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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTTGTTAGGATACGACGAGCACGTGAGTCAAATCAAGAAGCGGTTCTTCTTGCGCTCTGTTTGAAGACTTTCAAGCGAAGTGTTATCATTTTTAGgtctgtgttctgtataattataacttggtaaccttttgatatgaaatttagggatcctttacaggggacacattcaacactagctgttctactcattgtg...

Basic information

species Zea mays
transcript GRMZM5G804064_T01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G804064_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os12g29660.1 (Oryza sativa), 5'ss of exon 8
GGTTGTTAGGATACGACGAGCACGTGAGTCAAATCAAGAAGCGGTTCTTCTTGCGCTCTGTTTGAAGACTTTCAAGCGAAGTGTTATCATTTTTAGgtctgtgttctgta-----taattataacttggtaaccttttgatatgaaatttagggatcctttacaggggacacattcaacactagctgttctactcattgtg
||| ||||| |||||| ||||||| ||  ||||||||||||| ||||| ||||| |||||||||||||||||||||   |  || |||||||| ||||  |||||||| |     | ||| ||| ||       | ||| | |     | |  ||  |  |  |   |   |  |||    | |   || ||     | | 
GGTGGTTAGAATACGAAGAGCACGCGAAGCAAATCAAGAAGCTGTTCTGCTTGCTCTCTGTTTGAAGACTTTCAAGGATAAAGTAATCATTTTCAGgttagtgttctggaggacctgattgtaatttatggctttattgcttttg---tcaatgactcagtgtaacagttcc--tcagttttgggcattataagatgtata
















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|87151869|gb|DY396658.1|DY396658
EST:     CTTCTTGCGCTCTGTTTGAAGACTTTCAAGCGAAGTGTTATCATTTTTAG                         TGGCACAAAGCAATCCGCACACAGGTTAAAAATAATATTTGGTCTCTCTGG
genomic: CTTCTTGCGCTCTGTTTGAAGACTTTCAAGCGAAGTGTTATCATTTTTAGgtctgtgttc ... ccccctgcagTGGCACAAAGCAATCCGCACACAGGTTAAAAATAATATTTGGTCTCTCTGG
EST: gi|19057848|gb|BM736515.1|BM736515
EST:     CTTCTTGCGCTCTGTTTGAAGACTTTCAAGCGAAGTGTTATCATTTTTAG                         GGGCACAAAGCAATCCGCACACAGGTTAAAAATAATATTTGGNCTCTCTGG
genomic: CTTCTTGCGCTCTGTTTGAAGACTTTCAAGCGAAGTGTTATCATTTTTAGgtctgtgttc ... ccccctgcagTGGCACAAAGCAATCCGCACACAGGTTAAAAATAATATTTGGTCTCTCTGG
EST: gi|32808049|gb|CD960283.1|CD960283
EST:     CTTCTTGCGCTCTGTTTGAAGACTTTCAAGCGAAGTGTTATCATTTTTAG                         TGGCACAAAGCAATCCGCACACAGGTTA
genomic: CTTCTTGCGCTCTGTTTGAAGACTTTCAAGCGAAGTGTTATCATTTTTAGgtctgtgttc ... ccccctgcagTGGCACAAAGCAATCCGCACACAGGTTA
EST: gi|20301192|gb|BQ164135.1|BQ164135
EST:     CTTCTTGCGCTCTGTTTGAAGACTTTCAAGCGAAGTGTTATCATTTTTAG                         TGGCACAAAGCAATCCGCACACAGGTTAAAAATAATATTTGGTCTCTCTGG
genomic: CTTCTTGCGCTCTGTTTGAAGACTTTCAAGCGAAGTGTTATCATTTTTAGgtctgtgttc ... ccccctgcagTGGCACAAAGCAATCCGCACACAGGTTAAAAATAATATTTGGTCTCTCTGG
EST: gi|20300928|gb|BQ163871.1|BQ163871
EST:     CTTCTTGCGCTCTGTTTGAAGACTTTCAAGCGAAGTGTTATCATTTTTAG                         TGGCACAAAGCAATCCGCACACAGGTTAAAAATAATATTTGGTCTCTCTGG
genomic: CTTCTTGCGCTCTGTTTGAAGACTTTCAAGCGAAGTGTTATCATTTTTAGgtctgtgttc ... ccccctgcagTGGCACAAAGCAATCCGCACACAGGTTAAAAATAATATTTGGTCTCTCTGG
EST: gi|19058325|gb|BM736992.1|BM736992
EST:     CTTCTTGCGCTCTGTTTGAAGACTTTCAAGCGAAGTGTTATCATTTTTAG                         TGGCACAAAGCAATCCGCACACAGGTTAAAAATAATATTTGGTCTCTCTGG
genomic: CTTCTTGCGCTCTGTTTGAAGACTTTCAAGCGAAGTGTTATCATTTTTAGgtctgtgttc ... ccccctgcagTGGCACAAAGCAATCCGCACACAGGTTAAAAATAATATTTGGTCTCTCTGG
EST: gi|22490815|gb|BU050738.1|BU050738
EST:     CTTCTTGCGCTCTGTTTGAAGACTTTCAAGCGAAGTGTTATCATTTTTAG                         TGGCACAAAGCAATCCGCACACAGGTTAAAAATAATATTTGGTCTCTCTGG
genomic: CTTCTTGCGCTCTGTTTGAAGACTTTCAAGCGAAGTGTTATCATTTTTAGgtctgtgttc ... ccccctgcagTGGCACAAAGCAATCCGCACACAGGTTAAAAATAATATTTGGTCTCTCTGG

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: 46 (upstream exon), 48 (downstream exon)
Score: 47

GGTTGTTAGGATACGACGAGCACGTGAGTCAAATCAAGAAGCGGTTCTTCTTGCGCTCTGTTTGAAGACTTTCAAGCGAAGTGTTATCATTTTTAGgtctgtgttc ... ccccctgcagTGGCACAAAGCAATCCGCACACAGGTTAAAAATAATATTTGGTCTCTCTGGCATGAAAGCAGCTGAACTTCATGGCAACCTTACACAGGCCCAGCGGCTT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 39

GGTTGTTAGGATACGACGAGCACGTGAGTCAAATCAAGAAGCGGTTCTTCTTGCGCTCTGTTTGAAGACTTTCAAGCGAAGTGTTATCATTTTTAGgtctgtgttc ... ccccctgcagTGGCACAAAGCAATCCGCACACAGGTTAAAAATAATATTTGGTCTCTCTGGCATGAAAGCAGCTGAACTTCATGGCAACCTTACACAGGCCCAGCGGCTT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 39

GGTTGTTAGGATACGACGAGCACGTGAGTCAAATCAAGAAGCGGTTCTTCTTGCGCTCTGTTTGAAGACTTTCAAGCGAAGTGTTATCATTTTTAGgtctgtgttc ... ccccctgcagTGGCACAAAGCAATCCGCACACAGGTTAAAAATAATATTTGGTCTCTCTGGCATGAAAGCAGCTGAACTTCATGGCAACCTTACACAGGCCCAGCGGCTT


Block sizes: 47 (upstream exon), 45 (downstream exon)
Score: 29

GGTTGTTAGGATACGACGAGCACGTGAGTCAAATCAAGAAGCGGTTCTTCTTGCGCTCTGTTTGAAGACTTTCAAGCGAAGTGTTATCATTTTTAGgtctgtgttc ... ccccctgcagTGGCACAAAGCAATCCGCACACAGGTTAAAAATAATATTTGGTCTCTCTGGCATGAAAGCAGCTGAACTTCATGGCAACCTTACACAGGCCCAGCGGCTT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTTGTTAGGATACGACGAGCACGTGAGTCAAATCAAGAAGCGGTTCTTCTTGCGCTCTGTTTGAAGACTTTCAAGCGAAGTGTTATCATTTTTAGgtctgtgttctgtataattataacttggtaaccttttgatatgaaatttagggatcctttacaggggacacattcaacactagctgttctactcattgtg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA