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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGCGCTGGCGGCGCTGGCGGCCGTGGCGGCCGGAGGGGACATCGTGCACCAGGACGACGAGGCGCCCAAGATCCCCGGCTGCTCCAACGACTTCGTGCTGgtatggggtatagatggccaaaaagcacgaggcccgtgagcccggcacgaagcccgctttttgggcccggtccgagcacggcacggtagaataagcgggc...

Basic information

species Zea mays
transcript GRMZM2G096343_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G096343_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os02g57710.1 (Oryza sativa), 5'ss of exon 1
CGCGCTGGCGGCGCTGGCGGCCGTGGCGGCCGGAGGGGACATCGTGCACCAGGACGACGAGGCGCCCAAGATCCCCGGCTGCTCCAACGACTTCGTGCTGgtatggggtatagatggccaaaaagcacgaggcccgtgagcccggcacgaagcccgctttttgggcccggtccgagcacggcacggtagaataagcgggc
 |   ||||||| ||||| |  || |||||||| || |||||||| |||||||||||||||||||||||||||||||||||||||||||||||||| || ||| |     |    | |     | ||    ||  | | |       ||    ||  |  |  |   ||  ||||                |   |||| 
GGTCATGGCGGCTCTGGCCGGGGTCGCGGCCGGCGGCGACATCGTCCACCAGGACGACGAGGCGCCCAAGATCCCCGGCTGCTCCAACGACTTCGTCCTCgtacgccccttcccagactttctaccatctcgcttgcgcggtttcttcgcttgcccttagtacgatgcgacccgaattttcggttccgagctgcacggga
















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|149049844|gb|EE048531.2|EE048531
EST:     AGGACGACGAGGCGCCCAAGATCCCCGGCTGCTCCAACGACTTCGTGCTG                         GTAAAAGTGCAGACCTGGATCAACAAAAAAGATAAAGATGAGTTTGTTGGT
genomic: AGGACGACGAGGCGCCCAAGATCCCCGGCTGCTCCAACGACTTCGTGCTGgtatggggta ... ctgctgtcagGTAAAAGTGCAGACCTGGATCAACAAAAAAGATAAAGATGAGTTTGTTGGT
EST: gi|89758526|gb|DY687677.1|DY687677
EST:     AGGACGACGAGGCGCCCAAGATCCCCGGCTGCTCCAACGACTTCGTGCTG                         GTAAAAGTGCAGACCTGGATCAACAAAAAAGATAAAGATGAGTTTGTTGGT
genomic: AGGACGACGAGGCGCCCAAGATCCCCGGCTGCTCCAACGACTTCGTGCTGgtatggggta ... ctgctgtcagGTAAAAGTGCAGACCTGGATCAACAAAAAAGATAAAGATGAGTTTGTTGGT
EST: gi|76282122|gb|DV021690.1|DV021690
EST:     AGGACGACGAGGCGCCCAAGATCCCCGGCTGCTCCAACGACTTCGTGCTG                         GTAAAAGTGCAGACCTGGATCAACAAAAAAGATAAAGATGAGTTTGTTGGT
genomic: AGGACGACGAGGCGCCCAAGATCCCCGGCTGCTCCAACGACTTCGTGCTGgtatggggta ... ctgctgtcagGTAAAAGTGCAGACCTGGATCAACAAAAAAGATAAAGATGAGTTTGTTGGT
EST: gi|211324017|gb|FL189571.1|FL189571
EST:     AGGACGACGAGGCGCCCAAGATCCCCGGCTGCTCCAACGACTTCGTGCTG                         GTAAAAGTGCAGACCTGGATCAACAAAAAAGATAAAGATGAGTTTGTTGGT
genomic: AGGACGACGAGGCGCCCAAGATCCCCGGCTGCTCCAACGACTTCGTGCTGgtatggggta ... ctgctgtcagGTAAAAGTGCAGACCTGGATCAACAAAAAAGATAAAGATGAGTTTGTTGGT
EST: gi|71441951|gb|DR823001.1|DR823001
EST:     AGGACGACGAGGCGCCCAAGATCCCCGGCTGCTCCAACGACTTCGTGCTG                         GTAAAAGTGCAGACCTGGATCAACAAAAAAGATAAAGATGAGTTTGTTGGT
genomic: AGGACGACGAGGCGCCCAAGATCCCCGGCTGCTCCAACGACTTCGTGCTGgtatggggta ... ctgctgtcagGTAAAAGTGCAGACCTGGATCAACAAAAAAGATAAAGATGAGTTTGTTGGT
EST: gi|211324014|gb|FL189568.1|FL189568
EST:     AGGACGACGAGGCGCCCAAGATCCCCGGCTGCTCCAACGACTTCGTGCTG                         GTAAAAGTGCAGACCTGGATCAACAAAAAAGATAAAGATGAGTTTGTTGGT
genomic: AGGACGACGAGGCGCCCAAGATCCCCGGCTGCTCCAACGACTTCGTGCTGgtatggggta ... ctgctgtcagGTAAAAGTGCAGACCTGGATCAACAAAAAAGATAAAGATGAGTTTGTTGGT
EST: gi|148956514|gb|EC902353.2|EC902353
EST:     AGGACGACGAGGCGCCCAAGATCCCCGGCTGCTCCAACGACTTCGTGCTG                         GTAAAAGTGCAGACCTGGATCAACAAAAAAGATAAAGATGAGTTTGTTGGT
genomic: AGGACGACGAGGCGCCCAAGATCCCCGGCTGCTCCAACGACTTCGTGCTGgtatggggta ... ctgctgtcagGTAAAAGTGCAGACCTGGATCAACAAAAAAGATAAAGATGAGTTTGTTGGT
EST: gi|211324016|gb|FL189570.1|FL189570
EST:     AGGACGACGAGGCGCCCAAGATCCCCGGCTGCTCCAACGACTTCGTGCTG                         GTAAAAGTGCAGACCTGGATCAACAAAAAAGATAAAGATGAGTTTGTTGGT
genomic: AGGACGACGAGGCGCCCAAGATCCCCGGCTGCTCCAACGACTTCGTGCTGgtatggggta ... ctgctgtcagGTAAAAGTGCAGACCTGGATCAACAAAAAAGATAAAGATGAGTTTGTTGGT
EST: gi|149081128|gb|EE170234.2|EE170234
EST:     AGGACGACGAGGCGCCCAAGATCCCCGGCTGCTCCAACGACTTCGTGCTG                         GTAAAAGTGCAGACCTGGATCAACAAAAAAGATAAAGATGAGTTTGTTGGT
genomic: AGGACGACGAGGCGCCCAAGATCCCCGGCTGCTCCAACGACTTCGTGCTGgtatggggta ... ctgctgtcagGTAAAAGTGCAGACCTGGATCAACAAAAAAGATAAAGATGAGTTTGTTGGT
EST: gi|71422117|gb|DR805619.1|DR805619
EST:     AGGACGACGAGGCGCCCAAGATCCCCGGCTGCTCCAACGACTTCGTGCTG                         GTAAAAGTGCAGACCTGGATCAACAAAAAAGATAAAGATGAGTTTGTTGGT
genomic: AGGACGACGAGGCGCCCAAGATCCCCGGCTGCTCCAACGACTTCGTGCTGgtatggggta ... ctgctgtcagGTAAAAGTGCAGACCTGGATCAACAAAAAAGATAAAGATGAGTTTGTTGGT

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: 211

CGCGCTGGCGGCGCTGGCGGCCGTGGCGGCCGGAGGGGACATCGTGCACCAGGACGACGAGGCGCCCAAGATCCCCGGCTGCTCCAACGACTTCGTGCTGgtatggggta ... ctgctgtcagGTAAAAGTGCAGACCTGGATCAACAAAAAAGATAAAGATGAGTTTGTTGGTGTTGGTGCTCGATTTGGCCCCAAGATAGAGTCAAAGGAAAAGCATGCCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 549

CGCGCTGGCGGCGCTGGCGGCCGTGGCGGCCGGAGGGGACATCGTGCACCAGGACGACGAGGCGCCCAAGATCCCCGGCTGCTCCAACGACTTCGTGCTGgtatggggta ... ctgctgtcagGTAAAAGTGCAGACCTGGATCAACAAAAAAGATAAAGATGAGTTTGTTGGTGTTGGTGCTCGATTTGGCCCCAAGATAGAGTCAAAGGAAAAGCATGCCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 705

CGCGCTGGCGGCGCTGGCGGCCGTGGCGGCCGGAGGGGACATCGTGCACCAGGACGACGAGGCGCCCAAGATCCCCGGCTGCTCCAACGACTTCGTGCTGgtatggggta ... ctgctgtcagGTAAAAGTGCAGACCTGGATCAACAAAAAAGATAAAGATGAGTTTGTTGGTGTTGGTGCTCGATTTGGCCCCAAGATAGAGTCAAAGGAAAAGCATGCCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 395

CGCGCTGGCGGCGCTGGCGGCCGTGGCGGCCGGAGGGGACATCGTGCACCAGGACGACGAGGCGCCCAAGATCCCCGGCTGCTCCAACGACTTCGTGCTGgtatggggta ... ctgctgtcagGTAAAAGTGCAGACCTGGATCAACAAAAAAGATAAAGATGAGTTTGTTGGTGTTGGTGCTCGATTTGGCCCCAAGATAGAGTCAAAGGAAAAGCATGCCA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGCGCTGGCGGCGCTGGCGGCCGTGGCGGCCGGAGGGGACATCGTGCACCAGGACGACGAGGCGCCCAAGATCCCCGGCTGCTCCAACGACTTCGTGCTGgtatggggtatagatggccaaaaagcacgaggcccgtgagcccggcacgaagcccgctttttgggcccggtccgagcacggcacggtagaataagcgggc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaagca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cccggtcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agaataag