         ATATATTTGAGGTTGCCACAGAGGATGGTACAGTACTCGCCATGAAACTTC
genomic: GGGAGTTTTTGCTTCAGTTGGCCGTCAGATCGGTGTTGGAAAGGAGTCTGgtatgttgtg ... tgatatacagATATATTTGAGGTTGCCACAGAGGATGGTACAGTACTCGCCATGAAACTTC
EST: gi|20299997|gb|BQ162940.1|BQ162940
EST:     GGGAGTTTTTGCTTCAGTTGGCCGTCAGATCGGTGTTGGAAAGGAGTCTG                         ATATATTTGAGGTTGCC-CAGAGGATGGTACAGTACTCGCCATGAAACTTC
genomic: GGGAGTTTTTGCTTCAGTTGGCCGTCAGATCGGTGTTGGAAAGGAGTCTGgtatgttgtg ... tgatatacagATATATTTGAGGTTGCCACAGAGGATGGTACAGTACTCGCCATGAAACTTC
EST: gi|20300018|gb|BQ162961.1|BQ162961
EST:     GGGAGTTTTTGCTTCAGTTGGCCGTCAGATCGGTGTTGGAAAGGAGTCTG                         ATATATTTGAGGTTGCCACAGAGGATGGTACAGTACTCGCCATGAAACTTC
genomic: GGGAGTTTTTGCTTCAGTTGGCCGTCAGATCGGTGTTGGAAAGGAGTCTGgtatgttgtg ... tgatatacagATATATTTGAGGTTGCCACAGAGGATGGTACAGTACTCGCCATGAAACTTC
EST: gi|78120952|gb|DV539336.1|DV539336
EST:     GGGAGTTTTTGCTTCAGTTGGCCGTCAGATCGGTGTTGGAAAGGAGTCTG                         ATATATTTGAGGTTGCCACAGAGGATGGTACAGTACTCGCCATGAAACTTC
genomic: GGGAGTTTTTGCTTCAGTTGGCCGTCAGATCGGTGTTGGAAAGGAGTCTGgtatgttgtg ... tgatatacagATATATTTGAGGTTGCCACAGAGGATGGTACAGTACTCGCCATGAAACTTC
EST: gi|76014878|gb|DT942048.1|DT942048
EST:     GGGAGTTTTTGCTTCAGTTGGCCGTCAGATCGGTGTTGGAAAGGAGTCTG                         ATATATTTGAGGTTGCCACAGAGGATGGTACAGTACTCGCCATGAAACTTC
genomic: GGGAGTTTTTGCTTCAGTTGGCCGTCAGATCGGTGTTGGAAAGGAGTCTGgtatgttgtg ... tgatatacagATATATTTGAGGTTGCCACAGAGGATGGTACAGTACTCGCCATGAAACTTC
EST: gi|78112924|gb|DV531318.1|DV531318
EST:     GGGAGTTTTTGCTTCAGTTGGCCGTCAGATCGGTGTTGGAAAGGAGTCTG                         ATATATTTGAGGTTGCCACAGAGGATGGTACAGTACTCGCCATGAAACTTC
genomic: GGGAGTTTTTGCTTCAGTTGGCCGTCAGATCGGTGTTGGAAAGGAGTCTGgtatgttgtg ... tgatatacagATATATTTGAGGTTGCCACAGAGGATGGTACAGTACTCGCCATGAAACTTC
EST: gi|76014835|gb|DT942005.1|DT942005
EST:     GGGAGTTTTTGCTTCAGTTGGCCGTCAGATCGGTGTTGGAAAGGAGTCTG                         ATATATTTGAGGTTGCCACAGAGGATGGTACAGTACTCGCCATGAAACTTC
genomic: GGGAGTTTTTGCTTCAGTTGGCCGTCAGATCGGTGTTGGAAAGGAGTCTGgtatgttgtg ... tgatatacagATATATTTGAGGTTGCCACAGAGGATGGTACAGTACTCGCCATGAAACTTC
EST: gi|89106284|gb|DY576501.1|DY576501
EST:     GGGAGTTTTTGCTTCAGTTGGCCGTCAGATCGGTGTTGGAAAGGAGTCTG                         ATATATTTGAGGTTGCCACAGAGGATGGTACAGTACTCGCCATGAAACTTC
genomic: GGGAGTTTTTGCTTCAGTTGGCCGTCAGATCGGTGTTGGAAAGGAGTCTGgtatgttgtg ... tgatatacagATATATTTGAGGTTGCCACAGAGGATGGTACAGTACTCGCCATGAAACTTC
EST: gi|22489226|gb|BU049149.1|BU049149
EST:     GGGAGTTTTTGCTTCAGTTGGCCGTCAGATCGGTGTTGGAAAGGAGTCTG                         ATATATTTGAGGTTGCCACAGAGGATGGTACAGTACTCGCCATGAAACTTC
genomic: GGGAGTTTTTGCTTCAGTTGGCCGTCAGATCGGTGTTGGAAAGGAGTCTGgtatgttgtg ... tgatatacagATATATTTGAGGTTGCCACAGAGGATGGTACAGTACTCGCCATGAAACTTC
EST: gi|91056420|gb|EB166838.1|EB166838
EST:     GGGAGTTTTTGCTTCAGTTGGCCGTCAGATCGGTGTTGGAAAGGAGTCTG                         ATATATTTGAGGTTGCCACAGAGGATGGTACAGTACTCGCCATGAAACTTC
genomic: GGGAGTTTTTGCTTCAGTTGGCCGTCAGATCGGTGTTGGAAAGGAGTCTGgtatgttgtg ... tgatatacagATATATTTGAGGTTGCCACAGAGGATGGTACAGTACTCGCCATGAAACTTC
EST: gi|18383990|gb|BM417190.1|BM417190
EST:     GGGAGTTTTTGCTTCAGTTGGCCGTCAGATCGGTGTTGGAAAGGAGTCTG                         ATATATTTGAGGTTGCCACAGAGGATGGTACAGTACTCGCCATGAAACTTC
genomic: GGGAGTTTTTGCTTCAGTTGGCCGTCAGATCGGTGTTGGAAAGGAGTCTGgtatgttgtg ... tgatatacagATATATTTGAGGTTGCCACAGAGGATGGTACAGTACTCGCCATGAAACTTC
EST: gi|211277358|gb|FL192926.1|FL192926
EST:     GGGAGTTTTTGCTTCAGTTGGCCGTCAGATCGGTGTTGGAAAGGAGTCTG                         ATATATTTGAGGTTGCCACAGAGGATGGTACAGTACTCGCCATGAAACTTC
genomic: GGGAGTTTTTGCTTCAGTTGGCCGTCAGATCGGTGTTGGAAAGGAGTCTGgtatgttgtg ... tgatatacagATATATTTGAGGTTGCCACAGAGGATGGTACAGTACTCGCCATGAAACTTC

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: 49 (upstream exon), 49 (downstream exon)
Score: 104

CTCACCTATCTAGGATATGACTTCCTTGCCATCAAGACTTTGGTTAATCGGGGAGTTTTTGCTTCAGTTGGCCGTCAGATCGGTGTTGGAAAGGAGTCTGgtatgttgtg ... tgatatacagATATATTTGAGGTTGCCACAGAGGATGGTACAGTACTCGCCATGAAACTTCATAGGCTGGGAAGGACATCTTTTAGGGCTGTGAAATCTAAACGTGACTA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 84

CTCACCTATCTAGGATATGACTTCCTTGCCATCAAGACTTTGGTTAATCGGGGAGTTTTTGCTTCAGTTGGCCGTCAGATCGGTGTTGGAAAGGAGTCTGgtatgttgtg ... tgatatacagATATATTTGAGGTTGCCACAGAGGATGGTACAGTACTCGCCATGAAACTTCATAGGCTGGGAAGGACATCTTTTAGGGCTGTGAAATCTAAACGTGACTA


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 58

CTCACCTATCTAGGATATGACTTCCTTGCCATCAAGACTTTGGTTAATCGGGGAGTTTTTGCTTCAGTTGGCCGTCAGATCGGTGTTGGAAAGGAGTCTGgtatgttgtg ... tgatatacagATATATTTGAGGTTGCCACAGAGGATGGTACAGTACTCGCCATGAAACTTCATAGGCTGGGAAGGACATCTTTTAGGGCTGTGAAATCTAAACGTGACTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 79

CTCACCTATCTAGGATATGACTTCCTTGCCATCAAGACTTTGGTTAATCGGGGAGTTTTTGCTTCAGTTGGCCGTCAGATCGGTGTTGGAAAGGAGTCTGgtatgttgtg ... tgatatacagATATATTTGAGGTTGCCACAGAGGATGGTACAGTACTCGCCATGAAACTTCATAGGCTGGGAAGGACATCTTTTAGGGCTGTGAAATCTAAACGTGACTA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgtcatgtggctagcgcacatgaagttatttctaatatctctatgatatacagATATATTTGAGGTTGCCACAGAGGATGGTACAGTACTCGCCATGAAACTTCATAGGCTGGGAAGGACATCTTTTAGGGCTGTGAAATCTAAACGTGACTA
                               ttctaat  putative branch site (score: 79)
                                       tctctat  CT-rich tract
                        aagttatttctaatat  TA-rich tract