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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattgcattacagttatataaaaaaatggtatgtatgattcttcagataccaactaaattgttctttcttgcagTGTTGAATCTGGCCTTTTCCTTGAGCGTTTTTGGTTTTATGATTATGCATATTTCACTTGTTTCGGCTAATACGACGACAATTGAG

Basic information

species Zea mays
transcript GRMZM2G027307_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G027307_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os03g58960.1 (Oryza sativa), 3'ss of exon 4
gtaattgcattacagttat--ataaaaaaat-------ggtatgtatgattcttcagataccaactaaattgttctttcttgcagTGTTGAATCTGGCCTTTTCCTTGAGCGTTTTTGGTTTTATGATTATGCATATTTCACTTGTTTCGGCTAATACGACGACAATTGAG
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gtaattgcattactttcattcatgagaaattattcttgggcacgtttgactgaggattggcttataatattctttttctctgcagTGTTGAACCTGGCCTTTTCCTTGAGTGTTCTGGGTTTTATGATTATGCATGTTTCACTTGTTTCTGCTAATACAACAACAATTGAG
















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|5895854|gb|AW037100.1|AW037100
EST:     GAGATCCCAGGAGGGGGCTGCAGCACTTGCAACCACATTTCTCACCTTTG                         TGTTGAATCTGGCCTTTTCCTTGAGCGTTTTTGGTTTTATGATTATGCATA
genomic: GAGATCCCAGGA-AGTCCTGCAGCACTTGCAACCACATTTCTCACCTTTGgtaattgcat ... tttcttgcagTGTTGAATCTGGCCTTTTCCTTGAGCGTTTTTGGTTTTATGATTATGCATA
EST: gi|26455295|gb|CA826878.1|CA826878
EST:     CGAGATCCCAGGAAGTCCTGCAGCACTTGCAACCACATTTCTCACCTTTG                         TGTTGAATCTGGCCTTTTCCTTGAGCGTTTTTGGTTTTATGATTATGCATA
genomic: CGAGATCCCAGGAAGTCCTGCAGCACTTGCAACCACATTTCTCACCTTTGgtaattgcat ... tttcttgcagTGTTGAATCTGGCCTTTTCCTTGAGCGTTTTTGGTTTTATGATTATGCATA
EST: gi|149110923|gb|EE294421.2|EE294421
EST:     CGAGATCCCAGGAAGTCCTGCAGCACTTGCAACCACATTTCTCACCTTTG                         TGTTGAATCTGGCCTTTTCCTTGAGCGTTTTTGGTTTTATGATTATGCATA
genomic: CGAGATCCCAGGAAGTCCTGCAGCACTTGCAACCACATTTCTCACCTTTGgtaattgcat ... tttcttgcagTGTTGAATCTGGCCTTTTCCTTGAGCGTTTTTGGTTTTATGATTATGCATA
EST: gi|148933152|gb|EC876791.2|EC876791
EST:     CGAGATCCCAGGAAGTCCTGCAGCACTTGCAACCACATTTCTCACCTTTG                         TGTTGAATCTGGCCTTTTCCTTGAGCGTTTTTGGTTTTATGATTATGCATA
genomic: CGAGATCCCAGGAAGTCCTGCAGCACTTGCAACCACATTTCTCACCTTTGgtaattgcat ... tttcttgcagTGTTGAATCTGGCCTTTTCCTTGAGCGTTTTTGGTTTTATGATTATGCATA
EST: gi|89106782|gb|DY576999.1|DY576999
EST:     CGAGATCCCAGGAAGTCCTGCAGCACTTGCAACCACATTTCTCACCTTTG                         TGTTGAATCTGGCCTTTTCCTTGAGCGTTTTTGGTTTTATGATTATGCATA
genomic: CGAGATCCCAGGAAGTCCTGCAGCACTTGCAACCACATTTCTCACCTTTGgtaattgcat ... tttcttgcagTGTTGAATCTGGCCTTTTCCTTGAGCGTTTTTGGTTTTATGATTATGCATA
EST: gi|32797603|gb|CD949839.1|CD949839
EST:     GATCCCAGGAAGTCCTGCAGCACTTGCAACCACATTTCTCACCTTTG                         TGTTGAATCTGGCCTTTTCCTTGAGCGTTTTTGGTTTTATGATTATGCATA
genomic: GATCCCAGGAAGTCCTGCAGCACTTGCAACCACATTTCTCACCTTTGgtaattgcat ... tttcttgcagTGTTGAATCTGGCCTTTTCCTTGAGCGTTTTTGGTTTTATGATTATGCATA
EST: gi|61119340|gb|DN560301.1|DN560301
EST:     CGAGATCCCAGGAAGTCCTGCAGCACTTGCAACCACATTTCTCACCTTTG                         TGTTGAATCTGGCCTTTTCCTTGAGCGTTTTTGGTTTTATGATTATGCATA
genomic: CGAGATCCCAGGAAGTCCTGCAGCACTTGCAACCACATTTCTCACCTTTGgtaattgcat ... tttcttgcagTGTTGAATCTGGCCTTTTCCTTGAGCGTTTTTGGTTTTATGATTATGCATA
EST: gi|21390493|gb|BQ528542.1|BQ528542
EST:     CGAGATCCCAGGAAGTCCTGCAGCACTTGCAACCACATTTCTCACCTTTG                         TGTTGAATCTGGCCTTTTCCTTGAGCGTTTTTGGTTTTATGATTATGCATA
genomic: CGAGATCCCAGGAAGTCCTGCAGCACTTGCAACCACATTTCTCACCTTTGgtaattgcat ... tttcttgcagTGTTGAATCTGGCCTTTTCCTTGAGCGTTTTTGGTTTTATGATTATGCATA
EST: gi|89106688|gb|DY576905.1|DY576905
EST:     CGAGATCCCAGGAAGTCCTGCAGCACTTGCAACCACATTTCTCACCTTTG                         TGTTGAATCTGGCCTTTTCCTTGAGCGTTTTTGGTTTTATGATTATGCATA
genomic: CGAGATCCCAGGAAGTCCTGCAGCACTTGCAACCACATTTCTCACCTTTGgtaattgcat ... tttcttgcagTGTTGAATCTGGCCTTTTCCTTGAGCGTTTTTGGTTTTATGATTATGCATA
EST: gi|149072485|gb|EE160763.2|EE160763
EST:     AGATCCCAGGAAGTCCTGCAGCACTTGCAACCACATTTCTCACCTTTG                         TGTTGAATCTGGCCTTTTCCTTGAGCGTTTTTGGTTTTATGATTATGCATA
genomic: AGATCCCAGGAAGTCCTGCAGCACTTGCAACCACATTTCTCACCTTTGgtaattgcat ... tttcttgcagTGTTGAATCTGGCCTTTTCCTTGAGCGTTTTTGGTTTTATGATTATGCATA

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), 47 (downstream exon)
Score: 285

CTTGTCACACTCTCTTTATTGCCTCACTTCATAGCCTTCTTCAGTGATATCGAGATCCCAGGAAGTCCTGCAGCACTTGCAACCACATTTCTCACCTTTGgtaattgcat ... tttcttgcagTGTTGAATCTGGCCTTTTCCTTGAGCGTTTTTGGTTTTATGATTATGCATATTTCACTTGTTTCGGCTAATACGACGACAATTGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 298

CTTGTCACACTCTCTTTATTGCCTCACTTCATAGCCTTCTTCAGTGATATCGAGATCCCAGGAAGTCCTGCAGCACTTGCAACCACATTTCTCACCTTTGgtaattgcat ... tttcttgcagTGTTGAATCTGGCCTTTTCCTTGAGCGTTTTTGGTTTTATGATTATGCATATTTCACTTGTTTCGGCTAATACGACGACAATTGAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 342

CTTGTCACACTCTCTTTATTGCCTCACTTCATAGCCTTCTTCAGTGATATCGAGATCCCAGGAAGTCCTGCAGCACTTGCAACCACATTTCTCACCTTTGgtaattgcat ... tttcttgcagTGTTGAATCTGGCCTTTTCCTTGAGCGTTTTTGGTTTTATGATTATGCATATTTCACTTGTTTCGGCTAATACGACGACAATTGAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 273

CTTGTCACACTCTCTTTATTGCCTCACTTCATAGCCTTCTTCAGTGATATCGAGATCCCAGGAAGTCCTGCAGCACTTGCAACCACATTTCTCACCTTTGgtaattgcat ... tttcttgcagTGTTGAATCTGGCCTTTTCCTTGAGCGTTTTTGGTTTTATGATTATGCATATTTCACTTGTTTCGGCTAATACGACGACAATTGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaaaaatggtatgtatgattcttcagataccaactaaattgttctttcttgcagTGTTGAATCTGGCCTTTTCCTTGAGCGTTTTTGGTTTTATGATTATGCATATTTCACTTGTTTCGGCTAATACGACGACAATTGAG
                                aactaaa  putative branch site (score: 273)
                                       ttgttctttcttgc  CT-rich tract
                                aactaaatt  TA-rich tract