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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctactcagcatgtcaactgatttgtattctactatagtatcttggttcgtttccttttatgaaactgactgattagtgatttgtgtgtgatttcttctagTTCTTCTAAGCGAAAAAGAGGTGGACCTGGTGGTTTAAATAAAGTTTGCGCAATTTCACCTGAACTTCAGACCATTGTTGGTGAGACTGCCATGTCAAGA

Basic information

species Zea mays
transcript GRMZM2G124502_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G124502_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os04g56980.1 (Oryza sativa), 3'ss of exon 1
ctactcagcatgtcaactgatttgtattctactatagtatcttggttcgtttccttttatg-aaactgactgattagtgatttgtgtgtgatttcttctagTTCTTCTAAGCGAAAAAGAGGTGGACCTGGTGGTTTAAATAAAGTTTGCGCAATTTCACCTGAACTTCAGACCATTGTTGGTGAGACTGCCATGTCAAGA
    |     ||||   ||  |||||   |  |  |      |||    |   | |  ||| ||||||| || ||  | || | ||| | ||||| |||||| |||| ||||| ||| ||||||| ||||||||||||||||||||||| ||||| ||||||||||||||||| |||||||||||||||| ||||||||||
tagattcatgtgtcc-ttggattgtacattgattcaaacctgtggaatttactcatgcatgcaaactgattggtttatcatatctgtattatttcctctagTGCTTCAAAGCGGAAACGAGGTGGGCCTGGTGGTTTAAATAAAGTTTGTGCAATCTCACCTGAACTTCAGACTATTGTTGGTGAGACTGTCATGTCAAGA

upper sequence: GRMZM2G124502_T01 (Zea mays), 3'ss of exon 1
lower sequence: Vv19s0090g01460.t01 (Vitis vinifera), 3'ss of exon 1
-------ctactcagcatgtcaactgatttgtattctactatag-tatcttggttcgtttccttttatgaaactgactgattagtgatttgtgtgtgatttcttctagTTCTTCTAAGCGAAAAAGAGGTGGACCTGGTGGTTTAAATAAAGTTTGCGCAATTTCACCTGAACTTCAGACCATTGTTGGTGAGACTGCCATGTCAAGA
        ||     ||   |   |  | ||| || |  |||   |||     |  | | | |    | |   |  |   ||  |||||| | | ||   |  || ||  ||   |    || ||||||||| || || ||| |||| ||||||||||   ||||||||||||||||||||||||||||  || | ||  ||      
agagtgtgtatctgtcacaaccttttttatgtgttattatatgcctattgcattctgatgcttggcctaatgtttccatgttcatgatttttttctgcagTGCTCGAG--CTGGAACTAAAAGAAGAGGTGGTCCAGGGGGTCTAAACAAAGTTTGCGGTGTTTCACCTGAACTTCAGACCATTGTTGGCCAGCCAGCGCTG------
















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|74239586|gb|DT647500.1|DT647500
EST:     ACTGCTTCCCCCACCGCTGCACCGCAGGTCGCCGGCGACAACAAGGAAAG                         TTCTTCTAAGCGAAAAAGAGGTGGACCTGGTGGTTTAAATAAAGTTTGCGC
genomic: ACTGCTTCCCCCACCGCTGCACCGCAGGTCGCCGGCGACAACAAGGAAAGgtgagttgtc ... tttcttctagTTCTTCTAAGCGAAAAAGAGGTGGACCTGGTGGTTTAAATAAAGTTTGCGC
EST: gi|78111193|gb|DV529590.1|DV529590
EST:     ACTGCTTCCCCCACCGCTGCACCGCAGGTCGCCGGCGACAACAAGGAAAG                         TTCTTCTAAGCGAAAAAGAGGTGGACCTGGTGGTTTAAATAAAGTTTGCGC
genomic: ACTGCTTCCCCCACCGCTGCACCGCAGGTCGCCGGCGACAACAAGGAAAGgtgagttgtc ... tttcttctagTTCTTCTAAGCGAAAAAGAGGTGGACCTGGTGGTTTAAATAAAGTTTGCGC
EST: gi|71422220|gb|DR805652.1|DR805652
EST:     ACTGCTTCCCCCACCGCTGCACCGCAGGTCGCCGGCGACAACAAGGAAAG                         TTCTTCTAAGCGAAAAAGAGGTGGACCTGGTGGTTTAAATAAAGTTTGCGC
genomic: ACTGCTTCCCCCACCGCTGCACCGCAGGTCGCCGGCGACAACAAGGAAAGgtgagttgtc ... tttcttctagTTCTTCTAAGCGAAAAAGAGGTGGACCTGGTGGTTTAAATAAAGTTTGCGC
EST: gi|71440370|gb|DR821420.1|DR821420
EST:     ACTGCTTCCCCCACCGCTGCACCGCAGGTCGCCGGCGACAACAAGGAAAG                         TTCTTCTAAGCGAAAAAGAGGTGGACCTGGTGGTTTAAATAAAGTTTGCGC
genomic: ACTGCTTCCCCCACCGCTGCACCGCAGGTCGCCGGCGACAACAAGGAAAGgtgagttgtc ... tttcttctagTTCTTCTAAGCGAAAAAGAGGTGGACCTGGTGGTTTAAATAAAGTTTGCGC

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: 39 (upstream exon), 49 (downstream exon)
Score: 26

CCACGGGTGGGACCGTCTCCTTCCAGCAGCCAGCCCCTGGGGCTGGGGGCACTGCTTCCCCCACCGCTGCACCGCAGGTCGCCGGCGACAACAAGGAAAGgtgagttgtc ... tttcttctagTTCTTCTAAGCGAAAAAGAGGTGGACCTGGTGGTTTAAATAAAGTTTGCGCAATTTCACCTGAACTTCAGACCATTGTTGGTGAGACTGCCATGTCAAGA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 24

CCACGGGTGGGACCGTCTCCTTCCAGCAGCCAGCCCCTGGGGCTGGGGGCACTGCTTCCCCCACCGCTGCACCGCAGGTCGCCGGCGACAACAAGGAAAGgtgagttgtc ... tttcttctagTTCTTCTAAGCGAAAAAGAGGTGGACCTGGTGGTTTAAATAAAGTTTGCGCAATTTCACCTGAACTTCAGACCATTGTTGGTGAGACTGCCATGTCAAGA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 23

CCACGGGTGGGACCGTCTCCTTCCAGCAGCCAGCCCCTGGGGCTGGGGGCACTGCTTCCCCCACCGCTGCACCGCAGGTCGCCGGCGACAACAAGGAAAGgtgagttgtc ... tttcttctagTTCTTCTAAGCGAAAAAGAGGTGGACCTGGTGGTTTAAATAAAGTTTGCGCAATTTCACCTGAACTTCAGACCATTGTTGGTGAGACTGCCATGTCAAGA


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 16

CCACGGGTGGGACCGTCTCCTTCCAGCAGCCAGCCCCTGGGGCTGGGGGCACTGCTTCCCCCACCGCTGCACCGCAGGTCGCCGGCGACAACAAGGAAAGgtgagttgtc ... tttcttctagTTCTTCTAAGCGAAAAAGAGGTGGACCTGGTGGTTTAAATAAAGTTTGCGCAATTTCACCTGAACTTCAGACCATTGTTGGTGAGACTGCCATGTCAAGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcgtttccttttatgaaactgactgattagtgatttgtgtgtgatttcttctagTTCTTCTAAGCGAAAAAGAGGTGGACCTGGTGGTTTAAATAAAGTTTGCGCAATTTCACCTGAACTTCAGACCATTGTTGGTGAGACTGCCATGTCAAGA
                                             tttcttct  CT-rich tract
         ttttatgaaa  TA-rich tract