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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGGGGGAGGAGCCTGCTGCCGCTGCCGAGTTCCTCCTGCTTCCGTGGCTCCACGACGCCTTGCGATTGCGACGTTTCCGCAGTGGCGGTGGACGTCGAGgtaagggtgtttcctttccctcgcggtgctttcgaatctgtgcgtgttggaatgcggcgaatcaggcgaaggaagggtgttttcacaaatggagcgcgga...

Basic information

species Zea mays
transcript GRMZM2G060999_T01
intron # 1
splice site 5'
intron type U2

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|148999941|gb|EE037002.2|EE037002
EST:     CCACGACGCCTTGCGATTGCGACGTTTCCGCAGTGGCGGTGGACGTCGAG                         TGTAACAAGGGAGGGGAGACTGCAAGCCTACCTTCACTCACTCACACTACA
genomic: CCACGACGCCTTGCGATTGCGACGTTTCCGCAGTGGCGGTGGACGTCGAGgtaagggtgt ... atgtttctagTGTAACAAGGGAGGGGAGACTGCAAGCCTACCTTCACTCACTCACACTACA
EST: gi|78122499|gb|DV540883.1|DV540883
EST:     CCACGACGCCTTGCGATTGCGACGTTTCCGCAGTGGCGGTGGACGTCGAG                         TGTAACAAGGGAGGGGAGACTGCAAGCCTACCTTCTCTCTCTCACACTACA
genomic: CCACGACGCCTTGCGATTGCGACGTTTCCGCAGTGGCGGTGGACGTCGAGgtaagggtgt ... atgtttctagTGTAACAAGGGAGGGGAGACTGCAAGCCTACCTTCACTCACTCACACTACA
EST: gi|71771688|gb|DR969625.1|DR969625
EST:     CCACGACGCCTTGCGATTGCGACGTTTCCGCAGTGGCGGTGGACGTCGAG                         TGTAACAAGGGAGGGGAGACTGCAAGCCTACCTTCACTCACTCACACTACA
genomic: CCACGACGCCTTGCGATTGCGACGTTTCCGCAGTGGCGGTGGACGTCGAGgtaagggtgt ... atgtttctagTGTAACAAGGGAGGGGAGACTGCAAGCCTACCTTCACTCACTCACACTACA
EST: gi|148965243|gb|EE016048.2|EE016048
EST:     CCACGACGCCTTGCGATTGCGACGTTTCCGCAGTGGCGGTGGACGTCGAG                         TGTAACAAGGGAGGGGAGACTGCAAGCCTACCTTCACTCACTCACACTACA
genomic: CCACGACGCCTTGCGATTGCGACGTTTCCGCAGTGGCGGTGGACGTCGAGgtaagggtgt ... atgtttctagTGTAACAAGGGAGGGGAGACTGCAAGCCTACCTTCACTCACTCACACTACA
EST: gi|78076338|gb|DV504772.1|DV504772
EST:     CCACGACGCCTTGCGATTGCGACGTTTCCGCAGTGGCGGTGGACGTCGAG                         TGTAACAAGGGAGGGGAGACTGCAAGCCTACCTTCACTCACTCACACTACA
genomic: CCACGACGCCTTGCGATTGCGACGTTTCCGCAGTGGCGGTGGACGTCGAGgtaagggtgt ... atgtttctagTGTAACAAGGGAGGGGAGACTGCAAGCCTACCTTCACTCACTCACACTACA
EST: gi|211304570|gb|FL245482.1|FL245482
EST:     CCACGACGCCTTGCGATTGCGACGTTTCCGCAGTGGCGGTGGACGTCGAG                         TCTAACAAGGGAGGGGAGACTGCAAGCCTACCTTCACTCACTCACACTACA
genomic: CCACGACGCCTTGCGATTGCGACGTTTCCGCAGTGGCGGTGGACGTCGAGgtaagggtgt ... atgtttctagTGTAACAAGGGAGGGGAGACTGCAAGCCTACCTTCACTCACTCACACTACA
EST: gi|211304576|gb|FL245488.1|FL245488
EST:     CCACGACGCCTTGCGATTGCGACGTTTCCGCAGTGGCGGTGGACGTCGAG                         TCTAACAAGGGAGGGGAGACTGCAAGCCTACCTTCACTCACTCACACTACA
genomic: CCACGACGCCTTGCGATTGCGACGTTTCCGCAGTGGCGGTGGACGTCGAGgtaagggtgt ... atgtttctagTGTAACAAGGGAGGGGAGACTGCAAGCCTACCTTCACTCACTCACACTACA
EST: gi|148933432|gb|EC877117.2|EC877117
EST:     CCACGACGCCTTGCGATTGCGACGTTTCCGCAGTGGCGGTGGACGTCGAG                         TGTAACAAGGGAGGGGAGACTGCAAGCCTACCTTCACTCACTCACACTACA
genomic: CCACGACGCCTTGCGATTGCGACGTTTCCGCAGTGGCGGTGGACGTCGAGgtaagggtgt ... atgtttctagTGTAACAAGGGAGGGGAGACTGCAAGCCTACCTTCACTCACTCACACTACA
EST: gi|149082256|gb|EE171442.2|EE171442
EST:     CCACGACGCCTTGCGATTGCGACGTTTCCGCAGTGGCGGTGGACGTCGAG                         TGTAACAAGGGAGGGGAGACTGCAAGCCTACTTT-ACTCACTCACACTACA
genomic: CCACGACGCCTTGCGATTGCGACGTTTCCGCAGTGGCGGTGGACGTCGAGgtaagggtgt ... atgtttctagTGTAACAAGGGAGGGGAGACTGCAAGCCTACCTTCACTCACTCACACTACA
EST: gi|211304568|gb|FL245480.1|FL245480
EST:     CCACGACGCCTTGCGATTGCGACGTTTCCGCAGTGGCGGTGGACGTCGAG                         TCTAACAAGGGAGGGGAGACTGCAAGCCTACCTTCACTCACTCACACTACA
genomic: CCACGACGCCTTGCGATTGCGACGTTTCCGCAGTGGCGGTGGACGTCGAGgtaagggtgt ... atgtttctagTGTAACAAGGGAGGGGAGACTGCAAGCCTACCTTCACTCACTCACACTACA
EST: gi|211304572|gb|FL245484.1|FL245484
EST:     CCACGACGCCTTGCGATTGCGACGTTTCCGCAGTGGCGGTGGACGTCGAG                         TCTAACAAGGGAGGGGAGACTGCAAGCCTACCTTCACTCACTCACACTACA
genomic: CCACGACGCCTTGCGATTGCGACGTTTCCGCAGTGGCGGTGGACGTCGAGgtaagggtgt ... atgtttctagTGTAACAAGGGAGGGGAGACTGCAAGCCTACCTTCACTCACTCACACTACA
EST: gi|148956525|gb|EC902365.2|EC902365
EST:     CCACGACGCCTTGCGATTGCGACGTTTCCGCAGTGGCGGTGGACGTCGAG                         TGTAACAAGGGAGGGGAGACTGCAAGCCTACCTTCACTCACTCACACTACA
genomic: CCACGACGCCTTGCGATTGCGACGTTTCCGCAGTGGCGGTGGACGTCGAGgtaagggtgt ... atgtttctagTGTAACAAGGGAGGGGAGACTGCAAGCCTACCTTCACTCACTCACACTACA
EST: gi|211304566|gb|FL245478.1|FL245478
EST:     CCACGACGCCTTGCGATTGCGACGTTTCCGCAGTGGCGGTGGACGTCGAG                         TCTAACAAGGGAGGGGAGACTGCAAGCCTACCTTCACTCACTCACACTACA
genomic: CCACGACGCCTTGCGATTGCGACGTTTCCGCAGTGGCGGTGGACGTCGAGgtaagggtgt ... atgtttctagTGTAACAAGGGAGGGGAGACTGCAAGCCTACCTTCACTCACTCACACTACA
EST: gi|50331296|gb|CO526422.1|CO526422
EST:     CCACGACGCCTTGCGATTGCGACGTTTCCGCAGTGGCGGTGGACGTCGAG                         TGTAACAAGGGAGGGGAGACCGCAAGCCTACCTTCACTCACTCACACTACA
genomic: CCACGACGCCTTGCGATTGCGACGTTTCCGCAGTGGCGGTGGACGTCGAGgtaagggtgt ... atgtttctagTGTAACAAGGGAGGGGAGACTGCAAGCCTACCTTCACTCACTCACACTACA
EST: gi|71321709|gb|DR797549.1|DR797549
EST:     CCACGACGCCTTGCGATTGCGACGTTTCCGCAGTGGCGGTGGACGTCGAG                         TGTAACAAGGGAGGGGAGACTGCAAGCCTACCTTCACTCACTCACACTACA
genomic: CCACGACGCCTTGCGATTGCGACGTTTCCGCAGTGGCGGTGGACGTCGAGgtaagggtgt ... atgtttctagTGTAACAAGGGAGGGGAGACTGCAAGCCTACCTTCACTCACTCACACTACA

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: 47 (upstream exon), 44 (downstream exon)
Score: 47

GAGGGGGAGGAGCCTGCTGCCGCTGCCGAGTTCCTCCTGCTTCCGTGGCTCCACGACGCCTTGCGATTGCGACGTTTCCGCAGTGGCGGTGGACGTCGAGgtaagggtgt ... atgtttctagTGTAACAAGGGAGGGGAGACTGCAAGCCTACCTTCACTCACTCACACTACAAAATCTGATGAAGATGTTCTTGCAACGCCTAAGTCTCATCCCGGTGAAG


Block sizes: 37 (upstream exon), 47 (downstream exon)
Score: 16

GAGGGGGAGGAGCCTGCTGCCGCTGCCGAGTTCCTCCTGCTTCCGTGGCTCCACGACGCCTTGCGATTGCGACGTTTCCGCAGTGGCGGTGGACGTCGAGgtaagggtgt ... atgtttctagTGTAACAAGGGAGGGGAGACTGCAAGCCTACCTTCACTCACTCACACTACAAAATCTGATGAAGATGTTCTTGCAACGCCTAAGTCTCATCCCGGTGAAG


Block sizes: 37 (upstream exon), 37 (downstream exon)
Score: 4

GAGGGGGAGGAGCCTGCTGCCGCTGCCGAGTTCCTCCTGCTTCCGTGGCTCCACGACGCCTTGCGATTGCGACGTTTCCGCAGTGGCGGTGGACGTCGAGgtaagggtgt ... atgtttctagTGTAACAAGGGAGGGGAGACTGCAAGCCTACCTTCACTCACTCACACTACAAAATCTGATGAAGATGTTCTTGCAACGCCTAAGTCTCATCCCGGTGAAG


Block sizes: 30 (upstream exon), 44 (downstream exon)
Score: 8

GAGGGGGAGGAGCCTGCTGCCGCTGCCGAGTTCCTCCTGCTTCCGTGGCTCCACGACGCCTTGCGATTGCGACGTTTCCGCAGTGGCGGTGGACGTCGAGgtaagggtgt ... atgtttctagTGTAACAAGGGAGGGGAGACTGCAAGCCTACCTTCACTCACTCACACTACAAAATCTGATGAAGATGTTCTTGCAACGCCTAAGTCTCATCCCGGTGAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGGGGGAGGAGCCTGCTGCCGCTGCCGAGTTCCTCCTGCTTCCGTGGCTCCACGACGCCTTGCGATTGCGACGTTTCCGCAGTGGCGGTGGACGTCGAGgtaagggtgtttcctttccctcgcggtgctttcgaatctgtgcgtgttggaatgcggcgaatcaggcgaaggaagggtgttttcacaaatggagcgcgga

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccctcgc