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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTAAGAGCATCGGTGCAAAGCACATAGTTTTGGTGGGATCCATGGGAGGAACAGACATCAATCACCCGCTAAACAAGTTAGGAAATGCAAATATACTGgtacatagcatatttagcttttcttccaatttgttctattctctgtccttgtgcatgttttgtgtgcatgagaacatcaccttcgtgtctgcattgtttagcaacttcctagtcattttcttctaaattttcag

Basic information

species Zea mays
transcript GRMZM2G047219_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G047219_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os05g01970.1 (Oryza sativa), 5'ss of exon 4
CTAAGAGCATCGGTGCAAAGCACATAGTTTTGGTGGGATCCATGGGAGGAACAGACATCAATCACCCGCTAAACAAGTTAGGAAATGCAAATATACTGgtacatagcatattta--gcttttcttccaatttgttctattctctgtccttgtgcatgttttgtgtgcatgagaacatcaccttcgtgtctgcattgtttagcaacttcctagtcattt----tcttctaaattttcag
| |||||||| |||| ||| ||  | |||||||| ||||||||||| || |||||  |||||||||| ||||| ||||||||||||||||||||||||||| ||| ||| |  |  |  |||||| |   |  ||   |  ||| |   ||||| ||||   | || |||    ||| | |      | |||| |||||| |||  ||  | |  |||    |  | | ||||  |||
CCAAGAGCATTGGTGTAAAACAGGTGGTTTTGGTTGGATCCATGGGCGGCACAGATGTCAATCACCCACTAAATAAGTTAGGAAATGCAAATATACTGgtatataacatgtgcaaagtctttctttcttctaatttattcatctttatgtgtgcgtgttc-atatgtatgcatgcatgagcacatcatatgcactgttta-caagctcagaatactttaatgttctttgaattcgcag
















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|211142589|gb|FL359509.1|FL359509
EST:     AACAGACATCAATCACCCGCTAAACAAGTTAGGAAATGCAAATATANCTG                         GTGTGGAAGCGCAAGGCAGAACAGTACCTAGCAGACTCCGGTCTTCCATA
genomic: AACAGACATCAATCACCCGCTAAACAAGTTAGGAAATGCAAATATA-CTGgtacatagca ... aaattttcagGTGTGGAAGCGCAAGGCAGAACAGTACCTAGCAGACTCCGGTCTTCCATA
EST: gi|211529297|gb|FL356731.1|FL356731
EST:     CAGACATNCA-TCACCCGNNCTAA-CAAGT-AGGAAATGCAAATATACTG                         GGTGTGGGAGCGCAAGGCAGAACAGTACCTAGCAGACTCCGGTCTTCCATA
genomic: CAGACAT-CAATCACCCG--CTAAACAAGTTAGGAAATGCAAATATACTGgtacatagca ... aaattttcagG-TGTGGAAGCGCAAGGCAGAACAGTACCTAGCAGACTCCGGTCTTCCATA
EST: gi|17931616|gb|BM268576.1|BM268576
EST:     GAACAGACATCAATCACCCGCTAAACAAGTTAGGAAATGCAAATATACTG                         GTGTGGAAGCGCAAGGCAGAACAGTACCTAGCAGACTCCGGTCTTCCATAT
genomic: GAACAGACATCAATCACCCGCTAAACAAGTTAGGAAATGCAAATATACTGgtacatagca ... aaattttcagGTGTGGAAGCGCAAGGCAGAACAGTACCTAGCAGACTCCGGTCTTCCATAT
EST: gi|149015400|gb|EE045246.2|EE045246
EST:     GAACAGACATCAATCACCCGCTAAACAAGTTAGGAAATGCAAATATACTG                         GTGTGGAAGCGCAAGGCAGAACAGTACCCTAGCAGACTCCGGTCTTCCATA
genomic: GAACAGACATCAATCACCCGCTAAACAAGTTAGGAAATGCAAATATACTGgtacatagca ... aaattttcagGTGTGGAAGCGCAAGGCAGAACAGTACC-TAGCAGACTCCGGTCTTCCATA
EST: gi|94473462|gb|EB702420.1|EB702420
EST:     AACAGACATCAATCACTCGCTAAACAAGTTAGGAAAATGCAAATATACTG                         GTGTGGAAGCGCAAGGCAGAACAGTACCTAGCAGACTCCGGTCTTCCATAT
genomic: AACAGACATCAATCACCCGCTAAACAAGTTAGG-AAATGCAAATATACTGgtacatagca ... aaattttcagGTGTGGAAGCGCAAGGCAGAACAGTACCTAGCAGACTCCGGTCTTCCATAT
EST: gi|148966373|gb|EE017367.2|EE017367
EST:     GAACAGACATCAATCCCCCGCTAAACAAGTTAGGAAATGCAAATATACTG                         GTGTGGAAGCGCAAGGCAGAACAGTACCTAGCAGACTCCGGTCTTCCATAT
genomic: GAACAGACATCAATCACCCGCTAAACAAGTTAGGAAATGCAAATATACTGgtacatagca ... aaattttcagGTGTGGAAGCGCAAGGCAGAACAGTACCTAGCAGACTCCGGTCTTCCATAT
EST: gi|12045929|gb|BF728159.1|BF728159
EST:     GAACAGACATCAATCACCCGCTAAACAAGTTAGGAAATGCAAATATACTG                         GTGTGGAAGCGCAAGGCAGAACAGTACCTAGCAGACTCCGGTCTTCCATAT
genomic: GAACAGACATCAATCACCCGCTAAACAAGTTAGGAAATGCAAATATACTGgtacatagca ... aaattttcagGTGTGGAAGCGCAAGGCAGAACAGTACCTAGCAGACTCCGGTCTTCCATAT
EST: gi|211072521|gb|FL326767.1|FL326767
EST:     GAACAGACATCAATCACCCGCTAAACAAGTTAGGAAATGCAAATATACTG                         GTGTGGAAGCGCAAGGCAGAACAGTACCTAGCAGACTCCGGTCTTCCATAT
genomic: GAACAGACATCAATCACCCGCTAAACAAGTTAGGAAATGCAAATATACTGgtacatagca ... aaattttcagGTGTGGAAGCGCAAGGCAGAACAGTACCTAGCAGACTCCGGTCTTCCATAT
EST: gi|148996959|gb|EE035773.2|EE035773
EST:     GAACAGACATCAATCACCCGCTAAACAAGTTAGGAAATGCAAATATACTG                         GTGTGGAAGCGCAAGGCAGAACAGTACCTAGCAGACTCCGGTCTTCCATAT
genomic: GAACAGACATCAATCACCCGCTAAACAAGTTAGGAAATGCAAATATACTGgtacatagca ... aaattttcagGTGTGGAAGCGCAAGGCAGAACAGTACCTAGCAGACTCCGGTCTTCCATAT
EST: gi|211140552|gb|FL174090.1|FL174090
EST:     GAACAGACATCAATCACCCGCTAAACAAGTTAGGAAATGCAAATATACTG                         GTGTGGAAGCGCAAGGCATAACAGTACCTAGCAGACTCCGGTCTTCCATAT
genomic: GAACAGACATCAATCACCCGCTAAACAAGTTAGGAAATGCAAATATACTGgtacatagca ... aaattttcagGTGTGGAAGCGCAAGGCAGAACAGTACCTAGCAGACTCCGGTCTTCCATAT
EST: gi|16380015|gb|BI993261.1|BI993261
EST:     GAACAGACATCAATCACCCGCTAAACAAGTTAGGAAATGCAAATATACTG                         GTGTGGAAGCGCAAGGCAGAACAGTACCTAGCAGACTCCGGTCTTCCATAT
genomic: GAACAGACATCAATCACCCGCTAAACAAGTTAGGAAATGCAAATATACTGgtacatagca ... aaattttcagGTGTGGAAGCGCAAGGCAGAACAGTACCTAGCAGACTCCGGTCTTCCATAT
EST: gi|89251955|gb|DY623741.1|DY623741
EST:     GAACAGACATCAATCACCCGCTAAACAAGTTAGGAAATGCAAATATACTG                         GTGTGGAAGCGCAAGGCAGAACAGTACCTAGCAGACTCCGGTCTTCCATAT
genomic: GAACAGACATCAATCACCCGCTAAACAAGTTAGGAAATGCAAATATACTGgtacatagca ... aaattttcagGTGTGGAAGCGCAAGGCAGAACAGTACCTAGCAGACTCCGGTCTTCCATAT
EST: gi|76293497|gb|DV033065.1|DV033065
EST:     GAACAGACATCAATCACCCGCTAAACAAGTTAGGAAATGCAAATATACTG                         GTGTGGAAGCGCAAGGCAGAACAGTACCTAGCAGACTCCGGTCTTCCATAT
genomic: GAACAGACATCAATCACCCGCTAAACAAGTTAGGAAATGCAAATATACTGgtacatagca ... aaattttcagGTGTGGAAGCGCAAGGCAGAACAGTACCTAGCAGACTCCGGTCTTCCATAT
EST: gi|32848760|gb|CD988441.1|CD988441
EST:     GAACAGACATCAATCACCCGCTAAACAAGTTAGGAAATGCAAATATACTG                         GTGTGGAAGCGCAAGGCAGAACAGTA
genomic: GAACAGACATCAATCACCCGCTAAACAAGTTAGGAAATGCAAATATACTGgtacatagca ... aaattttcagGTGTGGAAGCGCAAGGCAGAACAGTA
EST: gi|148955762|gb|EC901460.2|EC901460
EST:     GAACAGACATCAATCACCCGCTAAACAAGTTAGGAAATGCAAATATACTG                         GTGTGGAAGCGCAAGGCAGAACAGTACCTAGCAGACTCCGGTCTTCCATAT
genomic: GAACAGACATCAATCACCCGCTAAACAAGTTAGGAAATGCAAATATACTGgtacatagca ... aaattttcagGTGTGGAAGCGCAAGGCAGAACAGTACCTAGCAGACTCCGGTCTTCCATAT
EST: gi|211394348|gb|FL351051.1|FL351051
EST:     TA-CAGACATCAATCAACCGCTAAACA-GTTAGGAAATGCAAATATACTG                         GGTGTGGAAGCGCAAGGCAGAACAGTACCTAGCAGACTCCGGGTCTTC-AT
genomic: GAACAGACATCAATCACCCGCTAAACAAGTTAGGAAATGCAAATATACTGgtacatagca ... aaattttcagG-TGTGGAAGCGCAAGGCAGAACAGTACCTAGCAGACTCCGG-TCTTCCAT
EST: gi|89762676|gb|DY690164.1|DY690164
EST:     GAACAGACATCAATCACCCGCTAAACAAGTTAGGAAATGCAAATATACTG                         GTGTGGAAGCGCAAGGCAGAACAGTACCTAGCAGACTCCGGTCTTCCATAT
genomic: GAACAGACATCAATCACCCGCTAAACAAGTTAGGAAATGCAAATATACTGgtacatagca ... aaattttcagGTGTGGAAGCGCAAGGCAGAACAGTACCTAGCAGACTCCGGTCTTCCATAT
EST: gi|74243387|gb|DT651301.1|DT651301
EST:     CCGCTAAACAAGTTAGGAAATGCAAATATACTG                         GTGTGGAAGCGCAAGGCAGAACAGTACCTAGCAGACTCCGGTCTTCCATAT
genomic: CCGCTAAACAAGTTAGGAAATGCAAATATACTGgtacatagca ... aaattttcagGTGTGGAAGCGCAAGGCAGAACAGTACCTAGCAGACTCCGGTCTTCCATAT
EST: gi|16919596|gb|BM074268.1|BM074268
EST:     GAACAGACATCAATCACCCGCTAAACAAGTTAGGAAATGCAAATATACTG                         GTGTGGAAGCGCAAGGCAGAACAGTACCTAGCAGACTCCGGTCTTCCATAT
genomic: GAACAGACATCAATCACCCGCTAAACAAGTTAGGAAATGCAAATATACTGgtacatagca ... aaattttcagGTGTGGAAGCGCAAGGCAGAACAGTACCTAGCAGACTCCGGTCTTCCATAT
EST: gi|6742502|gb|AW313317.1|AW313317
EST:     GAACAGACATCAATCACCCGCTAAACAAGTTAGGAAATGCAAATATACTG                         GTGTGGAAGCGCAAGGCAGAACAGTACCTAGCAGACTCCGGTCTTCCATAT
genomic: GAACAGACATCAATCACCCGCTAAACAAGTTAGGAAATGCAAATATACTGgtacatagca ... aaattttcagGTGTGGAAGCGCAAGGCAGAACAGTACCTAGCAGACTCCGGTCTTCCATAT
EST: gi|71774203|gb|DR972081.1|DR972081
EST:     GAACAGACATCAATCACCCGCTAAACAAGTTAGGAAATGCAAATATACTG                         GTGTGGAAGCGCAAGGCAGAACAGTACCTAGCAGACTCCGGTCTTCCATAT
genomic: GAACAGACATCAATCACCCGCTAAACAAGTTAGGAAATGCAAATATACTGgtacatagca ... aaattttcagGTGTGGAAGCGCAAGGCAGAACAGTACCTAGCAGACTCCGGTCTTCCATAT
EST: gi|91055640|gb|EB166058.1|EB166058
EST:     GAACAGACATCAATCACCCGCTAAACAAGTTAGGAAATGCAAATATACTG                         GTGTGGAAGCGCAAGGCAGAACAGTACCTAGCAGACTCCGGTCTTCCATAT
genomic: GAACAGACATCAATCACCCGCTAAACAAGTTAGGAAATGCAAATATACTGgtacatagca ... aaattttcagGTGTGGAAGCGCAAGGCAGAACAGTACCTAGCAGACTCCGGTCTTCCATAT

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), 37 (downstream exon)
Score: 49

CTAAGAGCATCGGTGCAAAGCACATAGTTTTGGTGGGATCCATGGGAGGAACAGACATCAATCACCCGCTAAACAAGTTAGGAAATGCAAATATACTGgtacatagca ... aaattttcagGTGTGGAAGCGCAAGGCAGAACAGTACCTAGCAGACTCCGGTCTTCCATATACAATTATAAG


Block sizes: 49 (upstream exon), 37 (downstream exon)
Score: 409

CTAAGAGCATCGGTGCAAAGCACATAGTTTTGGTGGGATCCATGGGAGGAACAGACATCAATCACCCGCTAAACAAGTTAGGAAATGCAAATATACTGgtacatagca ... aaattttcagGTGTGGAAGCGCAAGGCAGAACAGTACCTAGCAGACTCCGGTCTTCCATATACAATTATAAG


Block sizes: 49 (upstream exon), 35 (downstream exon)
Score: 18

CTAAGAGCATCGGTGCAAAGCACATAGTTTTGGTGGGATCCATGGGAGGAACAGACATCAATCACCCGCTAAACAAGTTAGGAAATGCAAATATACTGgtacatagca ... aaattttcagGTGTGGAAGCGCAAGGCAGAACAGTACCTAGCAGACTCCGGTCTTCCATATACAATTATAAG


Block sizes: 49 (upstream exon), 37 (downstream exon)
Score: 147

CTAAGAGCATCGGTGCAAAGCACATAGTTTTGGTGGGATCCATGGGAGGAACAGACATCAATCACCCGCTAAACAAGTTAGGAAATGCAAATATACTGgtacatagca ... aaattttcagGTGTGGAAGCGCAAGGCAGAACAGTACCTAGCAGACTCCGGTCTTCCATATACAATTATAAG