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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAATTGCCAGAATTCCTTGGTGGCACTTGTACCTGTCCTGAATACGGAGGTTGCCTTAAGGCTGAAAAGGGACCGTGGAAGGACCCAAACATACTTAAGgcatgtgtcattagagcacatcattgatcctcctagtatctgttctttgctaactacgcagtataaccttctcattctcatgtatttattatttgtcaccccttgtactgataccag

Basic information

species Zea mays
transcript GRMZM2G073571_T02
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G073571_T02 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os02g04020.1 (Oryza sativa), 5'ss of exon 9
TGAATTGCCAGAATTCCTTGGTGGCACTTGTACCTGTCCTGAATACGGAGGTTGCCTTAAGGCTGAAAAGGGACCGTGGAAGGACCCAAACATACTTAAGgcatgtgtcattagagcacatcattgatcctcctagtatctgttctttgctaactacgcagtataaccttctcattctcatgtatttattatttgtcaccccttgtactgataccag
||||||||| ||||||||||||||| ||||||||||||||||||| ||||| || ||||| |||||||| ||||| |||||||||| ||||||||| || | | || | |||      | | | || |  ||    |||   || |  |   | | |    |||| |||||    ||  |||| || || |||| |      || ||||||||||||
TGAATTGCCGGAATTCCTTGGTGGCGCTTGTACCTGTCCTGAATATGGAGGGTGTCTTAAAGCTGAAAAAGGACCATGGAAGGACCAAAACATACTCAATgtacgtttgatttc--ttccttactgtttgtc----tattcattatcagtgcattgctttctatacccttcc---tcatatgttttaataatttttt-----ttatactgataccag
















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|8383108|gb|BE055991.1|BE055991
EST:     GTTGCCTTAAGGCTGAAAAGGGACCGTGGAAGGACCCAAACATACTTAAG                         ATAGTCCAAAGTGGTGGGGTTCATTGTGCTCGTCAAATTGTAACTATTTCC
genomic: GTTGCCTTAAGGCTGAAAAGGGACCGTGGAAGGACCCAAACATACTTAAGgcatgtgtca ... ctgataccagATAGTCCAAAGTGGTGGGGTTCATTGTGCTCGTCAAATTGTAACTATTTCC
EST: gi|15177587|gb|BI398526.1|BI398526
EST:     GTTGCCTTAAGGCTGAAAAGGGACCGTGGAAGGACCCAAACATACTTAAG                         ATAGTCCAAAGTGGTGGGGTTCATTGTGCTCGTCAAATTGTAACTATTTCC
genomic: GTTGCCTTAAGGCTGAAAAGGGACCGTGGAAGGACCCAAACATACTTAAGgcatgtgtca ... ctgataccagATAGTCCAAAGTGGTGGGGTTCATTGTGCTCGTCAAATTGTAACTATTTCC
EST: gi|16137338|gb|BI894203.1|BI894203
EST:     GTTGCCTTAAGGCTGAAAAGGGACCGTGGAAGGACCCAAACATACTTAAG                         ATAGTCCAAAGTGGTGGGGTTCATTGTGCTCGTCAAATTGTAACTTATT-C
genomic: GTTGCCTTAAGGCTGAAAAGGGACCGTGGAAGGACCCAAACATACTTAAGgcatgtgtca ... ctgataccagATAGTCCAAAGTGGTGGGGTTCATTGTGCTCGTCAAATTGTAACT-ATTTC
EST: gi|3172014|gb|AJ006545.1|AJ006545
EST:     GTTGCCTTAAGGCTGAAAAGGGACCGTGGAAGGACCCAAACATACTTAAG                         ATAGTCCAAAGTGGTGGGGTTCATTGTGCTCGTCAAATTGTAACTATTTCC
genomic: GTTGCCTTAAGGCTGAAAAGGGACCGTGGAAGGACCCAAACATACTTAAGgcatgtgtca ... ctgataccagATAGTCCAAAGTGGTGGGGTTCATTGTGCTCGTCAAATTGTAACTATTTCC
EST: gi|15177586|gb|BI398525.1|BI398525
EST:     GTTGCCTTAAGGCTGAAAAGGGACCGTGGAAGGACCCAAACATACTTAAG                         ATAGTCCAAAGTGGTGGGGTTCATTGTGCTCGTCAAATTGTAACTATTTCC
genomic: GTTGCCTTAAGGCTGAAAAGGGACCGTGGAAGGACCCAAACATACTTAAGgcatgtgtca ... ctgataccagATAGTCCAAAGTGGTGGGGTTCATTGTGCTCGTCAAATTGTAACTATTTCC
EST: gi|15188204|gb|BI417181.1|BI417181
EST:     TTAAGGCTGAAAAGGGACCGTGGAAGGACCCAGGCATACTTAAG                         ATAGTCCAAAGTGGTGGGGTTCATTGTGCTCGTCAAATTGTAACTATTTCC
genomic: TTAAGGCTGAAAAGGGACCGTGGAAGGACCCAAACATACTTAAGgcatgtgtca ... ctgataccagATAGTCCAAAGTGGTGGGGTTCATTGTGCTCGTCAAATTGTAACTATTTCC
EST: gi|15323597|gb|BI478855.1|BI478855
EST:     TTGCCTTAAGGCTGAAAAGGGACCGTGGAAGGACCCAAACATACTTAAG                         ATAGTCCAAAGTGGTGGGGTTCATTGTGCTCGTCAAATTGTAACTAATTCC
genomic: TTGCCTTAAGGCTGAAAAGGGACCGTGGAAGGACCCAAACATACTTAAGgcatgtgtca ... ctgataccagATAGTCCAAAGTGGTGGGGTTCATTGTGCTCGTCAAATTGTAACTATTTCC
EST: gi|15323596|gb|BI478854.1|BI478854
EST:     GCTGAAAAGGGACCGTGGAAGGACCCAAACATACTTAAG                         ATAGTCCAAAGTGGTGGGGTTCATTGTGCTCGTCAAATTGTAACTATTTCC
genomic: GCTGAAAAGGGACCGTGGAAGGACCCAAACATACTTAAGgcatgtgtca ... ctgataccagATAGTCCAAAGTGGTGGGGTTCATTGTGCTCGTCAAATTGTAACTATTTCC
EST: gi|32832349|gb|CD972027.1|CD972027
EST:     GTTGCCTTAAGGCTGAAAAGGGACCGTGGAAGGACCCAAACATACTTAAG                         ATAGTCCAAAGTGGTGGGGTTCATTGTGCTCGTCAAATTGTAACTATTTCC
genomic: GTTGCCTTAAGGCTGAAAAGGGACCGTGGAAGGACCCAAACATACTTAAGgcatgtgtca ... ctgataccagATAGTCCAAAGTGGTGGGGTTCATTGTGCTCGTCAAATTGTAACTATTTCC
EST: gi|32847771|gb|CD987452.1|CD987452
EST:     GTTGCCTTAAGGCTGAAAAGGGACCGTGGAAGGACCCAAACATACTTAAG                         ATAGTCCAAAGTGGTGGGGTTCATTGTGCTCGTCAAATTGTAACTATTTCC
genomic: GTTGCCTTAAGGCTGAAAAGGGACCGTGGAAGGACCCAAACATACTTAAGgcatgtgtca ... ctgataccagATAGTCCAAAGTGGTGGGGTTCATTGTGCTCGTCAAATTGTAACTATTTCC

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), 48 (downstream exon)
Score: 162

TGAATTGCCAGAATTCCTTGGTGGCACTTGTACCTGTCCTGAATACGGAGGTTGCCTTAAGGCTGAAAAGGGACCGTGGAAGGACCCAAACATACTTAAGgcatgtgtca ... ctgataccagATAGTCCAAAGTGGTGGGGTTCATTGTGCTCGTCAAATTGTAACTATTTCCAATGGTGAGGAAAAATTTATTACTTACGCCAAACCGAAGCGCCACGCA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 119

TGAATTGCCAGAATTCCTTGGTGGCACTTGTACCTGTCCTGAATACGGAGGTTGCCTTAAGGCTGAAAAGGGACCGTGGAAGGACCCAAACATACTTAAGgcatgtgtca ... ctgataccagATAGTCCAAAGTGGTGGGGTTCATTGTGCTCGTCAAATTGTAACTATTTCCAATGGTGAGGAAAAATTTATTACTTACGCCAAACCGAAGCGCCACGCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 99

TGAATTGCCAGAATTCCTTGGTGGCACTTGTACCTGTCCTGAATACGGAGGTTGCCTTAAGGCTGAAAAGGGACCGTGGAAGGACCCAAACATACTTAAGgcatgtgtca ... ctgataccagATAGTCCAAAGTGGTGGGGTTCATTGTGCTCGTCAAATTGTAACTATTTCCAATGGTGAGGAAAAATTTATTACTTACGCCAAACCGAAGCGCCACGCA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 121

TGAATTGCCAGAATTCCTTGGTGGCACTTGTACCTGTCCTGAATACGGAGGTTGCCTTAAGGCTGAAAAGGGACCGTGGAAGGACCCAAACATACTTAAGgcatgtgtca ... ctgataccagATAGTCCAAAGTGGTGGGGTTCATTGTGCTCGTCAAATTGTAACTATTTCCAATGGTGAGGAAAAATTTATTACTTACGCCAAACCGAAGCGCCACGCA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGAATTGCCAGAATTCCTTGGTGGCACTTGTACCTGTCCTGAATACGGAGGTTGCCTTAAGGCTGAAAAGGGACCGTGGAAGGACCCAAACATACTTAAGgcatgtgtcattagagcacatcattgatcctcctagtatctgttctttgctaactacgcagtataaccttctcattctcatgtatttattatttgtcaccccttgtactgataccag

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