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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttacccacattactattccacctatttgctgccatatcctgatatcctcctttggtatctctgacggtttcttatagaaataactggtactgatttgctgttctgattgcagATTTTTCGTAAGGAACCATTTTTCTACGGGCATGACAACCATGATCAACTTGTTAAGATAGCCAAG

Basic information

species Zea mays
transcript GRMZM2G143602_T03
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G143602_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os07g02350.1 (Oryza sativa), 3'ss of exon 5
gtatttacccacattactattccacctatttgctgccatatcctgatatcctcctttggtatctctgacggtttcttata-----gaaataactggtactgatttgctgtt---------ctgattgcagATTTTTCGTAAGGAACCATTTTTCTACGGGCATGACAACCATGATCAACTTGTTAAGATAGCCAAG
            ||||| ||  ||  |||    | |  | ||    |       ||| |||   |    |  || || ||     ||| |||||||| |||||| |||  |          ||| ||||||| || || ||||| ||||||||||| || ||||||||||||||||||||||||||||| || |||
----------gtattaccatgacatttatacattactttttctcatttcatcaattttgtaatgcaactgcctttttctataaaagaattaactggtgctgattcgctaataatgtgttgttgagtgcagATCTTCCGCAAGGAGCCATTTTTCTATGGTCATGACAACCATGATCAACTTGTTAAGATCGCAAAG

upper sequence: GRMZM2G143602_T01 (Zea mays), 3'ss of exon 5
lower sequence: PP1S165_119V6.1 (Physcomitrella patens), 3'ss of exon 6
---------gtattta--cccacattactattccacctatttgctgccatatcctgatatcctcctttggtatctctgacggtttcttatagaaataactggta--ctgatttgctgttctgattgcagATTTTTCGTAAGGAACCATTTTTCTACGGGCATGACAACCATGATCAACTTGTTAAGATAGCCAAG
          |    |   | | ||| | ||    | |  ||    |  | |   | ||   |  |||| | | |      |||| | |     ||    | ||  | | |    ||   ||||||||||| ||||| ||||| ||||| || || |||||||||||  ||||||||||||| ||||| || |||
gtaaatttaattccaagttcaatatttcgatggtccttgattatcacagtttgtcgctacgttgatttgctttttggtttagtttttgagcttgattctcgttaaacaggtgaattgaagtgattgcagATATTTCGGAAGGAGCCATTCTTTTATGGGCATGACAATTATGATCAACTTGTGAAGATTGCTAAG
















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|211466861|gb|FL187159.1|FL187159
EST:     ATGATTACTCTTTGGACATGTGGAGTCTGGGCTGCATGTTTGCTGGGATG                         ATTTTTCGTAAGGAACCATTTTTCTACGGGCATGACAACCATGATCAACTT
genomic: ATGATTACTCTTTGGACATGTGGAGTCTGGGCTGCATGTTTGCTGGGATGgtatttaccc ... ctgattgcagATTTTTCGTAAGGAACCATTTTTCTACGGGCATGACAACCATGATCAACTT
EST: gi|19822196|gb|BQ048220.1|BQ048220
EST:     ATGATTACTCTTTGGACATGTGGAGTCTGGGCTGCATGTTTGCTGGGATG                         ATTTTTCGTAAGGAACCATTTTTCTACGGGCATGACAACCATGATCAACTT
genomic: ATGATTACTCTTTGGACATGTGGAGTCTGGGCTGCATGTTTGCTGGGATGgtatttaccc ... ctgattgcagATTTTTCGTAAGGAACCATTTTTCTACGGGCATGACAACCATGATCAACTT
EST: gi|21389960|gb|BQ528009.1|BQ528009
EST:     ATGATTACTCTTTGGACATGTGGAGTCTGGGCTGCATGTTTGCTGGGATG                         ATTTTTCGTAAGGAACCATTTTTCTACGGGCATGACAACCATGATCAACTT
genomic: ATGATTACTCTTTGGACATGTGGAGTCTGGGCTGCATGTTTGCTGGGATGgtatttaccc ... ctgattgcagATTTTTCGTAAGGAACCATTTTTCTACGGGCATGACAACCATGATCAACTT
EST: gi|29576768|gb|CB616880.1|CB616880
EST:     ATGATTACTCTTTGGACATGTGGAGTCTGGGCTGCATGTTTGCTGGGATG                         ATTTTTCGTAAGGA
genomic: ATGATTACTCTTTGGACATGTGGAGTCTGGGCTGCATGTTTGCTGGGATGgtatttaccc ... ctgattgcagATTTTTCGTAAGGA
EST: gi|20507674|gb|BQ279724.1|BQ279724
EST:     ATGATTACTCTTTGGACATGTGGAGTCTGGGCTGCATGTTTGCTGGGATG                         ATTTTTCGTAAGGAACCATTTTTCTACGGGCATGGCAACCATGATCAGCTT
genomic: ATGATTACTCTTTGGACATGTGGAGTCTGGGCTGCATGTTTGCTGGGATGgtatttaccc ... ctgattgcagATTTTTCGTAAGGAACCATTTTTCTACGGGCATGACAACCATGATCAACTT
EST: gi|60348663|gb|DN215636.1|DN215636
EST:     ATGATTACTCTTTGGACATGTGGAGTCTGGGCTGCATGTTTGCTGGGATG                         ATTTTTCGTAAGGAACCATTTTTCTACGGGCATGACAACCATGATCAACTT
genomic: ATGATTACTCTTTGGACATGTGGAGTCTGGGCTGCATGTTTGCTGGGATGgtatttaccc ... ctgattgcagATTTTTCGTAAGGAACCATTTTTCTACGGGCATGACAACCATGATCAACTT
EST: gi|87156472|gb|DY401261.1|DY401261
EST:     ATGATTACTCTTTGGACATGTGGAGTCTGGGCTGCATGTTTGCTGGGATG                         -TTTTTCGTAAGGAACCATTT
genomic: ATGATTACTCTTTGGACATGTGGAGTCTGGGCTGCATGTTTGCTGGGATGgtatttaccc ... ctgattgcagATTTTTCGTAAGGAACCATTT
EST: gi|71770653|gb|DR968590.1|DR968590
EST:     ATGATTACTCTTTGGACATGTGGAGTCTGGGCTGCATGTTTGCTGGGATG                         ATTTTTCGTAAGGAACCATTTTTCTACGGGCATGACAACTATGATCAACTT
genomic: ATGATTACTCTTTGGACATGTGGAGTCTGGGCTGCATGTTTGCTGGGATGgtatttaccc ... ctgattgcagATTTTTCGTAAGGAACCATTTTTCTACGGGCATGACAACCATGATCAACTT

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: 330

GTACTTCAAGGGGCCTGAGCTTCTTGTTGACTTGCAAGATTATGATTACTCTTTGGACATGTGGAGTCTGGGCTGCATGTTTGCTGGGATGgtatttaccc ... ctgattgcagATTTTTCGTAAGGAACCATTTTTCTACGGGCATGACAACCATGATCAACTTGTTAAGATAGCCAAG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 226

GTACTTCAAGGGGCCTGAGCTTCTTGTTGACTTGCAAGATTATGATTACTCTTTGGACATGTGGAGTCTGGGCTGCATGTTTGCTGGGATGgtatttaccc ... ctgattgcagATTTTTCGTAAGGAACCATTTTTCTACGGGCATGACAACCATGATCAACTTGTTAAGATAGCCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 281

GTACTTCAAGGGGCCTGAGCTTCTTGTTGACTTGCAAGATTATGATTACTCTTTGGACATGTGGAGTCTGGGCTGCATGTTTGCTGGGATGgtatttaccc ... ctgattgcagATTTTTCGTAAGGAACCATTTTTCTACGGGCATGACAACCATGATCAACTTGTTAAGATAGCCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 271

GTACTTCAAGGGGCCTGAGCTTCTTGTTGACTTGCAAGATTATGATTACTCTTTGGACATGTGGAGTCTGGGCTGCATGTTTGCTGGGATGgtatttaccc ... ctgattgcagATTTTTCGTAAGGAACCATTTTTCTACGGGCATGACAACCATGATCAACTTGTTAAGATAGCCAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctctgacggtttcttatagaaataactggtactgatttgctgttctgattgcagATTTTTCGTAAGGAACCATTTTTCTACGGGCATGACAACCATGATCAACTTGTTAAGATAGCCAAG
                                        ctgttct  CT-rich tract
          tttcttatagaaataa  TA-rich tract