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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtatttcttacgttattcaggttctgttttcccaagtcttatttgatcatggatctagcagGTTCCAAAAACCTTCAATTTTAGCTTATCTGGGGCTTCTTCAAGGTCTTGCAAATATGTCTTAAACACACTCATGCAG

Basic information

species Zea mays
transcript GRMZM2G009849_T03
intron # 24
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G009849_T02 (Zea mays), 3'ss of exon 25
lower sequence: LOC_Os01g60040.2 (Oryza sativa), 3'ss of exon 42
gttagtatttcttacgttattcaggttctgttttcccaagtcttatttgatcatgg---atctagcagGTTCCAAAAACCTTCAATTTTAGCTTATCTGGGGCTTCTTCAAGGTCTTGCAAATATGTCTTAAACACACTCATGCAG
|| || ||||  ||  || || |||||   ||||  ||       | ||||  |||   | ||  |||||||||||||| || ||||||||| ||||||||||||| ||||| |||||||||||||| ||||| || |||||||||
gtaagcatttgctattttctttaggttaacttttgtcactataactctgatgttggcaaacctttcagGTTCCAAAAACTTTTAATTTTAGCCTATCTGGGGCTTCGTCAAGATCTTGCAAATATGTTTTAAATACTCTCATGCAG
















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|18649605|gb|BM498424.1|BM498424
EST:     AAGATCTTATTAAGGAAGCTGACAGATTAGTGTCATGCTTGGCTGTTATG                         GNTCCAAAAACCTTCAATTTTAGCTTATCTGGGGCTTCTTCAAGGTCTTGC
genomic: AAGATCTTATTAAGGAAGCTGACAGATTAGTGTCATGCTTGGCTGTTATGgttagtattt ... gatctagcagGTTCCAAAAACCTTCAATTTTAGCTTATCTGGGGCTTCTTCAAGGTCTTGC
EST: gi|20301651|gb|BQ164594.1|BQ164594
EST:     AAGATCTTATTAAGGAAGCTGACAGATTAGTGTCATGCTTGGCTGTTATG                         GTTCCAAAAACCTTCAATTTTAGCTTATCTGGGGCTTCTTCAAGGTCTTGC
genomic: AAGATCTTATTAAGGAAGCTGACAGATTAGTGTCATGCTTGGCTGTTATGgttagtattt ... gatctagcagGTTCCAAAAACCTTCAATTTTAGCTTATCTGGGGCTTCTTCAAGGTCTTGC
EST: gi|61118500|gb|DN559461.1|DN559461
EST:     AAGATCTTATTAAGGAAGCTGACAGATTAGTGTCATGCTTGGCTGTTATG                         GTTCCAAAAACCTTCAGTTTTAGCTTATCTGGGGCTTCTTCAAGGTCTTGC
genomic: AAGATCTTATTAAGGAAGCTGACAGATTAGTGTCATGCTTGGCTGTTATGgttagtattt ... gatctagcagGTTCCAAAAACCTTCAATTTTAGCTTATCTGGGGCTTCTTCAAGGTCTTGC
EST: gi|18450492|gb|BM428770.1|BM428770
EST:     AAGATCTTATTAAGGAAGCTGACAGATTAGTGTCATGCTTGGCTGTTATG                         GTTCCAAAAACCTTCAATTTTAGCTTATCTGGGGCTTCTTCAAGGTCTTGC
genomic: AAGATCTTATTAAGGAAGCTGACAGATTAGTGTCATGCTTGGCTGTTATGgttagtattt ... gatctagcagGTTCCAAAAACCTTCAATTTTAGCTTATCTGGGGCTTCTTCAAGGTCTTGC
EST: gi|18649578|gb|BM498397.1|BM498397
EST:     AAGATCTTATTAAGGAAGCTGACAGATTAGTGTCATGCTTGGCTGTTATG                         GNTCCAAAAACCTTCAATTTTAGCTTATCTGGGGCTTCTTCAAG
genomic: AAGATCTTATTAAGGAAGCTGACAGATTAGTGTCATGCTTGGCTGTTATGgttagtattt ... gatctagcagGTTCCAAAAACCTTCAATTTTAGCTTATCTGGGGCTTCTTCAAG
EST: gi|19822548|gb|BQ048572.1|BQ048572
EST:     AAGATCTTATTAAGGAAGCTGACAGATTAGTGCCATGCTTGGCTGTTATG                         GTTCCAAAAACCTTCAATTTTAGCTTATCTGGGGCTTCTTCAAGGTCTTGC
genomic: AAGATCTTATTAAGGAAGCTGACAGATTAGTGTCATGCTTGGCTGTTATGgttagtattt ... gatctagcagGTTCCAAAAACCTTCAATTTTAGCTTATCTGGGGCTTCTTCAAGGTCTTGC
EST: gi|67035401|gb|CO463934.1|CO463934
EST:     AAGATCTTATTAAGGAAGCTGACAGATTAGTGTCATGCTTGGCTGTTATG                         GTTCCAAAAACCTTCAATTTTAGCTTATCTGGGGCTTCTTCAAGGTCTTGC
genomic: AAGATCTTATTAAGGAAGCTGACAGATTAGTGTCATGCTTGGCTGTTATGgttagtattt ... gatctagcagGTTCCAAAAACCTTCAATTTTAGCTTATCTGGGGCTTCTTCAAGGTCTTGC
EST: gi|18450764|gb|BM429042.1|BM429042
EST:     AAGATCTTATTAAGGAAGCTGACAGATTAGTGTCATGCTTGGCTGTTATG                         GTTCCAAAAACCTTCAATTTTAGCTTATCTGGGGCTTCTTCAAGGTCTTGC
genomic: AAGATCTTATTAAGGAAGCTGACAGATTAGTGTCATGCTTGGCTGTTATGgttagtattt ... gatctagcagGTTCCAAAAACCTTCAATTTTAGCTTATCTGGGGCTTCTTCAAGGTCTTGC
EST: gi|18648832|gb|BM497651.1|BM497651
EST:     AAGATCTTATTAAGGAAGCTGACAGATTAGTGTCATGCTTGGCTGTTATG                         GTTCCAAAAACCTTCAATTTTAGCTTATCTGGGGCTTCTTCAAGGTCTTGC
genomic: AAGATCTTATTAAGGAAGCTGACAGATTAGTGTCATGCTTGGCTGTTATGgttagtattt ... gatctagcagGTTCCAAAAACCTTCAATTTTAGCTTATCTGGGGCTTCTTCAAGGTCTTGC
EST: gi|18648721|gb|BM497540.1|BM497540
EST:     AAGATCTTATTAAGGAAGCTGACAGATTAGTGTCATGCTTGGCTGTTATG                         GTTCCAAAAACCTTCAATTTTAGCTTATCTGGGGCTTCTTCAAGGNCTTGC
genomic: AAGATCTTATTAAGGAAGCTGACAGATTAGTGTCATGCTTGGCTGTTATGgttagtattt ... gatctagcagGTTCCAAAAACCTTCAATTTTAGCTTATCTGGGGCTTCTTCAAGGTCTTGC

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: 47 (upstream exon), 46 (downstream exon)
Score: 113

TATATGCCATGAGCTAACACAGGCAGCTGATCCTGAAAGCACGGTGCTTGAAGATCTTATTAAGGAAGCTGACAGATTAGTGTCATGCTTGGCTGTTATGgttagtattt ... gatctagcagGTTCCAAAAACCTTCAATTTTAGCTTATCTGGGGCTTCTTCAAGGTCTTGCAAATATGTCTTAAACACACTCATGCAG


Block sizes: 46 (upstream exon), 44 (downstream exon)
Score: 24

TATATGCCATGAGCTAACACAGGCAGCTGATCCTGAAAGCACGGTGCTTGAAGATCTTATTAAGGAAGCTGACAGATTAGTGTCATGCTTGGCTGTTATGgttagtattt ... gatctagcagGTTCCAAAAACCTTCAATTTTAGCTTATCTGGGGCTTCTTCAAGGTCTTGCAAATATGTCTTAAACACACTCATGCAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 39

TATATGCCATGAGCTAACACAGGCAGCTGATCCTGAAAGCACGGTGCTTGAAGATCTTATTAAGGAAGCTGACAGATTAGTGTCATGCTTGGCTGTTATGgttagtattt ... gatctagcagGTTCCAAAAACCTTCAATTTTAGCTTATCTGGGGCTTCTTCAAGGTCTTGCAAATATGTCTTAAACACACTCATGCAG


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 74

TATATGCCATGAGCTAACACAGGCAGCTGATCCTGAAAGCACGGTGCTTGAAGATCTTATTAAGGAAGCTGACAGATTAGTGTCATGCTTGGCTGTTATGgttagtattt ... gatctagcagGTTCCAAAAACCTTCAATTTTAGCTTATCTGGGGCTTCTTCAAGGTCTTGCAAATATGTCTTAAACACACTCATGCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttacgttattcaggttctgttttcccaagtcttatttgatcatggatctagcagGTTCCAAAAACCTTCAATTTTAGCTTATCTGGGGCTTCTTCAAGGTCTTGCAAATATGTCTTAAACACACTCATGCAG
                                ttatttgat  TA-rich tract