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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGGCGCCGCAGAACGACCGGGTTCTCGTCCGTCTTGAGCAGATCCCTGAGgtctctccgctatcaatcgtgtctccactccaatacgcatggattgagacggatacgagtgtagccgtataaagcctaagtgctgtagttactctgactt...

Basic information

species Zea mays
transcript GRMZM2G050961_T02
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G050961_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os10g41710.1 (Oryza sativa), 5'ss of exon 2
GTGGCGCCGCAGAACGACCGGGTTCTCGTCCGTCTTGAGCAGATCCCTGAGgtctctccgctatcaatcgtgtctccactccaatacgcatggattg-agacggatacgagtgtagccgtataaagcctaagtgctgtagttactctgactt-
||||||||||||  ||||||||| |||||||| || || ||||| |||||||| |||| |   || || |  || | |  ||  |     ||   || |     ||  |   ||    | ||      ||| |||| |||  | | |   |  
GTGGCGCCGCAGTCCGACCGGGTGCTCGTCCGCCTCGAACAGATTCCTGAGgtatctc-gtgctccattgcctcgcaatgccctttaatttgctctgcattttaatttgttagttcaagcatttcagttaattgct-tagccattgtctgtgg
















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|13558469|gb|BG549825.1|BG549825
EST:     TGGCGCCGCAGAACGACCGGGTTCTCGTCCGTCTTGAGCAGATCCCTGAG                         AAATCTGCTGGCGGTGTATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGA
genomic: TGGCGCCGCAGAACGACCGGGTTCTCGTCCGTCTTGAGCAGATCCCTGAGgtctctccgc ... attcatgcagAAATCTGCTGGCGGTGTATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGA
EST: gi|13558000|gb|BG549356.1|BG549356
EST:     AGAACGACCGGGTTCTCGTCCGTCTTGAGCAGATCCCTGAG                         AAATCTGCTGGCGGTGTATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGA
genomic: AGAACGACCGGGTTCTCGTCCGTCTTGAGCAGATCCCTGAGgtctctccgc ... attcatgcagAAATCTGCTGGCGGTGTATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGA
EST: gi|148943634|gb|EC888698.2|EC888698
EST:     TGGCGCCGCAGAACGACCGGGTTCTCGTCCGTCTTGAGCAGATCCCTGAG                         AAATCTGCTGGCGGTGTATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGA
genomic: TGGCGCCGCAGAACGACCGGGTTCTCGTCCGTCTTGAGCAGATCCCTGAGgtctctccgc ... attcatgcagAAATCTGCTGGCGGTGTATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGA
EST: gi|211482968|gb|FK973427.1|FK973427
EST:     TGGCGCCGCAGAACGACCGGGTTCTCGTCCGTCTTGAGCAGATCCCTGAG                         AAATCTGCTGGCGGTGTATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGA
genomic: TGGCGCCGCAGAACGACCGGGTTCTCGTCCGTCTTGAGCAGATCCCTGAGgtctctccgc ... attcatgcagAAATCTGCTGGCGGTGTATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGA
EST: gi|15198996|gb|BI423600.1|BI423600
EST:     TGGCGCCGCAGAACGACCGGGTTCTCGTCCGTCTTGAGCAGATCCCTGAG                         AAATCTGCTGGCGGTGTGTTGCTACCAAAATCTGCTGTTAAGTTTGAGAGA
genomic: TGGCGCCGCAGAACGACCGGGTTCTCGTCCGTCTTGAGCAGATCCCTGAGgtctctccgc ... attcatgcagAAATCTGCTGGCGGTGTATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGA
EST: gi|13558001|gb|BG549357.1|BG549357
EST:     TGGCGCCGCAGAACGACCGGGTTCTCGTCCGTCTTGAGCAGATCCCTGAG                         AAATCTGCTGGCGGT
genomic: TGGCGCCGCAGAACGACCGGGTTCTCGTCCGTCTTGAGCAGATCCCTGAGgtctctccgc ... attcatgcagAAATCTGCTGGCGGT
EST: gi|148943633|gb|EC888697.2|EC888697
EST:     TGGCGCCGCAGAACGACCGGGTTCTCGTCCGTCTTGAGCAGATCCCTGAG                         AAATCTGCTGGCGGTGTATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGA
genomic: TGGCGCCGCAGAACGACCGGGTTCTCGTCCGTCTTGAGCAGATCCCTGAGgtctctccgc ... attcatgcagAAATCTGCTGGCGGTGTATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGA
EST: gi|211485846|gb|FK973438.1|FK973438
EST:     TGGCGCCGCAGAACGACCGGGTTCTCGTCCGTCTTGAGCAGATCCCTGAG                         AAATCTGCTGGCGGNGTATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGA
genomic: TGGCGCCGCAGAACGACCGGGTTCTCGTCCGTCTTGAGCAGATCCCTGAGgtctctccgc ... attcatgcagAAATCTGCTGGCGGTGTATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGA
EST: gi|29577011|gb|CB617123.1|CB617123
EST:     TGGCGCCGCAGAACGACCGGGTTCTCGTCCGTCTTGAGCAGATCCCTGAG                         AAATCTGCTGGCGGTGTATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGA
genomic: TGGCGCCGCAGAACGACCGGGTTCTCGTCCGTCTTGAGCAGATCCCTGAGgtctctccgc ... attcatgcagAAATCTGCTGGCGGTGTATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGA
EST: gi|211061029|gb|FL204116.1|FL204116
EST:     TGGCGCCGCAGAACGACCGGGTTCTCGTCCGTCTTGAGCAGATCCCTGAG                         AAATCTGCTGGCGGTGTATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGA
genomic: TGGCGCCGCAGAACGACCGGGTTCTCGTCCGTCTTGAGCAGATCCCTGAGgtctctccgc ... attcatgcagAAATCTGCTGGCGGTGTATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGA
EST: gi|6342692|gb|AW165516.1|AW165516
EST:     CCGTCTTGAGCAGATCCCTGAG                         AAATCTGCTGGCGGTGTATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGA
genomic: CCGTCTTGAGCAGATCCCTGAGgtctctccgc ... attcatgcagAAATCTGCTGGCGGTGTATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGA
EST: gi|29167933|gb|CB411193.1|CB411193
EST:     TGGCGCCGCAGAACGACCGGGTTCTCGTCCGTCTTGAGCAGATCCCTGAG                         AAATCTGCTGGCGGTGTATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGA
genomic: TGGCGCCGCAGAACGACCGGGTTCTCGTCCGTCTTGAGCAGATCCCTGAGgtctctccgc ... attcatgcagAAATCTGCTGGCGGTGTATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGA
EST: gi|15499585|gb|BI596098.1|BI596098
EST:     TCTCGTCCGTCTTGAGCAGATCCCTGAG                         AAATCTGCTGGCGGTGTGTTGCTACCAAAATCTGCTGTTAAGTTTGAGAGA
genomic: TCTCGTCCGTCTTGAGCAGATCCCTGAGgtctctccgc ... attcatgcagAAATCTGCTGGCGGTGTATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGA
EST: gi|19058714|gb|BM737381.1|BM737381
EST:     TGGCGCCGCAGAACGACCGGGTTCTCGTCCGTCTTGAGCAGATCCCTGAG                         AAATCTGCTGGCGGTGTGTTGCTACCAAAATCTGCTGTTAAGTTTGAGAGA
genomic: TGGCGCCGCAGAACGACCGGGTTCTCGTCCGTCTTGAGCAGATCCCTGAGgtctctccgc ... attcatgcagAAATCTGCTGGCGGTGTATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGA
EST: gi|13382241|gb|BG458916.1|BG458916
EST:     TGGCGCCGCAGAACGACCGGGTTCTCGTCCGTCTTGAGCAGATCCCTGAG                         AAATCTGCTGGCGGTGTATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGA
genomic: TGGCGCCGCAGAACGACCGGGTTCTCGTCCGTCTTGAGCAGATCCCTGAGgtctctccgc ... attcatgcagAAATCTGCTGGCGGTGTATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGA
EST: gi|161588442|gb|EY958454.1|EY958454
EST:     CGGGTTCTCGTCCGTCTTGAGCAGATCCCTGAG                         AAATCTGCTGGCGGTGTGTTGCTACCAAAATCTGCTGTTAAGTTTGAGAGA
genomic: CGGGTTCTCGTCCGTCTTGAGCAGATCCCTGAGgtctctccgc ... attcatgcagAAATCTGCTGGCGGTGTATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGA
EST: gi|29947167|gb|CB816515.1|CB816515
EST:     TGGCGCCGCAGAACGACCGGGTTCTCGTCCGTCTTGAGCAGATCCCTGAG                         AAATCTGCTGGCGGTGTATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGA
genomic: TGGCGCCGCAGAACGACCGGGTTCTCGTCCGTCTTGAGCAGATCCCTGAGgtctctccgc ... attcatgcagAAATCTGCTGGCGGTGTATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGA
EST: gi|13382242|gb|BG458917.1|BG458917
EST:     TGGCGCCGCAGAACGACCGGGTTCTCGTCCGTCTTGAGCAGATCCCTGAG                         AAATCTGCTGGCGGTGTATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGA
genomic: TGGCGCCGCAGAACGACCGGGTTCTCGTCCGTCTTGAGCAGATCCCTGAGgtctctccgc ... attcatgcagAAATCTGCTGGCGGTGTATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGA
EST: gi|211058063|gb|FL204109.1|FL204109
EST:     TGGCGCCGCAGAACGACCGGGTTCTCGTCCGTCTTGAGCAGATCCCTGAG                         AAATCTGCTGGCGGTGTATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGA
genomic: TGGCGCCGCAGAACGACCGGGTTCTCGTCCGTCTTGAGCAGATCCCTGAGgtctctccgc ... attcatgcagAAATCTGCTGGCGGTGTATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGA
EST: gi|32849976|gb|CD989657.1|CD989657
EST:     TGGCGCCGCAGAACGACCGGGTTCTCGTCCGTCTTGAGCAGATCCCTGAG                         AAATCTGCTGGCGGTGTGTTGCTACCAAAATCTGCTGTTAAGTTTGAGAGA
genomic: TGGCGCCGCAGAACGACCGGGTTCTCGTCCGTCTTGAGCAGATCCCTGAGgtctctccgc ... attcatgcagAAATCTGCTGGCGGTGTATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGA
EST: gi|13558470|gb|BG549826.1|BG549826
EST:     TGGCGCCGCAGAACGACCGGGTTCTCGTCCGTCTTGAGCAGATCCCTGAG                         AAATCTGCTGGCGGTGTATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGA
genomic: TGGCGCCGCAGAACGACCGGGTTCTCGTCCGTCTTGAGCAGATCCCTGAGgtctctccgc ... attcatgcagAAATCTGCTGGCGGTGTATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGA
EST: gi|13237244|gb|BG355258.1|BG355258
EST:     TGGCGCCGCAGAACGACCGGGTTCTCGTCCGTCTTGAGCAGATCCCTGAG                         AAATCTGCTGGCGGTGTATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGA
genomic: TGGCGCCGCAGAACGACCGGGTTCTCGTCCGTCTTGAGCAGATCCCTGAGgtctctccgc ... attcatgcagAAATCTGCTGGCGGTGTATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGA
EST: gi|29544990|gb|CB605168.1|CB605168
EST:     TGGCGCCGCAGAACGACCGGGTTCTCGTCCGTCTTGAGCAGATCCCTGAG                         AAATCTGCTGGCGGTGTATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGA
genomic: TGGCGCCGCAGAACGACCGGGTTCTCGTCCGTCTTGAGCAGATCCCTGAGgtctctccgc ... attcatgcagAAATCTGCTGGCGGTGTATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGA
EST: gi|26559456|gb|CA831691.1|CA831691
EST:     TGGCGCCGCAGAACGACCGGGTTCTCGTCCGTCTTGAGCAGATCCCTGAG                         AAATCTGCTGGCGGTGTATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGA
genomic: TGGCGCCGCAGAACGACCGGGTTCTCGTCCGTCTTGAGCAGATCCCTGAGgtctctccgc ... attcatgcagAAATCTGCTGGCGGTGTATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGA

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: 344

GTGGCGCCGCAGAACGACCGGGTTCTCGTCCGTCTTGAGCAGATCCCTGAGgtctctccgc ... attcatgcagAAATCTGCTGGCGGTGTATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGATATCTGATGGGTGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 823

GTGGCGCCGCAGAACGACCGGGTTCTCGTCCGTCTTGAGCAGATCCCTGAGgtctctccgc ... attcatgcagAAATCTGCTGGCGGTGTATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGATATCTGATGGGTGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 248

GTGGCGCCGCAGAACGACCGGGTTCTCGTCCGTCTTGAGCAGATCCCTGAGgtctctccgc ... attcatgcagAAATCTGCTGGCGGTGTATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGATATCTGATGGGTGAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 411

GTGGCGCCGCAGAACGACCGGGTTCTCGTCCGTCTTGAGCAGATCCCTGAGgtctctccgc ... attcatgcagAAATCTGCTGGCGGTGTATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGATATCTGATGGGTGAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGGCGCCGCAGAACGACCGGGTTCTCGTCCGTCTTGAGCAGATCCCTGAGgtctctccgctatcaatcgtgtctccactccaatacgcatggattgagacggatacgagtgtagccgtataaagcctaagtgctgtagttactctgactt

- - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - GCAGAT