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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAAGTGATTCTCGGTAAGAAGATGAAGgtatcgatcagtgaatccccatctgctgcttcactataccccctcttttacactcactgtgaagtacgtcaaccctttgcatctatgcttatttgctttgctattag

Basic information

species Zea mays
transcript GRMZM2G081682_T02
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G081682_T02 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os07g47290.1 (Oryza sativa), 5'ss of exon 4
GGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAAGTGATTCTCGGTAAGAAGATGAAGgtatcgatcagtgaatccccatctgctgcttcactataccccctcttttacact-cactgtgaagtacgtcaaccctttgcatctatgcttatttgctttgctattag
|||||||  ||||||||||| |||||||| |||||||| ||    |||||||||||||| || |||||||||||||||  | | | |||||    || |  || |  ||    ||   | ||      | |    || | ||| ||     |||| || |     ||| ||||| ||  ||||
GGTCCAAGCAGCAAGAACCCGCTTGCTTACAAGTGGTACAATGCTGAGGAAGTGATTCTTGGGAAGAAGATGAAGgtagggttta-tgaatt---atgtcttgttgaacagatccttttattcccttttgcgtcatggaatacatctgagttttgtattt-----tatctgctt-gcgtttag
















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|31349785|gb|CD434142.1|CD434142
EST:     CTTATAAGTGGTATAACCTGGAGGAAGTGATTCTCGGTAAGAAGATGAAG                         GATTGGATGCGCTTCAGTGTTGCGTTCTGGCACACGTTCCGCGGTACTGGC
genomic: CTTATAAGTGGTATAACAAGGAGGAAGTGATTCTCGGTAAGAAGATGAAGgtatcgatca ... ttgctattagGATTGGATGCGCTTCAGTGTTGCATTCTGGCACACGTTCCGTGGTACTGGC
EST: gi|211316223|gb|FL334911.1|FL334911
EST:     CTTATAAGTGGTATAACAAGGAGGAAGTGATTCTCGGTMAGAAGATGAAG                         GATTGGATGCGCTTCAGTGTTGCGTTCTGGCACACGTTCCGCGGTACTGGC
genomic: CTTATAAGTGGTATAACAAGGAGGAAGTGATTCTCGGTAAGAAGATGAAGgtatcgatca ... ttgctattagGATTGGATGCGCTTCAGTGTTGCATTCTGGCACACGTTCCGTGGTACTGGC
EST: gi|211075605|gb|FL344132.1|FL344132
EST:     CTTATAAGTGGTATAACAAGGAGGAAGTGATTCTCGGTAAGAAGATGAAG                         SATTGGATGCGCTTCAGTGTTGCGTTCTGGCACACGTTCCGCGGTACTGGC
genomic: CTTATAAGTGGTATAACAAGGAGGAAGTGATTCTCGGTAAGAAGATGAAGgtatcgatca ... ttgctattagGATTGGATGCGCTTCAGTGTTGCATTCTGGCACACGTTCCGTGGTACTGGC
EST: gi|211288683|gb|FL312634.1|FL312634
EST:     CTTATAAGTGGTATAACAAGGAGGAAGTGATTCTCGGTAAGAAGATGAAG                         GATTGGATGCGCTTCAGTGTTGCATTCTGGCACACGTTCCGTGGTACTGGC
genomic: CTTATAAGTGGTATAACAAGGAGGAAGTGATTCTCGGTAAGAAGATGAAGgtatcgatca ... ttgctattagGATTGGATGCGCTTCAGTGTTGCATTCTGGCACACGTTCCGTGGTACTGGC
EST: gi|211328969|gb|FL341564.1|FL341564
EST:     CTTATAAGTGGTATAACAAGGAGGAAGTGATTCTCGGTAAGAAGATGAAG                         GATTGGATGCGCTTCAGTGTTGCGTTCTGGCACACGTTCCGSGGTACTGGC
genomic: CTTATAAGTGGTATAACAAGGAGGAAGTGATTCTCGGTAAGAAGATGAAGgtatcgatca ... ttgctattagGATTGGATGCGCTTCAGTGTTGCATTCTGGCACACGTTCCGTGGTACTGGC
EST: gi|71426924|gb|DR807974.1|DR807974
EST:     CTTATAAGTGGTATAACAAGGAGGAAGTGATTCTCGGTAAGAAGATGAAG                         GATTGGATGCGCTTCAGTGTTGCATTCTGGCACACGTTCCGTGGTACTGGC
genomic: CTTATAAGTGGTATAACAAGGAGGAAGTGATTCTCGGTAAGAAGATGAAGgtatcgatca ... ttgctattagGATTGGATGCGCTTCAGTGTTGCATTCTGGCACACGTTCCGTGGTACTGGC
EST: gi|211416745|gb|FL321410.1|FL321410
EST:     CTTATAAGTGGTATAACAAGGAGGAAGTGATTCTCGGTAAGAAGATGAAG                         GATTGGATGCGCTTCAGTGTTGCGTTCTGG
genomic: CTTATAAGTGGTATAACAAGGAGGAAGTGATTCTCGGTAAGAAGATGAAGgtatcgatca ... ttgctattagGATTGGATGCGCTTCAGTGTTGCATTCTGG
EST: gi|74245361|gb|DT653275.1|DT653275
EST:     CTTATAAGTGGTATAACAAGGAGGAAGTGATTCTCGGTAAGAAGATGAAG                         GATTGGATGCGCTTCAGTGTTGCATTCTGGCACACGTTCCGTGGTACTGGC
genomic: CTTATAAGTGGTATAACAAGGAGGAAGTGATTCTCGGTAAGAAGATGAAGgtatcgatca ... ttgctattagGATTGGATGCGCTTCAGTGTTGCATTCTGGCACACGTTCCGTGGTACTGGC
EST: gi|74232804|gb|DT640718.1|DT640718
EST:     CTTATAAGTGGTATAACAAGGAGGAAGTGATTCTCGGTAAGAAGATGAAG                         GATTGGATGCGCTTCAGTGTTGCATTCTGGCACACGTTCCGTGGTACTGGC
genomic: CTTATAAGTGGTATAACAAGGAGGAAGTGATTCTCGGTAAGAAGATGAAGgtatcgatca ... ttgctattagGATTGGATGCGCTTCAGTGTTGCATTCTGGCACACGTTCCGTGGTACTGGC
EST: gi|211420503|gb|FL364960.1|FL364960
EST:     CTTATAAGTGGTATAACAAGGAGGAAGTGATTCTCGGTAAGAAGATGAAG                         GATTGGATGCGCTTCAGTGTTGCGTTCTGGCACACGTTCCGCGGTACTGGC
genomic: CTTATAAGTGGTATAACAAGGAGGAAGTGATTCTCGGTAAGAAGATGAAGgtatcgatca ... ttgctattagGATTGGATGCGCTTCAGTGTTGCATTCTGGCACACGTTCCGTGGTACTGGC
EST: gi|32866060|gb|CF005742.1|CF005742
EST:     CTTATAAGTGGTATAACAAGGAGGAAGTGATTCTCGGTAAGAAGATGAAG                         GATTGGATGCGCTTCAGTGTTGCATTCTGGCACACGTTC
genomic: CTTATAAGTGGTATAACAAGGAGGAAGTGATTCTCGGTAAGAAGATGAAGgtatcgatca ... ttgctattagGATTGGATGCGCTTCAGTGTTGCATTCTGGCACACGTTC
EST: gi|32909379|gb|CF014191.1|CF014191
EST:     CTTATAAGTGGTATAACAAGGAGGAAGTGATTCTCGGTAAGAAGATGAAG                         GATTGGATGCGCTTCAGTGTTGCATTCTGGCACACGTTCCGTGGTACTGGC
genomic: CTTATAAGTGGTATAACAAGGAGGAAGTGATTCTCGGTAAGAAGATGAAGgtatcgatca ... ttgctattagGATTGGATGCGCTTCAGTGTTGCATTCTGGCACACGTTCCGTGGTACTGGC
EST: gi|211310239|gb|FL338849.1|FL338849
EST:     CTTATAAGTGGTATAACAAGGAGGAAGTGATTCTCGGTAAGAAGATGAAG                         GATTGGATGCGCTTCAGTGTTGCGTTCTGGCACACGTTCCGCGGTACTGGC
genomic: CTTATAAGTGGTATAACAAGGAGGAAGTGATTCTCGGTAAGAAGATGAAGgtatcgatca ... ttgctattagGATTGGATGCGCTTCAGTGTTGCATTCTGGCACACGTTCCGTGGTACTGGC
EST: gi|211140891|gb|FL328471.1|FL328471
EST:     CTTATAAGTGGTATAACAAGGAGGAAGTGATTCTCGGTAAGAAGATGAAG                         GATTGGATGCGCTTCAGTGTTGCGTTCTGGCACACGTTCCGCGGTACTGGC
genomic: CTTATAAGTGGTATAACAAGGAGGAAGTGATTCTCGGTAAGAAGATGAAGgtatcgatca ... ttgctattagGATTGGATGCGCTTCAGTGTTGCATTCTGGCACACGTTCCGTGGTACTGGC
EST: gi|211320715|gb|FL358326.1|FL358326
EST:     CTTATAAGTGGTATAACAAGGAGGAAGTGATTCTCGGTAAGAAGATGAAG                         GATTGGATGCGCTTCAGTGTTGCGTTCTGGCACACGTTCCGCGGTACTGGC
genomic: CTTATAAGTGGTATAACAAGGAGGAAGTGATTCTCGGTAAGAAGATGAAGgtatcgatca ... ttgctattagGATTGGATGCGCTTCAGTGTTGCATTCTGGCACACGTTCCGTGGTACTGGC

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), 41 (downstream exon)
Score: 305

GGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAAGTGATTCTCGGTAAGAAGATGAAGgtatcgatca ... ttgctattagGATTGGATGCGCTTCAGTGTTGCATTCTGGCACACGTTCCGTGGTACTGGCGCTGATCCTTTCGGTGCTCCTACAAAGACTTGGCCTTGGGAGGACGGCA


Block sizes: 49 (upstream exon), 41 (downstream exon)
Score: 419

GGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAAGTGATTCTCGGTAAGAAGATGAAGgtatcgatca ... ttgctattagGATTGGATGCGCTTCAGTGTTGCATTCTGGCACACGTTCCGTGGTACTGGCGCTGATCCTTTCGGTGCTCCTACAAAGACTTGGCCTTGGGAGGACGGCA


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 440

GGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAAGTGATTCTCGGTAAGAAGATGAAGgtatcgatca ... ttgctattagGATTGGATGCGCTTCAGTGTTGCATTCTGGCACACGTTCCGTGGTACTGGCGCTGATCCTTTCGGTGCTCCTACAAAGACTTGGCCTTGGGAGGACGGCA


Block sizes: 49 (upstream exon), 41 (downstream exon)
Score: 392

GGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAAGTGATTCTCGGTAAGAAGATGAAGgtatcgatca ... ttgctattagGATTGGATGCGCTTCAGTGTTGCATTCTGGCACACGTTCCGTGGTACTGGCGCTGATCCTTTCGGTGCTCCTACAAAGACTTGGCCTTGGGAGGACGGCA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAAGTGATTCTCGGTAAGAAGATGAAGgtatcgatcagtgaatccccatctgctgcttcactataccccctcttttacactcactgtgaagtacgtcaaccctttgcatctatgcttatttgctttgctattag

- - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG