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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatagcaattactgattttttttacatcacgatgattcattgaacagtttattagaatgaatctaacttcatcccttgcccaatttcagCATGGCTGGTGTTACGACAGGAAATGTTGGTTACCTAGCAAATGCAATTCATGAGGTTACCAAACCAAATTGAGTTAGGGTCCTACCTTCTTTGGTCGAT

Basic information

species Zea mays
transcript GRMZM2G146677_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G146677_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os02g14110.1 (Oryza sativa), 3'ss of exon 9
gtatagcaattactgatttt--ttttacatcacgatgattcattgaacagtttattagaatga--atctaacttcatcccttgcccaatttcagCATGGCTGGTGTTACGACAGGAAATGTTGGTTACCTAGCAAATGCAATTCATGAGGTTACCAAACCAAATTGAGTTAGGGTCCTA--CCTTCTTTGGTCGAT
||| |  ||  | |  ||||  |||| |||   | ||| || |||     |||| | |||| |  |||||||||  |  | |  |   |||||||||||||||||| || ||||||||||| |  ||  | || ||||| ||||||||||| || ||| | || |||       ||||   || |||| || |   
gtacaataac-agtacttttagtttttcatgttgctgaatctttgt----tttaatcgaataaaaatctaactttctgtcatttc---tttcagCATGGCTGGTGTAACAACAGGAAATGTGGCGTATTTGGCTAATGCTATTCATGAGGTCACTAAAACGAAATGAAGCTACTTCCTCTTCCCTCTTCGGCCA--
















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|31349057|gb|CD433414.1|CD433414
EST:     CGTTTAACAAATGAATACCACATTTACATGACCCGCAATGGGAGGATAAG                         CATGGCTGGTGTAACGACAGGAAATGTTGGTTACCTAGCAAATGCAATTCA
genomic: CGTTTAACAAATGAATACCACATTTACATGACCCGCAATGGGAGGATAAGgtatagcaat ... ccaatttcagCATGGCTGGTGTTACGACAGGAAATGTTGGTTACCTAGCAAATGCAATTCA
EST: gi|31362346|gb|CD446703.1|CD446703
EST:     CGTTTAACAAATGAATACCACATTTACATGACCCGCAATGGGAGGATAAG                         CATGGCTGGTGTAACGACAGGAAATGTTGGTTACCTAGCAAATGCAATTCA
genomic: CGTTTAACAAATGAATACCACATTTACATGACCCGCAATGGGAGGATAAGgtatagcaat ... ccaatttcagCATGGCTGGTGTTACGACAGGAAATGTTGGTTACCTAGCAAATGCAATTCA
EST: gi|32833423|gb|CD973101.1|CD973101
EST:     CGTTTAACAAATGAATACCACATTTACATGACCCGCAATGGGAGGATAAG                         CATGGCTGGTGTAACGACAGGAAATGTTGGTTACCTAGCAAATGCAATTCA
genomic: CGTTTAACAAATGAATACCACATTTACATGACCCGCAATGGGAGGATAAGgtatagcaat ... ccaatttcagCATGGCTGGTGTTACGACAGGAAATGTTGGTTACCTAGCAAATGCAATTCA
EST: gi|31353746|gb|CD438103.1|CD438103
EST:     CGTTTAACAAATGAATACCACATTTACATGACCCGCAATGGGAGGATAAG                         CATGGCTGGGTGT-ACGACAGGAAAATGT-GGTTACCTAGCAAATGCAATT
genomic: CGTTTAACAAATGAATACCACATTTACATGACCCGCAATGGGAGGATAAGgtatagcaat ... ccaatttcagCATGGCTGG-TGTTACGACAGGAAA-TGTTGGTTACCTAGCAAATGCAATT
EST: gi|211235538|gb|FL127822.1|FL127822
EST:     CGTTTAACAAATGAATACCACATTTACATGACCCGCAATGGGAGGATAAG                         CATGGCTGGTGTTACGACAGGAAATGTTGGTTACCTAGCAAATGCAATTCA
genomic: CGTTTAACAAATGAATACCACATTTACATGACCCGCAATGGGAGGATAAGgtatagcaat ... ccaatttcagCATGGCTGGTGTTACGACAGGAAATGTTGGTTACCTAGCAAATGCAATTCA
EST: gi|5714296|gb|AI944281.1|AI944281
EST:     CGTTTAACAAATGAATACCACATTTACATGACCCGCAATGGGAGGATAAG                         CATGGCTGGTGTTACGACAGGAAATGTTGGTTACCTAGCAAATGCAATTCA
genomic: CGTTTAACAAATGAATACCACATTTACATGACCCGCAATGGGAGGATAAGgtatagcaat ... ccaatttcagCATGGCTGGTGTTACGACAGGAAATGTTGGTTACCTAGCAAATGCAATTCA
EST: gi|5847048|gb|AW000127.1|AW000127
EST:     CGTTTAACAAATGAATACCACATTTACATGACCCGCAATGGGAGGATAAG                         CATGGCTGGTGTTACGACAGGAAATGTTGGTTACCTAGCAAATGCAATTCA
genomic: CGTTTAACAAATGAATACCACATTTACATGACCCGCAATGGGAGGATAAGgtatagcaat ... ccaatttcagCATGGCTGGTGTTACGACAGGAAATGTTGGTTACCTAGCAAATGCAATTCA
EST: gi|31352769|gb|CD437126.1|CD437126
EST:     CGTTTAACAAATGAATACCACATTTACATGACCCGCAATGGGAGGATAAG                         CATGGCTGGTGTAACGACAGGAAATGTTGGTTACCTAGCAAATGCAATTCA
genomic: CGTTTAACAAATGAATACCACATTTACATGACCCGCAATGGGAGGATAAGgtatagcaat ... ccaatttcagCATGGCTGGTGTTACGACAGGAAATGTTGGTTACCTAGCAAATGCAATTCA
EST: gi|84977385|gb|DW475807.1|DW475807
EST:     CGTTTAACAAATGAATACCACATTTACATGACCCGCAATGGGAGGATAAG                         CATGGCTGGTGTAACGACAAGAAATGTTGGTTACCTAGCAAATGCAATTCA
genomic: CGTTTAACAAATGAATACCACATTTACATGACCCGCAATGGGAGGATAAGgtatagcaat ... ccaatttcagCATGGCTGGTGTTACGACAGGAAATGTTGGTTACCTAGCAAATGCAATTCA
EST: gi|50324321|gb|CO519447.1|CO519447
EST:     CGTTTAACAAATGAATACCACATTTACATGACCCGCAATGGGAGGATAAG                         CATGGCTGGTGTTACGACAGGAAATGTTGGTTACCTAGCAAATGCAATTCA
genomic: CGTTTAACAAATGAATACCACATTTACATGACCCGCAATGGGAGGATAAGgtatagcaat ... ccaatttcagCATGGCTGGTGTTACGACAGGAAATGTTGGTTACCTAGCAAATGCAATTCA
EST: gi|18172785|gb|BM348173.1|BM348173
EST:     CGTTTAACAAATGAATACCACATTTACATGACCCGCAATGGGAGGATAAG                         CATGGCTGGTGTTACGACAGGAAATGTTGGTTACCTAGCAAATGCAATTCA
genomic: CGTTTAACAAATGAATACCACATTTACATGACCCGCAATGGGAGGATAAGgtatagcaat ... ccaatttcagCATGGCTGGTGTTACGACAGGAAATGTTGGTTACCTAGCAAATGCAATTCA
EST: gi|211237763|gb|FL127823.1|FL127823
EST:     CGTTTAACAAATGAATACCACATTTACATGACCCGCAATGGGAGGATAAG                         CATGGCTGGTGTTACGACAGGAAATGTTGGTTACCTAGCAAATGCAATTCA
genomic: CGTTTAACAAATGAATACCACATTTACATGACCCGCAATGGGAGGATAAGgtatagcaat ... ccaatttcagCATGGCTGGTGTTACGACAGGAAATGTTGGTTACCTAGCAAATGCAATTCA
EST: gi|211237764|gb|FL127824.1|FL127824
EST:     CGTTTAACAAATGAATACCACATTTACATGACCCGCAATGGGAGGATAAG                         CATGGCTGGTGTAACGACAGGNAATGTTGGTTACCTAGCAAATGCAATTCA
genomic: CGTTTAACAAATGAATACCACATTTACATGACCCGCAATGGGAGGATAAGgtatagcaat ... ccaatttcagCATGGCTGGTGTTACGACAGGAAATGTTGGTTACCTAGCAAATGCAATTCA
EST: gi|5296287|gb|AI783057.1|AI783057
EST:     CGTTTAACAAATGAATACCACATTTACATGACCCGCAATGGGAGGATAAG                         CATGGCTGGTGT
genomic: CGTTTAACAAATGAATACCACATTTACATGACCCGCAATGGGAGGATAAGgtatagcaat ... ccaatttcagCATGGCTGGTGT
EST: gi|32834200|gb|CD973878.1|CD973878
EST:     CGTTTAACAAATGAATACCACATTTACATGACCCGCAATGGGAGGATAAG                         CATGGCTGGTGTAACGACAGGAAATGTTGGTTACCTAGCAAATGCAATTCA
genomic: CGTTTAACAAATGAATACCACATTTACATGACCCGCAATGGGAGGATAAGgtatagcaat ... ccaatttcagCATGGCTGGTGTTACGACAGGAAATGTTGGTTACCTAGCAAATGCAATTCA

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: 29

ATTGGAATGTTCTGCTACAGTGGGATGACACCTGAACAAGTTGACCGTTTAACAAATGAATACCACATTTACATGACCCGCAATGGGAGGATAAGgtatagcaat ... ccaatttcagCATGGCTGGTGTTACGACAGGAAATGTTGGTTACCTAGCAAATGCAATTCATGAGGTTACCAAACCAAATTGAGTTAGGGTCCTACCTTCTTTGGTCGAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 66

ATTGGAATGTTCTGCTACAGTGGGATGACACCTGAACAAGTTGACCGTTTAACAAATGAATACCACATTTACATGACCCGCAATGGGAGGATAAGgtatagcaat ... ccaatttcagCATGGCTGGTGTTACGACAGGAAATGTTGGTTACCTAGCAAATGCAATTCATGAGGTTACCAAACCAAATTGAGTTAGGGTCCTACCTTCTTTGGTCGAT


Block sizes: 43 (upstream exon), 48 (downstream exon)
Score: 33

ATTGGAATGTTCTGCTACAGTGGGATGACACCTGAACAAGTTGACCGTTTAACAAATGAATACCACATTTACATGACCCGCAATGGGAGGATAAGgtatagcaat ... ccaatttcagCATGGCTGGTGTTACGACAGGAAATGTTGGTTACCTAGCAAATGCAATTCATGAGGTTACCAAACCAAATTGAGTTAGGGTCCTACCTTCTTTGGTCGAT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 23

ATTGGAATGTTCTGCTACAGTGGGATGACACCTGAACAAGTTGACCGTTTAACAAATGAATACCACATTTACATGACCCGCAATGGGAGGATAAGgtatagcaat ... ccaatttcagCATGGCTGGTGTTACGACAGGAAATGTTGGTTACCTAGCAAATGCAATTCATGAGGTTACCAAACCAAATTGAGTTAGGGTCCTACCTTCTTTGGTCGAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attcattgaacagtttattagaatgaatctaacttcatcccttgcccaatttcagCATGGCTGGTGTTACGACAGGAAATGTTGGTTACCTAGCAAATGCAATTCATGAGGTTACCAAACCAAATTGAGTTAGGGTCCTACCTTCTTTGGTCGAT
                          atctaac  putative branch site (score: 23)
                                cttcatcccttgccc  CT-rich tract
             tttattagaatgaat  TA-rich tract