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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAGCGCGAGTCCGTGCCGTGGTACTCGAACGCCGTCATCCCGTACGCCTTGTTGAACGGGATGCCGCCGTCCAGCACCGCGTCCTTGAGATAGTACCTGgcagagtggcagtgatcagaatcagatcagcgcatacaagaaacagacaggacaagagtccccatctctatcagcatcagccaggcaggcagatactata...

Basic information

species Zea mays
transcript GRMZM5G814904_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|67012335|gb|CO441084.1|CO441084
EST:     TGTTGAACGGGATGCCGCCGTCCAGCACCGCGTCCTTGAGATAGTACCAG                         CTCTCCATGAGGACCTTGTCCTGGTTCATGAGCGCGAGGGCGGCCATGGAC
genomic: TGTTGAACGGGATGCCGCCGTCCAGCACCGCGTCCTTGAGATAGTACCTGgcagagtggc ... tactcaccagCTCTCCATGAGGACCTTGTCCTGGTTCATGAGCGCGAGGGCGGCCATGGAC
EST: gi|67031008|gb|CO459757.1|CO459757
EST:     TGTTGAACGGGATGCCGCCGTCCAGCACCGCGTCCTTGAGATAGTACCAG                         CTCTCCATGAGGACCTTGTCCTGGTTCATGAGCGCGAGGGCGGCCATGGAC
genomic: TGTTGAACGGGATGCCGCCGTCCAGCACCGCGTCCTTGAGATAGTACCTGgcagagtggc ... tactcaccagCTCTCCATGAGGACCTTGTCCTGGTTCATGAGCGCGAGGGCGGCCATGGAC
EST: gi|67033454|gb|CO462203.1|CO462203
EST:     TGTTGAACGGGATGCCGCCGTCCAGCACCGCGTCCTTGAGATAGTACCAG                         CTCTCCATGAGGACCTTGTCCTGGTTCATGAGCGCGAGGGCGGCCATGGAC
genomic: TGTTGAACGGGATGCCGCCGTCCAGCACCGCGTCCTTGAGATAGTACCTGgcagagtggc ... tactcaccagCTCTCCATGAGGACCTTGTCCTGGTTCATGAGCGCGAGGGCGGCCATGGAC
EST: gi|211209231|gb|FL034829.1|FL034829
EST:     TGTTGAACGGGATGCCGCCGTCCAGCACCGCGTCCTTGAGGTAGTACCAG                         CTCTCCATGAGGACCTTGTCCTGGTTCATGAGCGCGAGGGCGGCCATGGAC
genomic: TGTTGAACGGGATGCCGCCGTCCAGCACCGCGTCCTTGAGATAGTACCTGgcagagtggc ... tactcaccagCTCTCCATGAGGACCTTGTCCTGGTTCATGAGCGCGAGGGCGGCCATGGAC
EST: gi|8367436|gb|BE050381.1|BE050381
EST:     TGTTGAACGGGATGCCGCCGTCCAGCACCGTGTCCTTGAGGTAGTACCAG                         CTCTCCATGAGGACCTTGTCCTGGTTCATGAGCGCGAGGGCGGCCATGGAC
genomic: TGTTGAACGGGATGCCGCCGTCCAGCACCGCGTCCTTGAGATAGTACCTGgcagagtggc ... tactcaccagCTCTCCATGAGGACCTTGTCCTGGTTCATGAGCGCGAGGGCGGCCATGGAC
EST: gi|211164430|gb|FL159893.1|FL159893
EST:     TGTTGAACGGGATGCCGCCGTCCAGCACCGCGTCCTTGAGATAGTACCAG                         CTCTCCATGAGGACCTTGTCCTGGTTCATGAGCGCGAGGGCGGCCATGGAC
genomic: TGTTGAACGGGATGCCGCCGTCCAGCACCGCGTCCTTGAGATAGTACCTGgcagagtggc ... tactcaccagCTCTCCATGAGGACCTTGTCCTGGTTCATGAGCGCGAGGGCGGCCATGGAC
EST: gi|19436410|gb|BM952820.1|BM952820
EST:     TGTTGAACGGGATGCCGCCGTCCAGCACCGCGTCCTTGAGGTAGTGCCAG                         CTCTCCATGAGGACCTTGTCCTGGTTCATGAGCGCGAGGGCGGCCATGGAC
genomic: TGTTGAACGGGATGCCGCCGTCCAGCACCGCGTCCTTGAGATAGTACCTGgcagagtggc ... tactcaccagCTCTCCATGAGGACCTTGTCCTGGTTCATGAGCGCGAGGGCGGCCATGGAC
EST: gi|211159625|gb|FL159845.1|FL159845
EST:     TGTTGAACGGGATGCCGCCGTCCAGCACCGCGTCCTTGAGGTAGTACCAG                         CTCTCCATGAGGACCTTGTCCTGGTTCATGAGCGCGAGGGCGGCCATGGAC
genomic: TGTTGAACGGGATGCCGCCGTCCAGCACCGCGTCCTTGAGATAGTACCTGgcagagtggc ... tactcaccagCTCTCCATGAGGACCTTGTCCTGGTTCATGAGCGCGAGGGCGGCCATGGAC
EST: gi|211211788|gb|FL034836.1|FL034836
EST:     TGTTGAACGGGATGCCGCCGTCCAGCACCGCGTCCTTGAGGTAGTACCAG                         CTCTCCATGAGGACCTTGTCCTGGTTCATGAGCGCGAGGGCGGCCATGGAC
genomic: TGTTGAACGGGATGCCGCCGTCCAGCACCGCGTCCTTGAGATAGTACCTGgcagagtggc ... tactcaccagCTCTCCATGAGGACCTTGTCCTGGTTCATGAGCGCGAGGGCGGCCATGGAC

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 2 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 17

GAAGCGCGAGTCCGTGCCGTGGTACTCGAACGCCGTCATCCCGTACGCCTTGTTGAACGGGATGCCGCCGTCCAGCACCGCGTCCTTGAGATAGTACCTGgcagagtggc ... tactcaccagCTCTCCATGAGGACCTTGTCCTGGTTCATGAGCGCGAGGGCGGCCATGGACACGCCGTCCTCGTTGGGGGTGAGCCACTTGCAGACGGGCGCGGCGGAGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 31

GAAGCGCGAGTCCGTGCCGTGGTACTCGAACGCCGTCATCCCGTACGCCTTGTTGAACGGGATGCCGCCGTCCAGCACCGCGTCCTTGAGATAGTACCTGgcagagtggc ... tactcaccagCTCTCCATGAGGACCTTGTCCTGGTTCATGAGCGCGAGGGCGGCCATGGACACGCCGTCCTCGTTGGGGGTGAGCCACTTGCAGACGGGCGCGGCGGAGT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAGCGCGAGTCCGTGCCGTGGTACTCGAACGCCGTCATCCCGTACGCCTTGTTGAACGGGATGCCGCCGTCCAGCACCGCGTCCTTGAGATAGTACCTGgcagagtggcagtgatcagaatcagatcagcgcatacaagaaacagacaggacaagagtccccatctctatcagcatcagccaggcaggcagatactata

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