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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGCTTGATCTTTGAATATGTTAACAACACAGATTTCAAAGTGCTGTACCCAACATTAACAGATTATGACATTCGGTATTACATCTACGAGTTACTCAAGgtaaattctcatatttttgttacatctgtcactctgtgtaaacagctggtatattttcttctttaaagaagtctttgtaaccagtgtttgacaaggcggc...

Basic information

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

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G143602_T03 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os07g02350.1 (Oryza sativa), 5'ss of exon 3
CAGCTTGATCTTTGAATATGTTAACAACACAGATTTCAAAGTGCTGTACCCAACATTAACAGATTATGACATTCGGTATTACATCTACGAGTTACTCAAGg-----taaattctcatatttttgttacatctgtcactctgtgtaaacagctggt-atattttcttctttaaagaagtctttgtaaccagtgtttgacaaggcggc
 |||||||| ||||||||||| ||||||||||||||||||||||| ||||||||  | |||||||||||||| || ||||| ||||||||| |||| ||||     |   ||||||  |||||||||| | |  || |      ||  | ||  | ||       | ||  |     || || |        |   |         
AAGCTTGATATTTGAATATGTCAACAACACAGATTTCAAAGTGCTATACCCAACCCTGACAGATTATGACATCCGTTATTATATCTACGAGCTACTGAAGgttttattctttctcaattttttgttac-tgtaacattgccaacaagaaactacttattcagcacttttccagagtatcgttcttgttgaaatgaaatctt-----

upper sequence: GRMZM2G143602_T03 (Zea mays), 5'ss of exon 3
lower sequence: PP1S63_208V6.1 (Physcomitrella patens), 5'ss of exon 4
CAGCTTGATCTTTGAATATGTTAACAACACAGATTTCAAAGTGCTGTACCCAACATTAACAGATTATGACATTCGGTATTACATCTACGAGTTACTCAAGgtaaattctcatatttttgttacatctgtcactctgtgt--aaacagctggtatattttcttctttaaagaagtctttgtaaccagtgtttgacaaggcggc
|||  | || ||||| ||||| |||||||| |||||||||||||| ||||| ||| | ||||| | ||||||||| || |||||  | ||| |||||||||| | |  |  | ||  | ||   |||   |   || ||  | |||| | | | | |  | | | | |    | ||| |  | |  | ||            
CAGTCTTATATTTGAGTATGTGAACAACACGGATTTCAAAGTGCTCTACCCTACACTGACAGACTTTGACATTCGTTACTACATTCATGAGCTACTCAAGgtgagtaatttttttcatcttttttcttaaagcttgggtcgacacagattggagactcacgtttctgagtgtgactt-gctatctatattcatttttatct-
















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:     CAACATTAACAGATTATGACATTCGGTATTACATCTACGAGTTACTCAAG                         GCATTAGATTACTGCCATTCACAAGGTATTATGCACCGAGATGTGAAGCCC
genomic: CAACATTAACAGATTATGACATTCGGTATTACATCTACGAGTTACTCAAGgtaaattctc ... ggatatacagGCATTAGATTACTGCCATTCACAAGGTATTATGCACCGAGATGTGAAGCCC
EST: gi|19822196|gb|BQ048220.1|BQ048220
EST:     CAACATTAACAGATTATGACATTCGGTATTACATCTACGAGTTACTCAAG                         GCATTAGATTACTGCCATTCACAAGGTATTATGCACCGAGATGTGAAGCCC
genomic: CAACATTAACAGATTATGACATTCGGTATTACATCTACGAGTTACTCAAGgtaaattctc ... ggatatacagGCATTAGATTACTGCCATTCACAAGGTATTATGCACCGAGATGTGAAGCCC
EST: gi|23199704|gb|BU582269.1|BU582269
EST:     CAACATTAACAGATTATGACATTCGGTATTACATCTACGAGTTACTCAAG                         GCATTAGATTACTGCCATTCACAAGGTATTATGCACCGAGATGTGAAGCCC
genomic: CAACATTAACAGATTATGACATTCGGTATTACATCTACGAGTTACTCAAGgtaaattctc ... ggatatacagGCATTAGATTACTGCCATTCACAAGGTATTATGCACCGAGATGTGAAGCCC
EST: gi|21389960|gb|BQ528009.1|BQ528009
EST:     TGACATTCGGTATTACATCTACGAGTTACTCAAG                         GCATTAGATTACTGCCATTCACAAGGTATTATGCACCGAGATGTGAAGCCC
genomic: TGACATTCGGTATTACATCTACGAGTTACTCAAGgtaaattctc ... ggatatacagGCATTAGATTACTGCCATTCACAAGGTATTATGCACCGAGATGTGAAGCCC
EST: gi|148979084|gb|EE026504.2|EE026504
EST:     CAACATTAACAGATTATGACATTCGGTATTACATCTACGAGTTACTCAAG                         GCATTAGATTACTGCCATTCACAAGGTATTATGCACCGAGATGTGAAGCCC
genomic: CAACATTAACAGATTATGACATTCGGTATTACATCTACGAGTTACTCAAGgtaaattctc ... ggatatacagGCATTAGATTACTGCCATTCACAAGGTATTATGCACCGAGATGTGAAGCCC
EST: gi|13388534|gb|BG462212.1|BG462212
EST:     CAACATTAACAGATTATGACATTCGGTATTACATCTACGAGTTACTCAAG                         GCATTAGATTACTGCCATTCACAAGGTATTATGCACCGAGATGTGAAGCCC
genomic: CAACATTAACAGATTATGACATTCGGTATTACATCTACGAGTTACTCAAGgtaaattctc ... ggatatacagGCATTAGATTACTGCCATTCACAAGGTATTATGCACCGAGATGTGAAGCCC
EST: gi|29576768|gb|CB616880.1|CB616880
EST:     CAACATTAACAGATTATGACATTCGGTATTACATCTACGAGTTACTCAAG                         GCATTAGATTACTGCCATTCACAAGGTATTATGCACCGAGATGTGAAGCCC
genomic: CAACATTAACAGATTATGACATTCGGTATTACATCTACGAGTTACTCAAGgtaaattctc ... ggatatacagGCATTAGATTACTGCCATTCACAAGGTATTATGCACCGAGATGTGAAGCCC
EST: gi|20507676|gb|BQ279725.1|BQ279725
EST:     CAACATTAACAGATTATGACATTCGGTATTACATCTACGAGTTACTCAAG                         GCATTAGATTACTGCCATTCACAAG
genomic: CAACATTAACAGATTATGACATTCGGTATTACATCTACGAGTTACTCAAGgtaaattctc ... ggatatacagGCATTAGATTACTGCCATTCACAAG
EST: gi|87156472|gb|DY401261.1|DY401261
EST:     CAACATTAACAGATTATGACATTCGGTATTACATCTACGAGTTACTCAAG                         GCATTAGATTACTGCCATTCACAAGGTATTATGCACCGAGATGTGAAGCCC
genomic: CAACATTAACAGATTATGACATTCGGTATTACATCTACGAGTTACTCAAGgtaaattctc ... ggatatacagGCATTAGATTACTGCCATTCACAAGGTATTATGCACCGAGATGTGAAGCCC
EST: gi|71770653|gb|DR968590.1|DR968590
EST:     CAACATTAACAGATTATGACATTCGGTATTACATCTACGAGTTACTCAAG                         GCATTAGATTACTGCCATTCACAAGGTATTATGCACCGAGATGTGAAGCCC
genomic: CAACATTAACAGATTATGACATTCGGTATTACATCTACGAGTTACTCAAGgtaaattctc ... ggatatacagGCATTAGATTACTGCCATTCACAAGGTATTATGCACCGAGATGTGAAGCCC

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: 330

CAGCTTGATCTTTGAATATGTTAACAACACAGATTTCAAAGTGCTGTACCCAACATTAACAGATTATGACATTCGGTATTACATCTACGAGTTACTCAAGgtaaattctc ... ggatatacagGCATTAGATTACTGCCATTCACAAGGTATTATGCACCGAGATGTGAAGCCCCACAATGTTATGATAGATCATGAGCTTCGGAAACTCCGGCTGATAGACT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 218

CAGCTTGATCTTTGAATATGTTAACAACACAGATTTCAAAGTGCTGTACCCAACATTAACAGATTATGACATTCGGTATTACATCTACGAGTTACTCAAGgtaaattctc ... ggatatacagGCATTAGATTACTGCCATTCACAAGGTATTATGCACCGAGATGTGAAGCCCCACAATGTTATGATAGATCATGAGCTTCGGAAACTCCGGCTGATAGACT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 306

CAGCTTGATCTTTGAATATGTTAACAACACAGATTTCAAAGTGCTGTACCCAACATTAACAGATTATGACATTCGGTATTACATCTACGAGTTACTCAAGgtaaattctc ... ggatatacagGCATTAGATTACTGCCATTCACAAGGTATTATGCACCGAGATGTGAAGCCCCACAATGTTATGATAGATCATGAGCTTCGGAAACTCCGGCTGATAGACT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 159

CAGCTTGATCTTTGAATATGTTAACAACACAGATTTCAAAGTGCTGTACCCAACATTAACAGATTATGACATTCGGTATTACATCTACGAGTTACTCAAGgtaaattctc ... ggatatacagGCATTAGATTACTGCCATTCACAAGGTATTATGCACCGAGATGTGAAGCCCCACAATGTTATGATAGATCATGAGCTTCGGAAACTCCGGCTGATAGACT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAGCTTGATCTTTGAATATGTTAACAACACAGATTTCAAAGTGCTGTACCCAACATTAACAGATTATGACATTCGGTATTACATCTACGAGTTACTCAAGgtaaattctcatatttttgttacatctgtcactctgtgtaaacagctggtatattttcttctttaaagaagtctttgtaaccagtgtttgacaaggcggc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -taaagaag