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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTGAGAACAAATACATGGATGAAGCACGGAACTATCGAAGAGATGGCTATCTGCAGACCTTGTTGCATGCACTTATCATTTGGATATGTTCTGTTGCTTgtaagacaactagccagttgacattccattccctgtatacaatctttcctatggatttacaagatatacatgaaagtcttcttcatttcccttaattgtg...

Basic information

species Zea mays
transcript GRMZM2G151236_T03
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G151236_T03 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os12g44330.1 (Oryza sativa), 5'ss of exon 12
TCTGAGAACA-AATACATGGATGAAGCACGGAACTATCGAAGAGATGGCTATCT-GCAGACCTTGTTGCATGCACTTATCATTTGGATATGTTCTGTTGCTTgtaagacaactagccagttgacattccattccctgtatacaatctttcctatggatttacaagatatac--atgaaagtcttcttcatttcccttaattgtg
  ||||| || | ||  |||  ||||| ||||| ||| |||||||||||| |||  ||||||||| |||||||| |||||||||||||||||||||||||||||||||||||| ||||| || |||| |||| |||||||||| |||||||||||||||| ||||||||||  |||| | |  |||||||||  || ||  |  
--TGAGATCAGAGTATGTGGGCGAAGCTCGGAAATATGGAAGAGATGGCTGTCTTACAGACCTTGGTGCATGCAGTTATCATTTGGATATGTTCTGTTGCTTgtaagacaactggccagctggcatttcattacctgtatacattctttcctatggatttgcaagatatacacatgatatttctcttcattttgctcaacag--
















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|87155341|gb|DY400130.1|DY400130
EST:     TCTGCAGACCTTGTTGCATGCACTTATCATTTGGATATGTTCTGTTGCTT                         GATTCTGCCAGGGCCTCTGCTGTGTGTACACTTTATATGCTTAAGCGCCAA
genomic: TCTGCAGACCTTGTTGCATGCACTTATCATTTGGATATGTTCTGTTGCTTgtaagacaac ... ttccattcagGATTCTGCCAGGGCCTCTGCTGTGTGTACACTTTATATGCTTAAGCGCCAA
EST: gi|32802193|gb|CD954429.1|CD954429
EST:     TCTGCAGACCTTGTTGCATGCACTTATCATTTGGATATGTTCTGTTGCTT                         GATTCTGCCAGGTCCTCTGCTGTGTGTACACTTTATATGCTTA
genomic: TCTGCAGACCTTGTTGCATGCACTTATCATTTGGATATGTTCTGTTGCTTgtaagacaac ... ttccattcagGATTCTGCCAGGGCCTCTGCTGTGTGTACACTTTATATGCTTA
EST: gi|32804525|gb|CD956761.1|CD956761
EST:     TCTGCAGACCTTGTTGCATGCACTTATCATTTGGATATGTTCTGTTGCTT                         GATTCTGCCAGGTCCTCTGCTGTGTGTACACTTTATATACTTA
genomic: TCTGCAGACCTTGTTGCATGCACTTATCATTTGGATATGTTCTGTTGCTTgtaagacaac ... ttccattcagGATTCTGCCAGGGCCTCTGCTGTGTGTACACTTTATATGCTTA
EST: gi|32802413|gb|CD954649.1|CD954649
EST:     TCTGCAGACCTTGTTGCATGCACTTATCATTTGGATATGTTCTGTTGCTT                         GATTCTGCCAGGTACTCTGCTGTGTGTACACTTTATATGCTTA
genomic: TCTGCAGACCTTGTTGCATGCACTTATCATTTGGATATGTTCTGTTGCTTgtaagacaac ... ttccattcagGATTCTGCCAGGGCCTCTGCTGTGTGTACACTTTATATGCTTA
EST: gi|9731581|gb|BE510333.1|BE510333
EST:     TCTGCAGACCTTGTTGCATGCACTTATCATTTGGATATGTTCTGTTGCTT                         GATTCTGCCAGGGCCTCTGCTGTGTGTACACTTTATATGCTTAAGCGCCAA
genomic: TCTGCAGACCTTGTTGCATGCACTTATCATTTGGATATGTTCTGTTGCTTgtaagacaac ... ttccattcagGATTCTGCCAGGGCCTCTGCTGTGTGTACACTTTATATGCTTAAGCGCCAA

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: 48 (upstream exon), 49 (downstream exon)
Score: 129

TCTGAGAACAAATACATGGATGAAGCACGGAACTATCGAAGAGATGGCTATCTGCAGACCTTGTTGCATGCACTTATCATTTGGATATGTTCTGTTGCTTgtaagacaac ... ttccattcagGATTCTGCCAGGGCCTCTGCTGTGTGTACACTTTATATGCTTAAGCGCCAACATTTGAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 83

TCTGAGAACAAATACATGGATGAAGCACGGAACTATCGAAGAGATGGCTATCTGCAGACCTTGTTGCATGCACTTATCATTTGGATATGTTCTGTTGCTTgtaagacaac ... ttccattcagGATTCTGCCAGGGCCTCTGCTGTGTGTACACTTTATATGCTTAAGCGCCAACATTTGAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 108

TCTGAGAACAAATACATGGATGAAGCACGGAACTATCGAAGAGATGGCTATCTGCAGACCTTGTTGCATGCACTTATCATTTGGATATGTTCTGTTGCTTgtaagacaac ... ttccattcagGATTCTGCCAGGGCCTCTGCTGTGTGTACACTTTATATGCTTAAGCGCCAACATTTGAAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 84

TCTGAGAACAAATACATGGATGAAGCACGGAACTATCGAAGAGATGGCTATCTGCAGACCTTGTTGCATGCACTTATCATTTGGATATGTTCTGTTGCTTgtaagacaac ... ttccattcagGATTCTGCCAGGGCCTCTGCTGTGTGTACACTTTATATGCTTAAGCGCCAACATTTGAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTGAGAACAAATACATGGATGAAGCACGGAACTATCGAAGAGATGGCTATCTGCAGACCTTGTTGCATGCACTTATCATTTGGATATGTTCTGTTGCTTgtaagacaactagccagttgacattccattccctgtatacaatctttcctatggatttacaagatatacatgaaagtcttcttcatttcccttaattgtg

- - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG