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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtacatattctttgctttgttctttcgaaacttgaatatagatcttgatgcataatttttcttctgcgagaaagctggatttctgcttattttatggcataccatacacagGTAAGGGTTTCAGGATATGGTGGGTGGTTCTTGCTGAGGCTCTCTCTGCATGATCCTGTTCTTCCCCTAAACATTGAG

Basic information

species Zea mays
transcript GRMZM2G069676_T03
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G069676_T03 (Zea mays), 3'ss of exon 16
lower sequence: LOC_Os07g26610.1 (Oryza sativa), 3'ss of exon 16
gtatgtacatattctttgctttgttctttcgaaacttgaatatagatcttgatgca--taatttttcttctgcgagaaagctgga-tttctgcttatt---ttatggcataccat----acacagGTAAGGGTTTCAGGATATGGTGGGTGGTTCTTGCTGAGGCTCTCTCTGCATGATCCTGTTCTTCCCCTAAACATTGAG
||||||   |||||||||||| ||| |  | ||  |||| |||| ||||||||  |  ||  |||||||  |  |   ||||||  |||||  ||  |   | |||  |||   |    || |||||||| ||||||||||||||||| ||||||||  || || | || || ||||| || ||||||||||| ||||| |||
gtatgtcattattctttgctt-gttttcac-aagtttgagtatatatcttgatatatctaccttttcttgggtaaagtagctgggctttcttattgctgtatcatgctatatttttactacgcagGTAAGAGTTTCAGGATATGGTGGCTGGTTCTTATTGCGGTTATCCCTCCATGACCCAGTTCTTCCCCTTAACATCGAG
















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|211441849|gb|FL182586.1|FL182586
EST:     CAAAGACCCAAATCTCCATAAAGCCCCGGTGAACCATGAGGGC                         GTAAGGGTTTCAGGATATGGTGGGTGGTTCTTGCTGAGGCTCTCTCTGCAT
genomic: CAAAGACCCAAATCTCCGTAAAGCCCCGGTGAACCATGAGGGCgtatgtacat ... ccatacacagGTAAGGGTTTCAGGATATGGTGGGTGGTTCTTGCTGAGGCTCTCTCTGCAT
EST: gi|76289293|gb|DV028861.1|DV028861
EST:     CAATCAGCAAAGACCCAAATCTCCGTAAAGCCCCGGTGAACCATGAGGGC                         GTAAGGGTTTCAGGATATGGTGGGTGGTTCTTGCTGAGGCTCTCTCTGCAT
genomic: CAATCAGCAAAGACCCAAATCTCCGTAAAGCCCCGGTGAACCATGAGGGCgtatgtacat ... ccatacacagGTAAGGGTTTCAGGATATGGTGGGTGGTTCTTGCTGAGGCTCTCTCTGCAT
EST: gi|78112841|gb|DV531235.1|DV531235
EST:     CAATCAGCAAAGACCCAAATCTCCGTAAAGCCCCGGTGAACCATGAGGGC                         GTAAGGGTTTCAGGATATGGTGGGTGGTTCTTGCTGAGGCTCTCTCTGCAT
genomic: CAATCAGCAAAGACCCAAATCTCCGTAAAGCCCCGGTGAACCATGAGGGCgtatgtacat ... ccatacacagGTAAGGGTTTCAGGATATGGTGGGTGGTTCTTGCTGAGGCTCTCTCTGCAT
EST: gi|86465999|gb|DY232372.1|DY232372
EST:     CAATCAGCAAAGACCCAAATCTCCGTAAAGCCCCGGTGAACCATGAGGGC                         GTAAGGGTTTCAGGATATGGTGGGTGGTTCTTGCTGAGGCTCTCTCTGCAT
genomic: CAATCAGCAAAGACCCAAATCTCCGTAAAGCCCCGGTGAACCATGAGGGCgtatgtacat ... ccatacacagGTAAGGGTTTCAGGATATGGTGGGTGGTTCTTGCTGAGGCTCTCTCTGCAT
EST: gi|101389186|gb|EB816548.1|EB816548
EST:     CAATCAGCAAAGACCCAAATCTCCGTAAAGCCCCGGTGAACCATGAGGGC                         GTAAGGGTTTCAGGATATGGTGGGTGGTTCTTGCTGAGGCTCTCTCTGCAT
genomic: CAATCAGCAAAGACCCAAATCTCCGTAAAGCCCCGGTGAACCATGAGGGCgtatgtacat ... ccatacacagGTAAGGGTTTCAGGATATGGTGGGTGGTTCTTGCTGAGGCTCTCTCTGCAT
EST: gi|67018791|gb|CO447540.1|CO447540
EST:     CCAAATCTTCGTAAAGCCCCGTTGAACC-TGAGGGC                         GTAAGGGTTTCAGGATATGGTGGGTGGTTCTTGCTGAGGCTCTCTCTGCAT
genomic: CCAAATCTCCGTAAAGCCCCGGTGAACCATGAGGGCgtatgtacat ... ccatacacagGTAAGGGTTTCAGGATATGGTGGGTGGTTCTTGCTGAGGCTCTCTCTGCAT
EST: gi|20512826|gb|BQ280024.1|BQ280024
EST:     CAATCAGCAAAGACCCAAATCTCCATAAAGCCCCGGTGAACCATGAGGGC                         GTAAGGGTTTCAGGATATGGTGGGTGGTTCTTGCTGAGGCTCTCTCTGCAT
genomic: CAATCAGCAAAGACCCAAATCTCCGTAAAGCCCCGGTGAACCATGAGGGCgtatgtacat ... ccatacacagGTAAGGGTTTCAGGATATGGTGGGTGGTTCTTGCTGAGGCTCTCTCTGCAT
EST: gi|32928442|gb|CF033254.1|CF033254
EST:     CAATCAGCAAAGACCCAAATCTCCATAAAGCCCCGGTGAACCATGAGGGC                         GTAAGGGTTTCAGGATATGGTGGGTGGTTCTTGCTGAGGCTCTCTCTGCAT
genomic: CAATCAGCAAAGACCCAAATCTCCGTAAAGCCCCGGTGAACCATGAGGGCgtatgtacat ... ccatacacagGTAAGGGTTTCAGGATATGGTGGGTGGTTCTTGCTGAGGCTCTCTCTGCAT
EST: gi|32928208|gb|CF033020.1|CF033020
EST:     CAATCAGCAAAGACCCAAATCTCCATAAAGCCCCGGTGAACCATGAGGGC                         GTAAGGGTTTCAGGATATGGTGGGTGGTTCTTGCTGAGGCTCTCTCTGCAT
genomic: CAATCAGCAAAGACCCAAATCTCCGTAAAGCCCCGGTGAACCATGAGGGCgtatgtacat ... ccatacacagGTAAGGGTTTCAGGATATGGTGGGTGGTTCTTGCTGAGGCTCTCTCTGCAT
EST: gi|32929540|gb|CF034352.1|CF034352
EST:     CAATCAGCAAAGACCCAAATCTCCATAAAGCCCCGGTGAACCATGAGGGC                         GTAAGGGTTTCAGGATATGGTGGGTGGTTCTTGCTGAGGCTCTCTCTGCAT
genomic: CAATCAGCAAAGACCCAAATCTCCGTAAAGCCCCGGTGAACCATGAGGGCgtatgtacat ... ccatacacagGTAAGGGTTTCAGGATATGGTGGGTGGTTCTTGCTGAGGCTCTCTCTGCAT

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: 44 (upstream exon), 48 (downstream exon)
Score: 44

GTCCTTCCGTGACTATGGAGAATCCGTCTTGAGACATTTAGAGAATGCAATCAGCAAAGACCCAAATCTCCGTAAAGCCCCGGTGAACCATGAGGGCgtatgtacat ... ccatacacagGTAAGGGTTTCAGGATATGGTGGGTGGTTCTTGCTGAGGCTCTCTCTGCATGATCCTGTTCTTCCCCTAAACATTGAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 45

GTCCTTCCGTGACTATGGAGAATCCGTCTTGAGACATTTAGAGAATGCAATCAGCAAAGACCCAAATCTCCGTAAAGCCCCGGTGAACCATGAGGGCgtatgtacat ... ccatacacagGTAAGGGTTTCAGGATATGGTGGGTGGTTCTTGCTGAGGCTCTCTCTGCATGATCCTGTTCTTCCCCTAAACATTGAG


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 42

GTCCTTCCGTGACTATGGAGAATCCGTCTTGAGACATTTAGAGAATGCAATCAGCAAAGACCCAAATCTCCGTAAAGCCCCGGTGAACCATGAGGGCgtatgtacat ... ccatacacagGTAAGGGTTTCAGGATATGGTGGGTGGTTCTTGCTGAGGCTCTCTCTGCATGATCCTGTTCTTCCCCTAAACATTGAG


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

GTCCTTCCGTGACTATGGAGAATCCGTCTTGAGACATTTAGAGAATGCAATCAGCAAAGACCCAAATCTCCGTAAAGCCCCGGTGAACCATGAGGGCgtatgtacat ... ccatacacagGTAAGGGTTTCAGGATATGGTGGGTGGTTCTTGCTGAGGCTCTCTCTGCATGATCCTGTTCTTCCCCTAAACATTGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttcttctgcgagaaagctggatttctgcttattttatggcataccatacacagGTAAGGGTTTCAGGATATGGTGGGTGGTTCTTGCTGAGGCTCTCTCTGCATGATCCTGTTCTTCCCCTAAACATTGAG
                              ttattttat  TA-rich tract