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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaattcatattataatgaaagtaccctttgaagttcttttagtttgattggtcatgctattttcagGTGTTCCTGATGAACCTCTCTGCTCCCTTCATTTGTGAGTTCTTCC

Basic information

species Zea mays
transcript GRMZM2G540538_T02
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G540538_T02 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os02g41590.1 (Oryza sativa), 3'ss of exon 8
gtaaattcatattataatgaaagtaccctttgaagttctttt---agtttgattggtcatgctattttcagGTGTTCCTGATGAACCTCTCTGCTCCCTTCATTTGTGAGTTCTTCC-------------------------
|||||||| ||| |  |  | ||| |||||||||||  ||||   ||||||| |   | || | |||||||||||||||||||||||||||||| ||||| || |||||||| ||||                         
gtaaattc-tatcacta-aagagttccctttgaagtggtttttagagtttgactaaccgtgttgttttcagGTGTTCCTGATGAACCTCTCTGCACCCTTTATCTGTGAGTTTTTCCGTGATGCCCAGGAGAAGGTTCTTCC

upper sequence: GRMZM2G540538_T02 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA10G06580.1 (Glycine max), 3'ss of exon 8
-------gtaaattcatattataatgaaagtaccctttgaagttcttttagtttgattggtca--tgctattttcagGTGTTCCTGATGAACCTCTCTGCTCCCTTCATTTGTGAGTTCTTCC-------------------------
        | | || |  ||   ||    ||     | | |||| ||| || || | |  ||   | || | | ||| | ||| |||||||||| ||||||||||| || |||||||||||                           
gttagatatgatttgaacttggcattcctgttttactggcagtt-tttgagattaagtattctatttctgtatgcagATCTTCATGATGAACCTTTCTGCTCCCTTTATATGTGAGTTCTTTAAGGGTGCACTGGACAAAGTTCTGCC
















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|211299293|gb|FK964182.1|FK964182
EST:     CGCCTGATTCTATCCAGCTAGTCGCTGAGCATGCTGCAGCAAATAACAAG                         GTGTTCCTGATGAACCTCTCTGCTCCTTTCA
genomic: CGCCTGATTCTATCCAGCTAGTCGCTGAGCATGCTGCAGCAAATAACAAGgtaaattcat ... ctattttcagGTGTTCCTGATGAACCTCTCTGCTCCCTTCA
EST: gi|28361646|gb|CB240002.1|CB240002
EST:     CGCCTGATTCTATCCAGCTAGTCGCTGAGCATGCTGCAGCAAATAACAAG                         GTGTTCCTGATGAACCTCTCTGCTCCCTTCATT
genomic: CGCCTGATTCTATCCAGCTAGTCGCTGAGCATGCTGCAGCAAATAACAAGgtaaattcat ... ctattttcagGTGTTCCTGATGAACCTCTCTGCTCCCTTCATT
EST: gi|15313682|gb|BI478903.1|BI478903
EST:     CGCCTGATTCTATCCAGCTAGTCGCTGAGCATGCTGCAGCAAATAACAAG                         GTGTTCCTGATGAACCTCTCTGCTCCCTTCATTTGTGAGTTCTTCCGTGAT
genomic: CGCCTGATTCTATCCAGCTAGTCGCTGAGCATGCTGCAGCAAATAACAAGgtaaattcat ... ctattttcagGTGTTCCTGATGAACCTCTCTGCTCCCTTCATTTGTGAGTTCTTCCGTGAT
EST: gi|60358287|gb|DN225260.1|DN225260
EST:     CGCCTGATTCTATCCAGCTAGTCGCTGAGCATGCTGCAGCAAATAACAAG                         GTGTTCCTGATGAACCTCTCTGCTCCCTTCATTTGTGAGTTCTTCCGTGAT
genomic: CGCCTGATTCTATCCAGCTAGTCGCTGAGCATGCTGCAGCAAATAACAAGgtaaattcat ... ctattttcagGTGTTCCTGATGAACCTCTCTGCTCCCTTCATTTGTGAGTTCTTCCGTGAT
EST: gi|60355538|gb|DN222511.1|DN222511
EST:     CGCCTGATTCTATCCAGCTAGTTGCTGAGCATGCTGCAGCAAATAACAAG                         GTGTTCCTGATGAACCTCTCTGCTCCCTTCATCTGTGAGTTCTTCCGTGAT
genomic: CGCCTGATTCTATCCAGCTAGTCGCTGAGCATGCTGCAGCAAATAACAAGgtaaattcat ... ctattttcagGTGTTCCTGATGAACCTCTCTGCTCCCTTCATTTGTGAGTTCTTCCGTGAT
EST: gi|18649011|gb|BM497830.1|BM497830
EST:     CGCCTGATTCTATCCAGCTAGTCGCTGAGCATGCTGCAGCAAATAACAAG                         GNGTTCCTGATGAACCTCTCTGCTCCCTTCATTTGGGAGTTCTTCCGTGAT
genomic: CGCCTGATTCTATCCAGCTAGTCGCTGAGCATGCTGCAGCAAATAACAAGgtaaattcat ... ctattttcagGTGTTCCTGATGAACCTCTCTGCTCCCTTCATTTGTGAGTTCTTCCGTGAT
EST: gi|18654570|gb|BM499375.1|BM499375
EST:     CGCCTGATTCTATCCAGCTAGTCGCTGAGCATGCTGCAGCAAATAACAAG                         GTGTTCCTGATGAACCTCTCTGCTCCCTTCATTTGTGAGTTCTTCCGTGAT
genomic: CGCCTGATTCTATCCAGCTAGTCGCTGAGCATGCTGCAGCAAATAACAAGgtaaattcat ... ctattttcagGTGTTCCTGATGAACCTCTCTGCTCCCTTCATTTGTGAGTTCTTCCGTGAT
EST: gi|18654716|gb|BM499521.1|BM499521
EST:     CGCCTGATTCTATCCAGCTAGTCGCTGAGCATGCTGCAGCAAATAACAAG                         GTGTTCCTGATGAACCTCTCTGCTCCCTTCATTTGTGAGTTCTTCCGTGAT
genomic: CGCCTGATTCTATCCAGCTAGTCGCTGAGCATGCTGCAGCAAATAACAAGgtaaattcat ... ctattttcagGTGTTCCTGATGAACCTCTCTGCTCCCTTCATTTGTGAGTTCTTCCGTGAT
EST: gi|28361834|gb|CB240190.1|CB240190
EST:     CGCCTGATTCTATCCAGCTAGTCGCTGAGCATGCTGCAGCAAATAACAAG                         GTGTTCCTGATGAACCTCTCTGCTCCCTTCATTTGTGAGTTCTTCCGT
genomic: CGCCTGATTCTATCCAGCTAGTCGCTGAGCATGCTGCAGCAAATAACAAGgtaaattcat ... ctattttcagGTGTTCCTGATGAACCTCTCTGCTCCCTTCATTTGTGAGTTCTTCCGT
EST: gi|78544692|gb|DV622190.1|DV622190
EST:     CGCCTGATTCTATCCAGCTAGTCGCTGAGCATGCTGCAGCAAATAACAAG                         GTGTTCCTGATGAACCTCTCTGCTCCCTTCATTTGTGAGTTCTTCC
genomic: CGCCTGATTCTATCCAGCTAGTCGCTGAGCATGCTGCAGCAAATAACAAGgtaaattcat ... ctattttcagGTGTTCCTGATGAACCTCTCTGCTCCCTTCATTTGTGAGTTCTTCC
EST: gi|78543652|gb|DV621150.1|DV621150
EST:     CGCCTGATTCTATCCAGCTAGTCGCTGAGCATGCTGCAGCAAATAACAAG                         GTGTTCCTGATGAACCTCTCTGCTCCCTTCATTTGTGAGTTCTTCC
genomic: CGCCTGATTCTATCCAGCTAGTCGCTGAGCATGCTGCAGCAAATAACAAGgtaaattcat ... ctattttcagGTGTTCCTGATGAACCTCTCTGCTCCCTTCATTTGTGAGTTCTTCC
EST: gi|40335337|gb|CK369407.1|CK369407
EST:     CGCCTGATTCTATCCAGCTAGTCGCTGAGCATGCTGCAGCAAATAACAAG                         GTGTTCCCTGATGA-CCTCTCTGCTCCCTTCATTTGTGAGTTCTTCCGTGA
genomic: CGCCTGATTCTATCCAGCTAGTCGCTGAGCATGCTGCAGCAAATAACAAGgtaaattcat ... ctattttcagGTGTTCC-TGATGAACCTCTCTGCTCCCTTCATTTGTGAGTTCTTCCGTGA
EST: gi|21331346|gb|BQ486727.1|BQ486727
EST:     CGCCTGATTCTATCCAGCTAGTCGCTGAGCATGCTGCAGCAAATAACAAG                         GTGTTCCTGATGAACCTCTCTGCTCCCTTCATTTGTGAGTTCTTCC
genomic: CGCCTGATTCTATCCAGCTAGTCGCTGAGCATGCTGCAGCAAATAACAAGgtaaattcat ... ctattttcagGTGTTCCTGATGAACCTCTCTGCTCCCTTCATTTGTGAGTTCTTCC
EST: gi|9953243|gb|BE639826.1|BE639826
EST:     CGCCTGATTCTATCCAGCTAGTCGCTGAGCATGCTGCAGCAAATAACAAG                         GTGTTCCTGATGAACCTCTCTGCTCC
genomic: CGCCTGATTCTATCCAGCTAGTCGCTGAGCATGCTGCAGCAAATAACAAGgtaaattcat ... ctattttcagGTGTTCCTGATGAACCTCTCTGCTCC

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), 49 (downstream exon)
Score: 1408

TTGAAAAGGCAAAATACATCTACATTGCTGGATTTTTCCTTACAGTGTCGCCTGATTCTATCCAGCTAGTCGCTGAGCATGCTGCAGCAAATAACAAGgtaaattcat ... ctattttcagGTGTTCCTGATGAACCTCTCTGCTCCCTTCATTTGTGAGTTCTTCC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 1598

TTGAAAAGGCAAAATACATCTACATTGCTGGATTTTTCCTTACAGTGTCGCCTGATTCTATCCAGCTAGTCGCTGAGCATGCTGCAGCAAATAACAAGgtaaattcat ... ctattttcagGTGTTCCTGATGAACCTCTCTGCTCCCTTCATTTGTGAGTTCTTCC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 1091

TTGAAAAGGCAAAATACATCTACATTGCTGGATTTTTCCTTACAGTGTCGCCTGATTCTATCCAGCTAGTCGCTGAGCATGCTGCAGCAAATAACAAGgtaaattcat ... ctattttcagGTGTTCCTGATGAACCTCTCTGCTCCCTTCATTTGTGAGTTCTTCC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 2273

TTGAAAAGGCAAAATACATCTACATTGCTGGATTTTTCCTTACAGTGTCGCCTGATTCTATCCAGCTAGTCGCTGAGCATGCTGCAGCAAATAACAAGgtaaattcat ... ctattttcagGTGTTCCTGATGAACCTCTCTGCTCCCTTCATTTGTGAGTTCTTCC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataatgaaagtaccctttgaagttcttttagtttgattggtcatgctattttcagGTGTTCCTGATGAACCTCTCTGCTCCCTTCATTTGTGAGTTCTTCC
                              gtttgat  putative branch site (score: 2273)
                                             ctattttc  putative PPT
                         ttttagttt  TA-rich tract