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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAGGATGTGCACCTGGAACCAGTACCGTTTGACATGGACCGTGATTTGATCACCCCGACATACAAAAAGAAGCGTCCGCAACTGCTCAAGTACTACCAGgtactgctcatttaactattggcgcaaagttggtccagtatattctgtttattgccgcataacagtgtgttcgttgaaatgctcttgaattggttctgtg...

Basic information

species Zea mays
transcript GRMZM5G861300_T01
intron # 18
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G861300_T01 (Zea mays), 5'ss of exon 18
lower sequence: LOC_Os01g46750.1 (Oryza sativa), 5'ss of exon 18
AAAGGATGTGCACCTGGAACCAGTACCGTTTGACATGGACCGTGATTTGATCACCCCGACATACAAAAAGAAGCGTCCGCAACTGCTCAAGTACTACCAGgtactgctcatttaactattggcgcaaagttggtccagtatattctgtttat-tgccgcataacagtgtgttcgttgaaatgctcttgaattggttctgtg----
||||| ||| || || |||||||| || ||||||||||||||||||||||| || || ||||| ||||||||||| || ||| |||||||||||||||||||| |||||||| ||  |||  ||  |   || |   | ||||  ||||||  | |  ||     ||  |  ||||   ||  |  | | ||||| || ||    
AAAGGCTGTACATCTTGAACCAGTGCCATTTGACATGGACCGTGATTTGATTACTCCAACATATAAAAAGAAGCGCCCTCAATTGCTCAAGTACTACCAGgtattgctcattcaa--attctcgtcatactgat--ggcatatgttgtttacatacttcacgcgtgta-gaacgttctcattttgcttacttggtcctttgaatc
















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|211321071|gb|FL030628.1|FL030628
EST:     TCACCCCGACATACAAAAAGAAGCGTCCGCAACTGCTCAAGTACTACCAG                         GGCGTGATTGACAACATGTACAAAAGTGCTAAGTGAACTCACTCTACAGTA
genomic: TCACCCCGACATACAAAAAGAAGCGTCCGCAACTGCTCAAGTACTACCAGgtactgctca ... aattttgcagGGCGTGATTGACAACATGTACAAAAGTGCTAAGTGAACTCACTCTACAGTA
EST: gi|32867684|gb|CF007366.1|CF007366
EST:     TCACCCCGACATACAAAAAGAAGCGTCCGCAACTGCTCAAGTACTACCAG                         GGCGTGATTGACAACATGTACAAAAGTGCTAAGTGAACTCACTCTACAGTG
genomic: TCACCCCGACATACAAAAAGAAGCGTCCGCAACTGCTCAAGTACTACCAGgtactgctca ... aattttgcagGGCGTGATTGACAACATGTACAAAAGTGCTAAGTGAACTCACTCTACAGTA
EST: gi|166614032|gb|EG105313.1|EG105313
EST:     TCACCCCGACATACAAAAAGAAGCGTCCGCAACTGCTCAAGTACTACCAG                         GGCGTGATTGACAACATGTACAAAAGTGCTAAGTGAACTCACTCTAC
genomic: TCACCCCGACATACAAAAAGAAGCGTCCGCAACTGCTCAAGTACTACCAGgtactgctca ... aattttgcagGGCGTGATTGACAACATGTACAAAAGTGCTAAGTGAACTCACTCTAC
EST: gi|149085680|gb|EE175194.2|EE175194
EST:     TCACCCCGACATACAAAAAGAAGCGTCCGCAACTGCTCAAGTACTACCAG                         GGCGTGATTGACAACATGTACAAAAGTGCTAAGTGAACTCACTCTACAGTA
genomic: TCACCCCGACATACAAAAAGAAGCGTCCGCAACTGCTCAAGTACTACCAGgtactgctca ... aattttgcagGGCGTGATTGACAACATGTACAAAAGTGCTAAGTGAACTCACTCTACAGTA
EST: gi|60349480|gb|DN216453.1|DN216453
EST:     TCACCCCGACATACAAAAAGAAGCGTCCGCAACTGCTCAAGTACTACCAG                         GGCGTGATTGACAACATGTACAAAAGTGCTAAGTGAACTCACTCTACAGTA
genomic: TCACCCCGACATACAAAAAGAAGCGTCCGCAACTGCTCAAGTACTACCAGgtactgctca ... aattttgcagGGCGTGATTGACAACATGTACAAAAGTGCTAAGTGAACTCACTCTACAGTA
EST: gi|37375449|gb|CF624162.1|CF624162
EST:     TCACCCCGACATACAAAAAGAAGCGTCCGCAACTGCTCAAGTACTACCAG                         GGCGTGATTGACAACATGTACAAAAGTGCTAAGTGAACTCACTCTACAGTA
genomic: TCACCCCGACATACAAAAAGAAGCGTCCGCAACTGCTCAAGTACTACCAGgtactgctca ... aattttgcagGGCGTGATTGACAACATGTACAAAAGTGCTAAGTGAACTCACTCTACAGTA
EST: gi|5871186|gb|AW017657.1|AW017657
EST:     TCACCCCGACATACAAAAAGAAGCGTCCGCAACTGCTCAAGTACTACCAG                         GGCGTGATTGACAACATGTACAAAAGTGCTAAGTGAACTAACTAATACAGT
genomic: TCACCCCGACATACAAAAAGAAGCGTCCGCAACTGCTCAAGTACTACCAGgtactgctca ... aattttgcagGGCGTGATTGACAACATGTACAAAAGTGCTAAGTGAACTCACTC-TACAGT
EST: gi|12968428|gb|BG265374.1|BG265374
EST:     TCACCCCGACATACAAAAAGAAGCGTCCGCAACTGCTCAAGTACTACCAG                         GGCGTGATTGACAACATGTACAAAAGTGCTAAGTGAACTCACTCTACAGTA
genomic: TCACCCCGACATACAAAAAGAAGCGTCCGCAACTGCTCAAGTACTACCAGgtactgctca ... aattttgcagGGCGTGATTGACAACATGTACAAAAGTGCTAAGTGAACTCACTCTACAGTA
EST: gi|44900657|gb|CK827202.1|CK827202
EST:     TCACCCCGACATACAAAAAGAAGCGTCCGCAACTGCTCAAGTACTACCAG                         GGCGTGATTGACAACATGTACAAAAGTGCTAAGTGAACTCACTCTACAGTA
genomic: TCACCCCGACATACAAAAAGAAGCGTCCGCAACTGCTCAAGTACTACCAGgtactgctca ... aattttgcagGGCGTGATTGACAACATGTACAAAAGTGCTAAGTGAACTCACTCTACAGTA
EST: gi|60341396|gb|DN208369.1|DN208369
EST:     TCACCCCGACATACAAAAAGAAGCGTCCGCAACTGCTCAAGTACTACCAG                         GGCGTGATTGACAACATGTACAAAAGTGCTAAGTGAACTCACTCTACAGTA
genomic: TCACCCCGACATACAAAAAGAAGCGTCCGCAACTGCTCAAGTACTACCAGgtactgctca ... aattttgcagGGCGTGATTGACAACATGTACAAAAGTGCTAAGTGAACTCACTCTACAGTA
EST: gi|9825060|gb|BE575262.1|BE575262
EST:     TCACCCCGACATACAAAAAGAAGCGTCCGCAACTGCTCAAGTACTACCAG                         GGCGTGATTGACAACATGTACAAAAGTGCTAAGTGAACTCACTCTACAGTA
genomic: TCACCCCGACATACAAAAAGAAGCGTCCGCAACTGCTCAAGTACTACCAGgtactgctca ... aattttgcagGGCGTGATTGACAACATGTACAAAAGTGCTAAGTGAACTCACTCTACAGTA
EST: gi|37377443|gb|CF625326.1|CF625326
EST:     GCAACTGCTCAAGTACTACCAG                         GGCGTGATTGACAACATGTACAAAAGTGCTAAGTGAACTCACTCTACAGTA
genomic: GCAACTGCTCAAGTACTACCAGgtactgctca ... aattttgcagGGCGTGATTGACAACATGTACAAAAGTGCTAAGTGAACTCACTCTACAGTA
EST: gi|5650372|gb|AI920732.1|AI920732
EST:     TCACCCCGACATACAAAAAGAAGCGTCCGCAACTGCTCAAGTACTACCAG                         GGCGTGATTGACAACATGTACAAAAGTGCTAAGTGAACTCACTCTACAGTA
genomic: TCACCCCGACATACAAAAAGAAGCGTCCGCAACTGCTCAAGTACTACCAGgtactgctca ... aattttgcagGGCGTGATTGACAACATGTACAAAAGTGCTAAGTGAACTCACTCTACAGTA
EST: gi|71431663|gb|DR812713.1|DR812713
EST:     TCACCCCGACATACAAAAAGAAGCGTCCGCAACTGCTCAAGTACTACCAG                         GGCGTGATTGACAACATGTACAAAAGTGCTAAGTGAACTCACTCTACAGTA
genomic: TCACCCCGACATACAAAAAGAAGCGTCCGCAACTGCTCAAGTACTACCAGgtactgctca ... aattttgcagGGCGTGATTGACAACATGTACAAAAGTGCTAAGTGAACTCACTCTACAGTA
EST: gi|7227832|gb|AW566473.1|AW566473
EST:     TCACCCCGACATACAAAAAGAAGCGTCCGCAACTGCTCAAGTACTACCAG                         GGCGTGATTGACAACATGTACAAAAGTGCTAAGTGAACTCACTCTACAGTA
genomic: TCACCCCGACATACAAAAAGAAGCGTCCGCAACTGCTCAAGTACTACCAGgtactgctca ... aattttgcagGGCGTGATTGACAACATGTACAAAAGTGCTAAGTGAACTCACTCTACAGTA
EST: gi|60355518|gb|DN222491.1|DN222491
EST:     TCACCCCGACATACAAAAAGAAGCGTCCGCAACTGCTCAAGTACTACCAG                         GGCGTGATTGACAACATGTACAAAAGTGCTAAGTGAACTCACTCTACAGTA
genomic: TCACCCCGACATACAAAAAGAAGCGTCCGCAACTGCTCAAGTACTACCAGgtactgctca ... aattttgcagGGCGTGATTGACAACATGTACAAAAGTGCTAAGTGAACTCACTCTACAGTA
EST: gi|26558144|gb|CA830379.1|CA830379
EST:     TCACCCCGACATACAAAAAGAAGCGTCCGCAACTGCTCAAGTACTACCAG                         GGCGTGATTGACAACATGTACAAAAGTGCTAAGTGAACTCACTCTACAGTA
genomic: TCACCCCGACATACAAAAAGAAGCGTCCGCAACTGCTCAAGTACTACCAGgtactgctca ... aattttgcagGGCGTGATTGACAACATGTACAAAAGTGCTAAGTGAACTCACTCTACAGTA
EST: gi|32868239|gb|CF007921.1|CF007921
EST:     TCACCCCGACATACAAAAAGAAGCGTCCGCAACTGCTCAAGTACTACCAG                         GGCGTGATTGACAACATGTACAAAAGTGCTAAGTGAACTCACTCTACAGTG
genomic: TCACCCCGACATACAAAAAGAAGCGTCCGCAACTGCTCAAGTACTACCAGgtactgctca ... aattttgcagGGCGTGATTGACAACATGTACAAAAGTGCTAAGTGAACTCACTCTACAGTA
EST: gi|32867685|gb|CF007367.1|CF007367
EST:     TCACCCCGACATACAAAAAGAAGCGTCCGCAACTGCTCAAGTACTACCAG                         GGCGTGATTGACAACATGTACAAAAGTGCTAAGTGAACTCACTCTACAGTG
genomic: TCACCCCGACATACAAAAAGAAGCGTCCGCAACTGCTCAAGTACTACCAGgtactgctca ... aattttgcagGGCGTGATTGACAACATGTACAAAAGTGCTAAGTGAACTCACTCTACAGTA
EST: gi|28982597|gb|BQ538182.2|BQ538182
EST:     TCACCCCGACATACAAAAAGAAGCGTCCGCAACTGCTCAAGTACTACCAG                         GGCGTGATTGACAACATGTACAAAAGTGCTAAGTGAACTCACTCTACAGTA
genomic: TCACCCCGACATACAAAAAGAAGCGTCCGCAACTGCTCAAGTACTACCAGgtactgctca ... aattttgcagGGCGTGATTGACAACATGTACAAAAGTGCTAAGTGAACTCACTCTACAGTA

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: 183

AAAGGATGTGCACCTGGAACCAGTACCGTTTGACATGGACCGTGATTTGATCACCCCGACATACAAAAAGAAGCGTCCGCAACTGCTCAAGTACTACCAGgtactgctca ... aattttgcagGGCGTGATTGACAACATGTACAAAAGTGCTAAGTGAACTCACTCTACAGTACACATCCCGATGAAGATTCCCAACGTTGAATCTTGTTTGAGCAGCCAGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 258

AAAGGATGTGCACCTGGAACCAGTACCGTTTGACATGGACCGTGATTTGATCACCCCGACATACAAAAAGAAGCGTCCGCAACTGCTCAAGTACTACCAGgtactgctca ... aattttgcagGGCGTGATTGACAACATGTACAAAAGTGCTAAGTGAACTCACTCTACAGTACACATCCCGATGAAGATTCCCAACGTTGAATCTTGTTTGAGCAGCCAGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 125

AAAGGATGTGCACCTGGAACCAGTACCGTTTGACATGGACCGTGATTTGATCACCCCGACATACAAAAAGAAGCGTCCGCAACTGCTCAAGTACTACCAGgtactgctca ... aattttgcagGGCGTGATTGACAACATGTACAAAAGTGCTAAGTGAACTCACTCTACAGTACACATCCCGATGAAGATTCCCAACGTTGAATCTTGTTTGAGCAGCCAGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 98

AAAGGATGTGCACCTGGAACCAGTACCGTTTGACATGGACCGTGATTTGATCACCCCGACATACAAAAAGAAGCGTCCGCAACTGCTCAAGTACTACCAGgtactgctca ... aattttgcagGGCGTGATTGACAACATGTACAAAAGTGCTAAGTGAACTCACTCTACAGTACACATCCCGATGAAGATTCCCAACGTTGAATCTTGTTTGAGCAGCCAGA


Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAAGGATGTGCACCTGGAACCAGTACCGTTTGACATGGACCGTGATTTGATCACCCCGACATACAAAAAGAAGCGTCCGCAACTGCTCAAGTACTACCAGgtactgctcatttaactattggcgcaaagttggtccagtatattctgtttattgccgcataacagtgtgttcgttgaaatgctcttgaattggttctgtg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC