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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttataggaactctatttcattgctagtctaattaatacttgtggaaaaaacaagttgtaaattgtaaatgtaatgttacattctgtgagcagTGAGAGGGCCTCTGAAACAAACAACTTCGGTCAAAAGCTTAGAGATGGAGCCAACATCAACCGATCACTCCTAGCATTAGCAAACTGCATCAATGCCCTA

Basic information

species Zea mays
transcript GRMZM5G837018_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G837018_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os03g56260.1 (Oryza sativa), 3'ss of exon 8
--------gttataggaactctatttc--attgctagtctaattaatacttgtggaaaaaacaagttgtaaattgtaaatgtaatgttacattctgtgagcagTGAGAGGGCCTCTGAAACAAACAACTTCGGTCAAAAGCTTAGAGATGGAGCCAACATCAACCGATCACTCCTAGCATTAGCAAACTGCATCAATGCCCTA
         | |||   ||||  |||   |||| |  ||| |||    | ||   | |||  ||| | ||||  | ||   | || ||| |         |||||||||||||||||||||||||||||| || |||||||||||||||||||||||||| ||||| ||||| |||||  |||| ||||||||||||||||| 
gtaatacactaatacctactcctttttggattgtttttctcatttcaccctgctaagaaagtaagctataaa--gcaacgcttatattata--------acagTGAGAGGGCCTCTGAAACAAACAACTTTGGGCAAAAGCTTAGAGATGGAGCCAACATTAACCGTTCACTTCTAGCGCTAGCGAACTGCATCAATGCCCTT

upper sequence: GRMZM5G837018_T01 (Zea mays), 3'ss of exon 8
lower sequence: Vv07s0205g00140.t01 (Vitis vinifera), 3'ss of exon 8
-----gttataggaactctatttcattgctagtctaattaatacttgtggaaaaaacaagttgtaaattgtaaatgtaatgttaca----ttctgtga-gcagTGAGAGGGCCTCTGAAACAAACAACTTCGGTCAAAAGCTTAGAGATGGAGCCAACATCAACCGATCACTCCTAGCATTAGCAAACTGCATCAATGCCCTA
      |  |  |   | | |||  |  |    ||   || |   | || |  | |      |||||| |||   ||  ||  | |    |  | ||| |||||||  | || ||||||||| | |     ||||||||||| |||||||||||||| || || || || || || || || ||||||||||||||||| || 
gtaagttcgttagctttattttttgtcccccacctctctactgtctttgtatcatattttaagtaaatggtatgagttctgccataaaaatgatttgatgcagTGAACGAGCTTCTGAAACACATAGTGGTGGTCAAAAGCTGAGAGATGGAGCCAATATTAATCGTTCGCTTCTTGCTTTGGCAAACTGCATCAATGCTCTG
















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|22490695|gb|BU050618.1|BU050618
EST:     GGTAACCAAGTTCTTCGTGGAAAGCTTGCCTTGGTTGATCTTGCGGGCAG                         TGAGAGGGCCTCTGAAACAAACAACTTCGGTCAAAAGCTTAGAGATGGAGC
genomic: GGTAACCAAGTTCTTCGTGGAAAGCTTGCCTTGGTTGATCTTGCGGGCAGgttataggaa ... ctgtgagcagTGAGAGGGCCTCTGAAACAAACAACTTCGGTCAAAAGCTTAGAGATGGAGC
EST: gi|87152314|gb|DY397103.1|DY397103
EST:     GGTAACCAAGTTCTTCGTGGAAAGCTTGCCTTGGTTGATCTTGCGGGCAG                         TGAGAGGGCCTCTGAAACAAACAACTTCGGTCAAAAGCTTAGAGATGGAGC
genomic: GGTAACCAAGTTCTTCGTGGAAAGCTTGCCTTGGTTGATCTTGCGGGCAGgttataggaa ... ctgtgagcagTGAGAGGGCCTCTGAAACAAACAACTTCGGTCAAAAGCTTAGAGATGGAGC

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), 49 (downstream exon)
Score: 131

CACATGCTGTACTTGAGATTACCGTAAAGCGAAAGCAGAAAGGCCAATATGGTAACCAAGTTCTTCGTGGAAAGCTTGCCTTGGTTGATCTTGCGGGCAGgttataggaa ... ctgtgagcagTGAGAGGGCCTCTGAAACAAACAACTTCGGTCAAAAGCTTAGAGATGGAGCCAACATCAACCGATCACTCCTAGCATTAGCAAACTGCATCAATGCCCTA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 40

CACATGCTGTACTTGAGATTACCGTAAAGCGAAAGCAGAAAGGCCAATATGGTAACCAAGTTCTTCGTGGAAAGCTTGCCTTGGTTGATCTTGCGGGCAGgttataggaa ... ctgtgagcagTGAGAGGGCCTCTGAAACAAACAACTTCGGTCAAAAGCTTAGAGATGGAGCCAACATCAACCGATCACTCCTAGCATTAGCAAACTGCATCAATGCCCTA


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 15

CACATGCTGTACTTGAGATTACCGTAAAGCGAAAGCAGAAAGGCCAATATGGTAACCAAGTTCTTCGTGGAAAGCTTGCCTTGGTTGATCTTGCGGGCAGgttataggaa ... ctgtgagcagTGAGAGGGCCTCTGAAACAAACAACTTCGGTCAAAAGCTTAGAGATGGAGCCAACATCAACCGATCACTCCTAGCATTAGCAAACTGCATCAATGCCCTA


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 53

CACATGCTGTACTTGAGATTACCGTAAAGCGAAAGCAGAAAGGCCAATATGGTAACCAAGTTCTTCGTGGAAAGCTTGCCTTGGTTGATCTTGCGGGCAGgttataggaa ... ctgtgagcagTGAGAGGGCCTCTGAAACAAACAACTTCGGTCAAAAGCTTAGAGATGGAGCCAACATCAACCGATCACTCCTAGCATTAGCAAACTGCATCAATGCCCTA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgtggaaaaaacaagttgtaaattgtaaatgtaatgttacattctgtgagcagTGAGAGGGCCTCTGAAACAAACAACTTCGGTCAAAAGCTTAGAGATGGAGCCAACATCAACCGATCACTCCTAGCATTAGCAAACTGCATCAATGCCCTA
                    taaattgtaaatgtaa  TA-rich tract