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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGGAGCCGCTCGGCGGCGAAGCTGAAGCAGAGCAAGCGCGACACACGCCGTGAGCAGTTTCTGTCTAGGGGGCAAGgtctgatctcatgtctggtctgtgcgatacattagtcttaatccgtgtttgtgattttggggatttctggttttcgattgacgattcggcagtggtgtgc...

Basic information

species Zea mays
transcript GRMZM2G029001_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G029001_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os04g38970.2 (Oryza sativa), 5'ss of exon 2
GGGAGCCGCTCGGCGGCGAAGCTGAAGCAGAGCAAGCGCGACACACGCCGTGAGCAGTTTCTGTCTAGGGGGCAAGgtctgatctcatgtctggtctgtgcgatacattagtcttaatccgtgtttgt-gattttggggatttctggttttc----gattgacgattcggcagtggtgtgc
|||| ||| ||| ||||||||||||||||| |||||| |||| | ||||| |||||||  || ||      ||||||||||||||| || ||    |||| |  |  || |||| | |   | ||| | |   |||  | |     ||||||    | |||  | || |||  ||      
GGGAACCGGTCGTCGGCGAAGCTGAAGCAGTGCAAGCTCGACGCGCGCCGCGAGCAGTGGCTTTC------GCAAGgtctgatctcgtgcctcccttgtgggg-atgttcgtctgatttttttttttttggggttgttgctcgggcgttttctcaggtttgggggttgggcgatgcg----
















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|211436608|gb|FL392571.1|FL392571
EST:     GCAGAGCAAGCGCGACACACGCCGTGAGCAGTTTCTGTCTAGGGGGCAAG                         GCAATAAGGATGCCAAATCTGCAGCTTCGCCAACAGGAGCAGTTTCTGGGT
genomic: GCAGAGCAAGCGCGACACACGCCGTGAGCAGTTTCTGTCTAGGGGGCAAGgtctgatctc ... attggttcagGCAATAAGGATGCCAAATCTGCAGCTTCGCCAACAGGAGCAGTTTCTGGGT
EST: gi|211019418|gb|FL374988.1|FL374988
EST:     GCAGAGCAAGCGCGACACACGCCGTGAGCAGTTTCTGTCTAGGGGGCAAG                         GCAATAAGGATGCCAAATCTGCAGCTTCGCCAACAGGAGCAGTTTCTGGGT
genomic: GCAGAGCAAGCGCGACACACGCCGTGAGCAGTTTCTGTCTAGGGGGCAAGgtctgatctc ... attggttcagGCAATAAGGATGCCAAATCTGCAGCTTCGCCAACAGGAGCAGTTTCTGGGT
EST: gi|29946923|gb|CB816392.1|CB816392
EST:     GCAGAGCAAGCGCGACACACGCCGTGAGCAGTTTCTGTCTAGGGGGCAAG                         GCAATAAGGATGCCAAATCTGCAGCTTCGCCAACAGGAGCAGTTTCTGGGT
genomic: GCAGAGCAAGCGCGACACACGCCGTGAGCAGTTTCTGTCTAGGGGGCAAGgtctgatctc ... attggttcagGCAATAAGGATGCCAAATCTGCAGCTTCGCCAACAGGAGCAGTTTCTGGGT
EST: gi|211324131|gb|FL423220.1|FL423220
EST:     GCAGAGCAAGCGCGACACACGCCGTGAGCAGTTTCTGTCTAGGGGGCAAG                         GCAATAAGGATGCCAAATCTGCAGCTTCGCCAACAGGAGCAGTTTCTGGGT
genomic: GCAGAGCAAGCGCGACACACGCCGTGAGCAGTTTCTGTCTAGGGGGCAAGgtctgatctc ... attggttcagGCAATAAGGATGCCAAATCTGCAGCTTCGCCAACAGGAGCAGTTTCTGGGT
EST: gi|211153480|gb|FL406041.1|FL406041
EST:     GCAGAGCAAGCGCGACACACGCCGTGAGCAGTTTCTGTCTAGGGGGCAAG                         GCAATAAGGATGCCAAATCTGCAGCTTCGCCAACAGGAGCAGTTTCTGGGT
genomic: GCAGAGCAAGCGCGACACACGCCGTGAGCAGTTTCTGTCTAGGGGGCAAGgtctgatctc ... attggttcagGCAATAAGGATGCCAAATCTGCAGCTTCGCCAACAGGAGCAGTTTCTGGGT
EST: gi|211189289|gb|FL377648.1|FL377648
EST:     GCAGAGCAAGCGCGACACACGCCGTGAGCAGTTTCTGTCTAGGGGGCAAG                         GCAATAAGGATGCCAAATCTGCAGCTTCGCCAACAGGAGCAGTTTCTGGGT
genomic: GCAGAGCAAGCGCGACACACGCCGTGAGCAGTTTCTGTCTAGGGGGCAAGgtctgatctc ... attggttcagGCAATAAGGATGCCAAATCTGCAGCTTCGCCAACAGGAGCAGTTTCTGGGT
EST: gi|211094859|gb|FL386834.1|FL386834
EST:     GCAGAGCAAGCGCGACACACGCCGTGAGCAGTTTCTGTCTAGGGGGCAAG                         GCAATAAGGATGCCAAATCTGCAGCTTCGCCAACAGGAGCAGTTTCTGGGT
genomic: GCAGAGCAAGCGCGACACACGCCGTGAGCAGTTTCTGTCTAGGGGGCAAGgtctgatctc ... attggttcagGCAATAAGGATGCCAAATCTGCAGCTTCGCCAACAGGAGCAGTTTCTGGGT
EST: gi|211225982|gb|FL407836.1|FL407836
EST:     GCAGAGCAAGCGCGACACACGCCGTGAGCAGTTTCTGTCTAGGGGGCAAG                         GCAATAAGGATGCCAAATCTGCAGCTTCGCCAACAGGAGCAGTTTCTGGGT
genomic: GCAGAGCAAGCGCGACACACGCCGTGAGCAGTTTCTGTCTAGGGGGCAAGgtctgatctc ... attggttcagGCAATAAGGATGCCAAATCTGCAGCTTCGCCAACAGGAGCAGTTTCTGGGT
EST: gi|33771137|gb|CF272798.1|CF272798
EST:     GCAGAGCAAGCGCGACACACGCCGTGAGCAGTTTCTGTCTAGGGGGCAAG                         ACAATAAGGATGCCAAATCTGCAGCTTCGCCAACAGGAGCAGTTTCTGGGT
genomic: GCAGAGCAAGCGCGACACACGCCGTGAGCAGTTTCTGTCTAGGGGGCAAGgtctgatctc ... attggttcagGCAATAAGGATGCCAAATCTGCAGCTTCGCCAACAGGAGCAGTTTCTGGGT
EST: gi|86471572|gb|DY237942.1|DY237942
EST:     GCAGAGCAAGCGCGACACACGCCGTGAGCAGTTTCTGTCTAGGGGGCAAG                         GCAATAAGGATGCCAAATCTGCAGCTTCGCCAACAGGAGCAGTTTCTGGGT
genomic: GCAGAGCAAGCGCGACACACGCCGTGAGCAGTTTCTGTCTAGGGGGCAAGgtctgatctc ... attggttcagGCAATAAGGATGCCAAATCTGCAGCTTCGCCAACAGGAGCAGTTTCTGGGT
EST: gi|211458924|gb|FL402427.1|FL402427
EST:     GCAGAGCAAGCGCGACACACGCCGTGAGCAGTTTCTGTCTAGGGGGCAAG                         GCAATAAGGATGCCAAATCTGCAGCTTCGCCAACAGGAGCAGTTTCTGGGT
genomic: GCAGAGCAAGCGCGACACACGCCGTGAGCAGTTTCTGTCTAGGGGGCAAGgtctgatctc ... attggttcagGCAATAAGGATGCCAAATCTGCAGCTTCGCCAACAGGAGCAGTTTCTGGGT
EST: gi|88754727|gb|DY538868.1|DY538868
EST:     GCAGAGCAAGCGCGACACACGCCGTGAGCAGTTTCTGTCTAGGGGGCAAG                         GCAATAAGGATGCCAAATCTGCAGCTTCGCCAACAGGAGCAGTTTCTGGGT
genomic: GCAGAGCAAGCGCGACACACGCCGTGAGCAGTTTCTGTCTAGGGGGCAAGgtctgatctc ... attggttcagGCAATAAGGATGCCAAATCTGCAGCTTCGCCAACAGGAGCAGTTTCTGGGT
EST: gi|211273339|gb|FL390038.1|FL390038
EST:     GCAGAGCAAGCGCGACACACGCCGTGAGCAGTTTCTGTCTAGGGGGCAAG                         GCAATAAGGATGCCAAATCTGCAGCTTCGCCAACAGGAGCAGTTTCTGGGT
genomic: GCAGAGCAAGCGCGACACACGCCGTGAGCAGTTTCTGTCTAGGGGGCAAGgtctgatctc ... attggttcagGCAATAAGGATGCCAAATCTGCAGCTTCGCCAACAGGAGCAGTTTCTGGGT
EST: gi|40286936|gb|CK327328.1|CK327328
EST:     GCAGAGCAAGCGCGACACACGCCGTGAGCAGTTTCTGTCTAGGGGGCAAG                         GCAATAAGGATGCCAAATCTGCAGCTTCGCCAACAGGAGCAGTTTCTGGGT
genomic: GCAGAGCAAGCGCGACACACGCCGTGAGCAGTTTCTGTCTAGGGGGCAAGgtctgatctc ... attggttcagGCAATAAGGATGCCAAATCTGCAGCTTCGCCAACAGGAGCAGTTTCTGGGT
EST: gi|211111984|gb|FL388628.1|FL388628
EST:     GCAGAGCAAGCGCGACACACGCCGTGAGCAGTTTCTGTCTAGGGGGCAAG                         GCAATAAGGATGCCAAATCTGCAGCTTCGCCAACAGGAGCAGTTTCTGGGT
genomic: GCAGAGCAAGCGCGACACACGCCGTGAGCAGTTTCTGTCTAGGGGGCAAGgtctgatctc ... attggttcagGCAATAAGGATGCCAAATCTGCAGCTTCGCCAACAGGAGCAGTTTCTGGGT
EST: gi|33770932|gb|CF273226.1|CF273226
EST:     GCAGAGCAAGCGCGACACACGCCGTGAGCAGTTTCTGTCTAGGGGGCAAG                         GCAATAAGGATGCCAAATCTGCAGCTTCGCCAACAGGAGCAGTTTCTGGGT
genomic: GCAGAGCAAGCGCGACACACGCCGTGAGCAGTTTCTGTCTAGGGGGCAAGgtctgatctc ... attggttcagGCAATAAGGATGCCAAATCTGCAGCTTCGCCAACAGGAGCAGTTTCTGGGT

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: 45 (upstream exon), 48 (downstream exon)
Score: 54

GGGAGCCGCTCGGCGGCGAAGCTGAAGCAGAGCAAGCGCGACACACGCCGTGAGCAGTTTCTGTCTAGGGGGCAAGgtctgatctc ... attggttcagGCAATAAGGATGCCAAATCTGCAGCTTCGCCAACAGGAGCAGTTTCTGGGTCGCCCATACTCGCTTCCCCGCACCCTCCACTTCCTCGTCGCCGTGCTGA


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 61

GGGAGCCGCTCGGCGGCGAAGCTGAAGCAGAGCAAGCGCGACACACGCCGTGAGCAGTTTCTGTCTAGGGGGCAAGgtctgatctc ... attggttcagGCAATAAGGATGCCAAATCTGCAGCTTCGCCAACAGGAGCAGTTTCTGGGTCGCCCATACTCGCTTCCCCGCACCCTCCACTTCCTCGTCGCCGTGCTGA


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

GGGAGCCGCTCGGCGGCGAAGCTGAAGCAGAGCAAGCGCGACACACGCCGTGAGCAGTTTCTGTCTAGGGGGCAAGgtctgatctc ... attggttcagGCAATAAGGATGCCAAATCTGCAGCTTCGCCAACAGGAGCAGTTTCTGGGTCGCCCATACTCGCTTCCCCGCACCCTCCACTTCCTCGTCGCCGTGCTGA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 65

GGGAGCCGCTCGGCGGCGAAGCTGAAGCAGAGCAAGCGCGACACACGCCGTGAGCAGTTTCTGTCTAGGGGGCAAGgtctgatctc ... attggttcagGCAATAAGGATGCCAAATCTGCAGCTTCGCCAACAGGAGCAGTTTCTGGGTCGCCCATACTCGCTTCCCCGCACCCTCCACTTCCTCGTCGCCGTGCTGA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGGAGCCGCTCGGCGGCGAAGCTGAAGCAGAGCAAGCGCGACACACGCCGTGAGCAGTTTCTGTCTAGGGGGCAAGgtctgatctcatgtctggtctgtgcgatacattagtcttaatccgtgtttgtgattttggggatttctggttttcgattgacgattcggcagtggtgtgc

- - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG