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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcaactgagtcatattatatttgtatcccttgatacttaggcctccttttgagaaagcatgttctgtatcatatcctctgatgtggtaatttgaatcgggactaattttctgttttggtttcttggcacatagGACTCCTCATTCTCAAACATCGCATCATATGAAACACCAAGTTCAGCACGTGGGAATAGACAGCAAATATTTATGGAGTCTCCAGTTGGCTTGAGACCAC

Basic information

species Zea mays
transcript GRMZM2G180704_T01
intron # 8
splice site 3'
intron type U2

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|6095545|gb|AW120212.1|AW120212
EST:     GGCTCCGTACAACCAGTGGCTATCTTGGAGCTGAATGTCAAGAAGCTATG                         GACTCCTCATTCTCAAACATCGCATCATATGAAACACCAAGTTCAGCACGT
genomic: GGCTCCGTACAACCAGTGGCTATCTTGGAGCTGAATGTCAAGAAGCTATGgtgagcaact ... tggcacatagGACTCCTCATTCTCAAACATCGCATCATATGAAACACCAAGTTCAGCACGT
EST: gi|211339633|gb|FL428844.1|FL428844
EST:     GGCTCCGTACAACCAGTGGCTATCTTGGAGCTGAATGTCAAGAAGCTATG                         GACTCCTCATTCTCAAACATCGCATCATATGAAACACCAAGTTCAGCACGT
genomic: GGCTCCGTACAACCAGTGGCTATCTTGGAGCTGAATGTCAAGAAGCTATGgtgagcaact ... tggcacatagGACTCCTCATTCTCAAACATCGCATCATATGAAACACCAAGTTCAGCACGT
EST: gi|67022796|gb|CO451545.1|CO451545
EST:     GGCTCCGTACAACCAGTGGCTATCTTGGAGCTGAATGTCAAGAAGCTATG                         GACTCCTCATTCTCAAACATCGCATCATATGAAACACCAAGTTCAGCACGT
genomic: GGCTCCGTACAACCAGTGGCTATCTTGGAGCTGAATGTCAAGAAGCTATGgtgagcaact ... tggcacatagGACTCCTCATTCTCAAACATCGCATCATATGAAACACCAAGTTCAGCACGT
EST: gi|94477170|gb|EB706128.1|EB706128
EST:     GGCTCCGTACAACCAGTGGCTATCTTGGAGCTGAATGTCAAGAAGCTATG                         GACTCCTCATTCTCAAACATCGCATCATATGAAACACCAAGTTCAGCACGT
genomic: GGCTCCGTACAACCAGTGGCTATCTTGGAGCTGAATGTCAAGAAGCTATGgtgagcaact ... tggcacatagGACTCCTCATTCTCAAACATCGCATCATATGAAACACCAAGTTCAGCACGT
EST: gi|6031408|gb|AW076310.1|AW076310
EST:     GGCTCCGTACAACCAGTGGCTATCTTGGAGCTGAATGTCAAGAAGCTATG                         GACTCCTCATTCTCAAACATCGCATCATATGAAACACCAAGTTCAGCACGT
genomic: GGCTCCGTACAACCAGTGGCTATCTTGGAGCTGAATGTCAAGAAGCTATGgtgagcaact ... tggcacatagGACTCCTCATTCTCAAACATCGCATCATATGAAACACCAAGTTCAGCACGT
EST: gi|6994173|gb|AW453387.1|AW453387
EST:     GGCTCCGTACAACCAGTGGCTATCTTGGAGCTGAATGTCAAGAAGCTATG                         GACTCCTCATTCTCAAACATCGCATCATATGAAACACCAAGTTCAGCACGT
genomic: GGCTCCGTACAACCAGTGGCTATCTTGGAGCTGAATGTCAAGAAGCTATGgtgagcaact ... tggcacatagGACTCCTCATTCTCAAACATCGCATCATATGAAACACCAAGTTCAGCACGT
EST: gi|116827763|gb|EC871704.1|EC871704
EST:     GGCTCCGTACAACCAGTGGCTATCTTGGAGCTGAATGTCAAGAAGCTATG                         GACTCCTCATTCTCAAACATCGCATCATATGAAACACCAAGTTCAGCACGT
genomic: GGCTCCGTACAACCAGTGGCTATCTTGGAGCTGAATGTCAAGAAGCTATGgtgagcaact ... tggcacatagGACTCCTCATTCTCAAACATCGCATCATATGAAACACCAAGTTCAGCACGT
EST: gi|76015667|gb|DT942837.1|DT942837
EST:     GGCTCCGTACAACCAGTGGCTATCTTGGAGCTGAATGTCAAGAAGCTATG                         GACTCCTCATTCTCAAACATCGCATCATATGAAACACCAAGTTCAGCACGT
genomic: GGCTCCGTACAACCAGTGGCTATCTTGGAGCTGAATGTCAAGAAGCTATGgtgagcaact ... tggcacatagGACTCCTCATTCTCAAACATCGCATCATATGAAACACCAAGTTCAGCACGT
EST: gi|211368668|gb|FL393818.1|FL393818
EST:     GGCTCCGTACAACCAGTGGCTATCTTGGAGCTGAATGTCAAGAAGCTATG                         GACTCCTCATTCTCAAACATCGCATCATATGAAACACCAAGTTCAGCACGT
genomic: GGCTCCGTACAACCAGTGGCTATCTTGGAGCTGAATGTCAAGAAGCTATGgtgagcaact ... tggcacatagGACTCCTCATTCTCAAACATCGCATCATATGAAACACCAAGTTCAGCACGT
EST: gi|211092258|gb|FL379383.1|FL379383
EST:     GGCTCCGTACAACCAGTGGCTATCTTGGAGCTGAATGTCAAGAAGCTATG                         GACTCCTCATTCTCAAACATCGCATCATATGAAACACCAAGTTCAGCACGT
genomic: GGCTCCGTACAACCAGTGGCTATCTTGGAGCTGAATGTCAAGAAGCTATGgtgagcaact ... tggcacatagGACTCCTCATTCTCAAACATCGCATCATATGAAACACCAAGTTCAGCACGT
EST: gi|32847442|gb|CD987123.1|CD987123
EST:     ACAACCAGTGGCTATCTTGGAGCTGAATGTCAAGAAGCTATG                         GACTCCTCATTCTCAAACATCGCATCATATGAAACACCAAGTTCAGCACGT
genomic: ACAACCAGTGGCTATCTTGGAGCTGAATGTCAAGAAGCTATGgtgagcaact ... tggcacatagGACTCCTCATTCTCAAACATCGCATCATATGAAACACCAAGTTCAGCACGT

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: 48 (upstream exon), 49 (downstream exon)
Score: 288

GCAACTGTTGCATATTACTTACTCTTGGACAATAGGCTCCGTACAACCAGTGGCTATCTTGGAGCTGAATGTCAAGAAGCTATGgtgagcaact ... tggcacatagGACTCCTCATTCTCAAACATCGCATCATATGAAACACCAAGTTCAGCACGTGGGAATAGACAGCAAATATTTATGGAGTCTCCAGTTGGCTTGAGACCAC


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 115

GCAACTGTTGCATATTACTTACTCTTGGACAATAGGCTCCGTACAACCAGTGGCTATCTTGGAGCTGAATGTCAAGAAGCTATGgtgagcaact ... tggcacatagGACTCCTCATTCTCAAACATCGCATCATATGAAACACCAAGTTCAGCACGTGGGAATAGACAGCAAATATTTATGGAGTCTCCAGTTGGCTTGAGACCAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 175

GCAACTGTTGCATATTACTTACTCTTGGACAATAGGCTCCGTACAACCAGTGGCTATCTTGGAGCTGAATGTCAAGAAGCTATGgtgagcaact ... tggcacatagGACTCCTCATTCTCAAACATCGCATCATATGAAACACCAAGTTCAGCACGTGGGAATAGACAGCAAATATTTATGGAGTCTCCAGTTGGCTTGAGACCAC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 203

GCAACTGTTGCATATTACTTACTCTTGGACAATAGGCTCCGTACAACCAGTGGCTATCTTGGAGCTGAATGTCAAGAAGCTATGgtgagcaact ... tggcacatagGACTCCTCATTCTCAAACATCGCATCATATGAAACACCAAGTTCAGCACGTGGGAATAGACAGCAAATATTTATGGAGTCTCCAGTTGGCTTGAGACCAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatgtggtaatttgaatcgggactaattttctgttttggtttcttggcacatagGACTCCTCATTCTCAAACATCGCATCATATGAAACACCAAGTTCAGCACGTGGGAATAGACAGCAAATATTTATGGAGTCTCCAGTTGGCTTGAGACCAC
                     gactaat  putative branch site (score: 203)
                                        tttctt  putative PPT
                        taattttctgtttt  TA-rich tract