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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgtacccaagcttggagctgaaacgagttcacatccgcgttggaattcggttctctgaatctgttttgtgttttcgtctttttttttgcttttcatttcagGCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGGCGGTGATGATCCCGACAGTGTTGGTTCCCATGATGGGCGGCGACGAT

Basic information

species Zea mays
transcript GRMZM2G437859_T04
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G437859_T03 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g55500.3 (Oryza sativa), 3'ss of exon 1
----gtgcgtacccaagc--ttggagctgaaacgagttcacatccgcgttggaattcggttctctgaatctgttttgtgttttcgtctttttttttgcttttcatttcagGCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGGCGGTGATGATCCCGACAGTGTTGGTTCCCATGATGGGCGGCGACGAT--
    ||| |  || ||||    |  |||| |  |  ||     | || | || |||  |   ||||||||        || || |      ||||||||     ||||||| ||||||||||||||||| |||||||||||||| |||||||||||||||||||||||||||||| | ||| |||| ||||||||||||||   |||   
gtgcgtgagagccgaagcggcggcggctgcattgcattttttcctgc-tcgggatttcgcattctgaatccac-----gtcttgga-----tttttgct----gtttcagGGGAGGCGATCATACTGGGATTCCAGCACTACATCCTGGCGCTGGGCACGGCGGTGATGATCCCGGCGGTGCTGGTGCCCATGATGGGCGGGAGCGACGT

upper sequence: GRMZM2G437859_T03 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g55500.4 (Oryza sativa), 3'ss of exon 1
----gtgcgtacccaagc--ttggagctgaaacgagttcacatccgcgttggaattcggttctctgaatctgttttgtgttttcgtctttttttttgcttttcatttcagGCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGGCGGTGATGATCCCGACAGTGTTGGTTCCCATGATGGGCGGCGACGAT
    ||| |  || ||||    |  |||| |  |  ||     | || | || |||  |   ||||||||        || || |      ||||||||     ||||||| ||||||||||||||||| |||||||||||||| |||||||||||||||||||||||||||||| | ||| |||| ||||||||||||||   ||| 
gtgcgtgagagccgaagcggcggcggctgcattgcattttttcctgc-tcgggatttcgcattctgaatccac-----gtcttgga-----tttttgct----gtttcagGGGAGGCGATCATACTGGGATTCCAGCACTACATCCTGGCGCTGGGCACGGCGGTGATGATCCCGGCGGTGCTGGTGCCCATGATGGGCGGGAGCGAC
















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|211100341|gb|FL069922.1|FL069922
EST:     GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGG                         GCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG
genomic: GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGGgtgcgtaccc ... ttcatttcagGCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG
EST: gi|50339069|gb|CO534195.1|CO534195
EST:     GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGG                         GCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG
genomic: GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGGgtgcgtaccc ... ttcatttcagGCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG
EST: gi|71449525|gb|DR830575.1|DR830575
EST:     GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGG                         GCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG
genomic: GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGGgtgcgtaccc ... ttcatttcagGCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG
EST: gi|74244049|gb|DT651963.1|DT651963
EST:     GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGG                         GCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG
genomic: GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGGgtgcgtaccc ... ttcatttcagGCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG
EST: gi|149001123|gb|EE038382.2|EE038382
EST:     GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGG                         GCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG
genomic: GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGGgtgcgtaccc ... ttcatttcagGCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG
EST: gi|78084450|gb|DV512843.1|DV512843
EST:     GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGG                         GCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG
genomic: GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGGgtgcgtaccc ... ttcatttcagGCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG
EST: gi|211102812|gb|FL069930.1|FL069930
EST:     GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGG                         GCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG
genomic: GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGGgtgcgtaccc ... ttcatttcagGCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG
EST: gi|211100342|gb|FL069923.1|FL069923
EST:     GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGG                         GCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG
genomic: GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGGgtgcgtaccc ... ttcatttcagGCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG
EST: gi|71439895|gb|DR820945.1|DR820945
EST:     GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGG                         GCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG
genomic: GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGGgtgcgtaccc ... ttcatttcagGCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG
EST: gi|50331687|gb|CO526813.1|CO526813
EST:     GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGG                         GCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG
genomic: GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGGgtgcgtaccc ... ttcatttcagGCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG
EST: gi|91878994|gb|EB408951.1|EB408951
EST:     GGAGCAGCTCCAGGGGTTCCAGTACTGCATCGACTCCCACCCTCCCTGGG                         GCGAGGCGATCATACTG
genomic: GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGGgtgcgtaccc ... ttcatttcagGCGAGGCGATCATACTG
EST: gi|74243489|gb|DT651403.1|DT651403
EST:     GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGG                         GCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG
genomic: GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGGgtgcgtaccc ... ttcatttcagGCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG
EST: gi|76923378|gb|DV169457.1|DV169457
EST:     GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGG                         GCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG
genomic: GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGGgtgcgtaccc ... ttcatttcagGCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG
EST: gi|74238882|gb|DT646796.1|DT646796
EST:     GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGG                         GCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG
genomic: GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGGgtgcgtaccc ... ttcatttcagGCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG
EST: gi|149071736|gb|EE160129.2|EE160129
EST:     GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGG                         GCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG
genomic: GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGGgtgcgtaccc ... ttcatttcagGCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG
EST: gi|74240437|gb|DT648351.1|DT648351
EST:     GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGG                         GCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG
genomic: GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGGgtgcgtaccc ... ttcatttcagGCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG
EST: gi|33467816|gb|CF244865.1|CF244865
EST:     GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGG                         GCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG
genomic: GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGGgtgcgtaccc ... ttcatttcagGCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG
EST: gi|91049745|gb|EB160163.1|EB160163
EST:     GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGG                         GCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG
genomic: GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGGgtgcgtaccc ... ttcatttcagGCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG
EST: gi|211102810|gb|FL069928.1|FL069928
EST:     GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGG                         GCGAGGCGATCATACTGGGCTTCCAGCACT
genomic: GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGGgtgcgtaccc ... ttcatttcagGCGAGGCGATCATACTGGGCTTCCAGCACT
EST: gi|211102809|gb|FL069927.1|FL069927
EST:     GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGG                         GCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG
genomic: GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGGgtgcgtaccc ... ttcatttcagGCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG
EST: gi|93016333|gb|EB641853.1|EB641853
EST:     GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGG                         GCGAGGCGATCATACTGGG
genomic: GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGGgtgcgtaccc ... ttcatttcagGCGAGGCGATCATACTGGG
EST: gi|78081194|gb|DV509606.1|DV509606
EST:     GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGG                         GCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG
genomic: GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGGgtgcgtaccc ... ttcatttcagGCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG
EST: gi|211100339|gb|FL069920.1|FL069920
EST:     GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGG                         GCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG
genomic: GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGGgtgcgtaccc ... ttcatttcagGCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG
EST: gi|211100340|gb|FL069921.1|FL069921
EST:     GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGG                         GCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG
genomic: GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGGgtgcgtaccc ... ttcatttcagGCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG
EST: gi|211102808|gb|FL069926.1|FL069926
EST:     GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGG                         GCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG
genomic: GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGGgtgcgtaccc ... ttcatttcagGCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG
EST: gi|211100336|gb|FL069917.1|FL069917
EST:     GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGG                         GCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG
genomic: GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGGgtgcgtaccc ... ttcatttcagGCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG
EST: gi|71310987|gb|DR791795.1|DR791795
EST:     GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGG                         GCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG
genomic: GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGGgtgcgtaccc ... ttcatttcagGCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG
EST: gi|71431026|gb|DR812076.1|DR812076
EST:     GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGG                         GCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG
genomic: GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGGgtgcgtaccc ... ttcatttcagGCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG
EST: gi|71438783|gb|DR819833.1|DR819833
EST:     GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGG                         GCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG
genomic: GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGGgtgcgtaccc ... ttcatttcagGCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG

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), 48 (downstream exon)
Score: 289

GGTAGGGAAATGGCGGAGGTGAAGCCGGAGGAGATAAGCCATCCGCCCATGGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGGgtgcgtaccc ... ttcatttcagGCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGGCGGTGATGATCCCGACAGTGTTGGTTCCCATGATGGGCGGCGACGAT


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

GGTAGGGAAATGGCGGAGGTGAAGCCGGAGGAGATAAGCCATCCGCCCATGGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGGgtgcgtaccc ... ttcatttcagGCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGGCGGTGATGATCCCGACAGTGTTGGTTCCCATGATGGGCGGCGACGAT


Block sizes: 46 (upstream exon), 47 (downstream exon)
Score: 27

GGTAGGGAAATGGCGGAGGTGAAGCCGGAGGAGATAAGCCATCCGCCCATGGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGGgtgcgtaccc ... ttcatttcagGCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGGCGGTGATGATCCCGACAGTGTTGGTTCCCATGATGGGCGGCGACGAT


Block sizes: 46 (upstream exon), 46 (downstream exon)
Score: 60

GGTAGGGAAATGGCGGAGGTGAAGCCGGAGGAGATAAGCCATCCGCCCATGGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGGgtgcgtaccc ... ttcatttcagGCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGGCGGTGATGATCCCGACAGTGTTGGTTCCCATGATGGGCGGCGACGAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcggttctctgaatctgttttgtgttttcgtctttttttttgcttttcatttcagGCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGGCGGTGATGATCCCGACAGTGTTGGTTCCCATGATGGGCGGCGACGAT
                 ttttgtgttttcgtct  CT-rich tract
                                tttttttttgctttt  TA-rich tract