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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggagaacctatatcgtgtaccaagtggcaaattttcttagtctttaagatgcttaattctcttattttcctcttgactttttttcacatatcaaatgcagGGCTGAAAAGGGAAATCTTGGAGTGCCACTGCTGCCAGGCCAAGGTTGCTCGTTTTATAGCTTCAAGACAAACACATACAAACTGAACTTCATGGAGAGC

Basic information

species Zea mays
transcript GRMZM2G039373_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G039373_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g33020.1 (Oryza sativa), 3'ss of exon 1
ggagaacctatatcgtgtaccaagt-ggcaaattttcttagtctttaagatgctta--attctcttattttcctcttgactttttttcacatatcaaatgcagGGCTGAAAAGGGAAATCTTGGAGTGCCACTGCTGCCAGGCCAAGGTTGCTCGTTTTATAGCTTCAAGACAAACACATACAAACTGAACTTCATGGAGAGC
       | | || || |||||  | |   ||||   | | |||  |    |||||  ||  | | | | | ||| |||    | | |||||  | | ||||| || |||||||| |||||||| |||||||| ||||| ||||| |||||||| ||||| |||||||||||||||||||||||| |||||||| | ||||||
-tgcccacgagattgt-taccattttgatgaattaggtgaatctaaattgagcttaaaatgttatcagtgttctcatgatcactctgcacatcacta-tgcagAGCAGAAAAGGGGAATCTTGGGGTGCCACTACTGCCGGGCCAGGGTTGCTCATTTTACAGCTTCAAGACAAACACATACAAATTGAACTTCCTAGAGAGC
















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|211273203|gb|FL267866.1|FL267866
EST:     GGACTCCTCTTCTCCCTTCGCTCCTTCACCGCCAAGATCGACCCAACCAC                         GGCTGAAAAGGGAAATCTTGGAGTGCCACTGCTGCCAGGCCAAGGTTGCTC
genomic: GGACTCCTCTTCTCCCTTCGCTCCTTCACCGCCAAGATCGACCCAACCACgtacgtccta ... tcaaatgcagGGCTGAAAAGGGAAATCTTGGAGTGCCACTGCTGCCAGGCCAAGGTTGCTC
EST: gi|148956259|gb|EC902056.2|EC902056
EST:     GGACTCCTCTTCTCCCTTCGCTCCTTCACCGCCAAGATCGACCCAACCAC                         GGCTGAAAAGGGAAATCTTGGAGTGCCACTGCTGCCAGGCCAAGGTTGCTC
genomic: GGACTCCTCTTCTCCCTTCGCTCCTTCACCGCCAAGATCGACCCAACCACgtacgtccta ... tcaaatgcagGGCTGAAAAGGGAAATCTTGGAGTGCCACTGCTGCCAGGCCAAGGTTGCTC
EST: gi|211273196|gb|FL267859.1|FL267859
EST:     GGACTCCTCTTCTCCCTTCGCTCCTTCACCGSCAAGATCGACCCAACCAC                         GGCTGAAAAGGGAAATCTTGGAGTGCCACTGSTGCCAGGCCAAGGTTGCTC
genomic: GGACTCCTCTTCTCCCTTCGCTCCTTCACCGCCAAGATCGACCCAACCACgtacgtccta ... tcaaatgcagGGCTGAAAAGGGAAATCTTGGAGTGCCACTGCTGCCAGGCCAAGGTTGCTC
EST: gi|211273198|gb|FL267861.1|FL267861
EST:     GGACTCCTCTTCTCCCTTCGCTCCTTCACCGCCAAGATCGACCCAACCAC                         GGCTGAAAAGGGAAATCTTGGAGTGCCACTGCTGCCAGGCCAAGGTTGCTC
genomic: GGACTCCTCTTCTCCCTTCGCTCCTTCACCGCCAAGATCGACCCAACCACgtacgtccta ... tcaaatgcagGGCTGAAAAGGGAAATCTTGGAGTGCCACTGCTGCCAGGCCAAGGTTGCTC
EST: gi|211273200|gb|FL267863.1|FL267863
EST:     GGACTCCTCTTCTCCCTTCGCTCCTTCACCGCCAAGATCGACCCAACCAC                         GGCTGANAAGGGAAATCTTGGAGTGCCACTGCTGCCAGGCCAAGGTTGCTC
genomic: GGACTCCTCTTCTCCCTTCGCTCCTTCACCGCCAAGATCGACCCAACCACgtacgtccta ... tcaaatgcagGGCTGAAAAGGGAAATCTTGGAGTGCCACTGCTGCCAGGCCAAGGTTGCTC
EST: gi|211273197|gb|FL267860.1|FL267860
EST:     GGACTCCTCTTCTCCCTTCGCTCCTTCACCGCCAAGATCGACCCAACCAC                         GGNTGAAAAGGGAAATCTTGGAG
genomic: GGACTCCTCTTCTCCCTTCGCTCCTTCACCGCCAAGATCGACCCAACCACgtacgtccta ... tcaaatgcagGGCTGAAAAGGGAAATCTTGGAG
EST: gi|94473829|gb|EB702787.1|EB702787
EST:     GGACTCCTCTTCTCCCTTCGCTCTTTCACCGCCAAGATCGACCCAACCAC                         GGCTGAAAAGGGAAATCTTGGAGTGCCACTGCTGCCAGGCCAAGGTTGCTC
genomic: GGACTCCTCTTCTCCCTTCGCTCCTTCACCGCCAAGATCGACCCAACCACgtacgtccta ... tcaaatgcagGGCTGAAAAGGGAAATCTTGGAGTGCCACTGCTGCCAGGCCAAGGTTGCTC
EST: gi|211273201|gb|FL267864.1|FL267864
EST:     GGACTCCTCTTCTCCCTTCGCTCCTTCACCGCCAAGATCGACCCAACCAC                         GGCTGAAAAGGGAAATCTTGGAGTGCCACTGCTGCCAGGCCAAGGTTGCTC
genomic: GGACTCCTCTTCTCCCTTCGCTCCTTCACCGCCAAGATCGACCCAACCACgtacgtccta ... tcaaatgcagGGCTGAAAAGGGAAATCTTGGAGTGCCACTGCTGCCAGGCCAAGGTTGCTC

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), 49 (downstream exon)
Score: 39

ATCGCCCGCTCCGCACGCTCGATCCCACCCAGGACCACAAGCTCATGTTCGGACTCCTCTTCTCCCTTCGCTCCTTCACCGCCAAGATCGACCCAACCACgtacgtccta ... tcaaatgcagGGCTGAAAAGGGAAATCTTGGAGTGCCACTGCTGCCAGGCCAAGGTTGCTCGTTTTATAGCTTCAAGACAAACACATACAAACTGAACTTCATGGAGAGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 55

ATCGCCCGCTCCGCACGCTCGATCCCACCCAGGACCACAAGCTCATGTTCGGACTCCTCTTCTCCCTTCGCTCCTTCACCGCCAAGATCGACCCAACCACgtacgtccta ... tcaaatgcagGGCTGAAAAGGGAAATCTTGGAGTGCCACTGCTGCCAGGCCAAGGTTGCTCGTTTTATAGCTTCAAGACAAACACATACAAACTGAACTTCATGGAGAGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 67

ATCGCCCGCTCCGCACGCTCGATCCCACCCAGGACCACAAGCTCATGTTCGGACTCCTCTTCTCCCTTCGCTCCTTCACCGCCAAGATCGACCCAACCACgtacgtccta ... tcaaatgcagGGCTGAAAAGGGAAATCTTGGAGTGCCACTGCTGCCAGGCCAAGGTTGCTCGTTTTATAGCTTCAAGACAAACACATACAAACTGAACTTCATGGAGAGC


Block sizes: 47 (upstream exon), 44 (downstream exon)
Score: 74

ATCGCCCGCTCCGCACGCTCGATCCCACCCAGGACCACAAGCTCATGTTCGGACTCCTCTTCTCCCTTCGCTCCTTCACCGCCAAGATCGACCCAACCACgtacgtccta ... tcaaatgcagGGCTGAAAAGGGAAATCTTGGAGTGCCACTGCTGCCAGGCCAAGGTTGCTCGTTTTATAGCTTCAAGACAAACACATACAAACTGAACTTCATGGAGAGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagatgcttaattctcttattttcctcttgactttttttcacatatcaaatgcagGGCTGAAAAGGGAAATCTTGGAGTGCCACTGCTGCCAGGCCAAGGTTGCTCGTTTTATAGCTTCAAGACAAACACATACAAACTGAACTTCATGGAGAGC
                         tcttgac  putative branch site (score: 74)
       ttaattctcttatttt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggagaacctatatcgtgtaccaagtggcaaattttcttagtctttaagatgcttaattctcttattttcctcttgactttttttcacatatcaaatgcagGGCTGAAAAGGGAAATCTTGGAGTGCCACTGCTGCCAGGCCAAGGTTGCTCGTTTTATAGCTTCAAGACAAACACATACAAACTGAACTTCATGGAGAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - -tgtacca