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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAAAGACAAGGAGTTCTATTCCTTTTATGATCAGTGCTTTGAGACCAAGGAAGGAAAgtatgtatattatcatccaatcttttttgtctgccccttctgtttttattgctttttattatttggttctaatttatgaactggtatccttatggatag

Basic information

species Zea mays
transcript GRMZM2G052875_T02
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G052875_T02 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os01g16970.1 (Oryza sativa), 5'ss of exon 11
GCAAAGACAAGGAGTTCTATTCCTTTTATGATCAGTGCTTTGAGACCAAGGAAGGAAAgtatgtatatta-tcatccaatcttttttgtctgccccttctgtttttattgc-----tttttattatttggtt-----ctaatttatgaactggta--tccttatggatag----------------
| || || ||||||||||||| ||||||||||||||||||||||| |||||| || ||||| |||||||| |||||||| ||    ||    | |  ||| | | | | |      |||  ||  |||  ||     | | | |||    || ||  ||||  |  || |                
GTAAGGAGAAGGAGTTCTATTACTTTTATGATCAGTGCTTTGAGAGCAAGGAGGGCAAgtacgtatattagtcatccaacctcacatgcgctctctctctctctctctcgtaaatatttccatggtttactttattaccattctatattttgttaattcctcgtttattgttattcttattgatag
















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|211535329|gb|FL357693.1|FL357693
EST:     AAGGAGTTCTATTCCTTTTATGATCAGTGCTTTGAGACCAAGGAAGGAAA                         GTATACTTACAAGGTCTGTGCATATAAGAAAGCATCACAGGCTGAAGGGCA
genomic: AAGGAGTTCTATTCCTTTTATGATCAGTGCTTTGAGACCAAGGAAGGAAAgtatgtatat ... ttatggatagGTATACTTACAAGGTCTGTGCATATAAGAAAGCATCACAGGCTGAAGGGCA
EST: gi|211178585|gb|FL326372.1|FL326372
EST:     AAGGAGTTCTATTCCTTTTATGATCAGNGCTTTGAGACCAAGGAAGGAAA                         GTATACTTACAAGGTC
genomic: AAGGAGTTCTATTCCTTTTATGATCAGTGCTTTGAGACCAAGGAAGGAAAgtatgtatat ... ttatggatagGTATACTTACAAGGTC
EST: gi|211376351|gb|FL146644.1|FL146644
EST:     AAGGAGTTCTATTCCTTTTATGATCAGTGCTTTGAGACCAAGGAAGGAAA                         GTATACTTAC-ATGTCTGTGCATATAAGAAAGCATCACAGGCTGAAGGGCA
genomic: AAGGAGTTCTATTCCTTTTATGATCAGTGCTTTGAGACCAAGGAAGGAAAgtatgtatat ... ttatggatagGTATACTTACAAGGTCTGTGCATATAAGAAAGCATCACAGGCTGAAGGGCA
EST: gi|211084967|gb|FL399106.1|FL399106
EST:     AAGGAGTTCTATTCCTTTTATGATCAGTGCTTTGAGACCAAGGAAGGAAA                         GTATACTTACAAGGTCTGTGCATATAAGAAAGCATCACAGGCTGAAGGGCA
genomic: AAGGAGTTCTATTCCTTTTATGATCAGTGCTTTGAGACCAAGGAAGGAAAgtatgtatat ... ttatggatagGTATACTTACAAGGTCTGTGCATATAAGAAAGCATCACAGGCTGAAGGGCA
EST: gi|211376352|gb|FL146645.1|FL146645
EST:     AAGGAGTTCTATTCCTTTTATGATCAGTGCTTTGAGACCAAGGAAGGAAA                         GTWTACTTAC-ATGTCTGTGCATATAAGATAGCATCACAGGCTGAAGGGCA
genomic: AAGGAGTTCTATTCCTTTTATGATCAGTGCTTTGAGACCAAGGAAGGAAAgtatgtatat ... ttatggatagGTATACTTACAAGGTCTGTGCATATAAGAAAGCATCACAGGCTGAAGGGCA
EST: gi|211072830|gb|FL342711.1|FL342711
EST:     AAGGAGTTCTATTCCTTTTATGATCAGTGCTTTGAGACCAAGGAAGGAAA                         GTATACTTACAAGGTCTGTGCATATAAGAAAGCATCACAGGCTGAAGGGCA
genomic: AAGGAGTTCTATTCCTTTTATGATCAGTGCTTTGAGACCAAGGAAGGAAAgtatgtatat ... ttatggatagGTATACTTACAAGGTCTGTGCATATAAGAAAGCATCACAGGCTGAAGGGCA
EST: gi|31359162|gb|CD443519.1|CD443519
EST:     AAGGAGTTCTATTCCTTTTATGATCAGTGCTTTGAGACCAAGGAAGGAAA                         GTATACTTACAAGGTCTGTGCATATAAGAAAGCATCACAGGCTGAAGGGCA
genomic: AAGGAGTTCTATTCCTTTTATGATCAGTGCTTTGAGACCAAGGAAGGAAAgtatgtatat ... ttatggatagGTATACTTACAAGGTCTGTGCATATAAGAAAGCATCACAGGCTGAAGGGCA
EST: gi|67026048|gb|CO454797.1|CO454797
EST:     AAGGAGTTCTATTCCTTTTATGATCAGTGCTTTGAGACCAAGGAAGGAAA                         GTATACTTACAAGGTCTGTGCATATAAGAAAGCATCACAGGCTGAAGGGCA
genomic: AAGGAGTTCTATTCCTTTTATGATCAGTGCTTTGAGACCAAGGAAGGAAAgtatgtatat ... ttatggatagGTATACTTACAAGGTCTGTGCATATAAGAAAGCATCACAGGCTGAAGGGCA

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), 47 (downstream exon)
Score: 111

GCAAAGACAAGGAGTTCTATTCCTTTTATGATCAGTGCTTTGAGACCAAGGAAGGAAAgtatgtatat ... ttatggatagGTATACTTACAAGGTCTGTGCATATAAGAAAGCATCACAGGCTGAAGGGCACAGTTCCACCAACCTGGG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 97

GCAAAGACAAGGAGTTCTATTCCTTTTATGATCAGTGCTTTGAGACCAAGGAAGGAAAgtatgtatat ... ttatggatagGTATACTTACAAGGTCTGTGCATATAAGAAAGCATCACAGGCTGAAGGGCACAGTTCCACCAACCTGGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 114

GCAAAGACAAGGAGTTCTATTCCTTTTATGATCAGTGCTTTGAGACCAAGGAAGGAAAgtatgtatat ... ttatggatagGTATACTTACAAGGTCTGTGCATATAAGAAAGCATCACAGGCTGAAGGGCACAGTTCCACCAACCTGGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 131

GCAAAGACAAGGAGTTCTATTCCTTTTATGATCAGTGCTTTGAGACCAAGGAAGGAAAgtatgtatat ... ttatggatagGTATACTTACAAGGTCTGTGCATATAAGAAAGCATCACAGGCTGAAGGGCACAGTTCCACCAACCTGGG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCAAAGACAAGGAGTTCTATTCCTTTTATGATCAGTGCTTTGAGACCAAGGAAGGAAAgtatgtatattatcatccaatcttttttgtctgccccttctgtttttattgctttttattatttggttctaatttatgaactggtatccttatggatag

- - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA