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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAATTTTGAACCAGCCAACGTGCTCCTCGACAATAGATGCTCAGTGCGTGTTGCTGAATGTGGGCTGGCACAATTGATGGCGTCTGGTTCTGTTACACAGgtaacctcttcgattcagctttgccgttatcaataatacaaaattgtggctgaaagaactgaactcatagcgcatacacttcatggtgcacggatcacgg...

Basic information

species Zea mays
transcript GRMZM2G335638_T01
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G335638_T01 (Zea mays), 5'ss of exon 14
lower sequence: LOC_Os02g07960.2 (Oryza sativa), 5'ss of exon 14
GAATTTTGAACCAGCCAACGTGCTCCTCGACAATAGATGCTCAGTGCGTGTTGCTGAATGTGGGCTGGCACAATTGATGGCGTCTGGTTCTGTTACACAGgtaacctcttcgatt------cagctttgccgttatcaataatacaaaattgtggctgaaagaactgaactcatagcgcatacacttcatggtgcacggatcacgg
||||||||| |||||||| |||||||| |  ||| ||| |||||| ||||| ||||||||||| |||||| |||||| |  ||| |||||||||||||||||||| |||    ||      || | |||  ||| |  ||| | |    ||   |  | ||| | |      | |   | || | ||| ||  |  |   |     
GAATTTTGAGCCAGCCAATGTGCTCCTTGGTAATGGATTCTCAGTACGTGTCGCTGAATGTGGACTGGCAGAATTGACGCTGTCAGGTTCTGTTACACAGgtaacatctagtgttgtacaccaaccttgtggttgt-gatacttcggcttttccgtcgcaagcagttctgatacatttcctaaaattcctgaagtccaatt-----
















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|148967602|gb|EE018855.2|EE018855
EST:     TTGCTGAATGTGGGCTGGCACAATTGATGGCGTCTGGTTCTGTTACACAG                         CTATCAGGCCGTATGAGAGCTTTACTCAATTATGAAGCACCTGAAATCCAT
genomic: TTGCTGAATGTGGGCTGGCACAATTGATGGCGTCTGGTTCTGTTACACAGgtaacctctt ... tttatctcagCTATCAGGCCGTATGAGAGCTCTACTCAATTATGAAGCACCTGAAATCCAT
EST: gi|78179795|gb|DV550168.1|DV550168
EST:     TTGCTGAATGTGGGCTGGCACAATTGATGGCGTCTGGTTCTGTTACACAG                         CTATCAGGCCGTATGAGAGCTCTACTCAATTATGAAGCACCTGAAA
genomic: TTGCTGAATGTGGGCTGGCACAATTGATGGCGTCTGGTTCTGTTACACAGgtaacctctt ... tttatctcagCTATCAGGCCGTATGAGAGCTCTACTCAATTATGAAGCACCTGAAA
EST: gi|32850663|gb|CD990344.1|CD990344
EST:     TTGCTGAATGTGGGCTGGCACAATTGATGGCGTCTGGTTCTGTTACACAG                         CTATCAGGCCGTATGAGAGCTCTACTCAATTATGAAGCACCTGAAATCCAT
genomic: TTGCTGAATGTGGGCTGGCACAATTGATGGCGTCTGGTTCTGTTACACAGgtaacctctt ... tttatctcagCTATCAGGCCGTATGAGAGCTCTACTCAATTATGAAGCACCTGAAATCCAT
EST: gi|44682246|gb|CK787294.1|CK787294
EST:     TTGCTGAATGTGGGCTGGCACAATTGATGGTGTCTGGTTCTGTTACACAG                         CTATCAGGCCGTATGCGAGCTCTACTCAATTATGAAGCACCTGAAATCCAT
genomic: TTGCTGAATGTGGGCTGGCACAATTGATGGCGTCTGGTTCTGTTACACAGgtaacctctt ... tttatctcagCTATCAGGCCGTATGAGAGCTCTACTCAATTATGAAGCACCTGAAATCCAT
EST: gi|40302989|gb|CK347376.1|CK347376
EST:     TTGCTGAATGTGGGCTGGCACAATTGATGGCGTCTGGTTCTGTTACACAG                         CTATCAGGCCGTATGAGAGCTCTACTCAATTATGAAGCACCTGAAATCCAT
genomic: TTGCTGAATGTGGGCTGGCACAATTGATGGCGTCTGGTTCTGTTACACAGgtaacctctt ... tttatctcagCTATCAGGCCGTATGAGAGCTCTACTCAATTATGAAGCACCTGAAATCCAT

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: 231

GAATTTTGAACCAGCCAACGTGCTCCTCGACAATAGATGCTCAGTGCGTGTTGCTGAATGTGGGCTGGCACAATTGATGGCGTCTGGTTCTGTTACACAGgtaacctctt ... tttatctcagCTATCAGGCCGTATGAGAGCTCTACTCAATTATGAAGCACCTGAAATCCATGAATCTGAGCCTTTTACTCGTCAAAGCGACGTATATAGTTTGGGTGTGG


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 134

GAATTTTGAACCAGCCAACGTGCTCCTCGACAATAGATGCTCAGTGCGTGTTGCTGAATGTGGGCTGGCACAATTGATGGCGTCTGGTTCTGTTACACAGgtaacctctt ... tttatctcagCTATCAGGCCGTATGAGAGCTCTACTCAATTATGAAGCACCTGAAATCCATGAATCTGAGCCTTTTACTCGTCAAAGCGACGTATATAGTTTGGGTGTGG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 172

GAATTTTGAACCAGCCAACGTGCTCCTCGACAATAGATGCTCAGTGCGTGTTGCTGAATGTGGGCTGGCACAATTGATGGCGTCTGGTTCTGTTACACAGgtaacctctt ... tttatctcagCTATCAGGCCGTATGAGAGCTCTACTCAATTATGAAGCACCTGAAATCCATGAATCTGAGCCTTTTACTCGTCAAAGCGACGTATATAGTTTGGGTGTGG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 273

GAATTTTGAACCAGCCAACGTGCTCCTCGACAATAGATGCTCAGTGCGTGTTGCTGAATGTGGGCTGGCACAATTGATGGCGTCTGGTTCTGTTACACAGgtaacctctt ... tttatctcagCTATCAGGCCGTATGAGAGCTCTACTCAATTATGAAGCACCTGAAATCCATGAATCTGAGCCTTTTACTCGTCAAAGCGACGTATATAGTTTGGGTGTGG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAATTTTGAACCAGCCAACGTGCTCCTCGACAATAGATGCTCAGTGCGTGTTGCTGAATGTGGGCTGGCACAATTGATGGCGTCTGGTTCTGTTACACAGgtaacctcttcgattcagctttgccgttatcaataatacaaaattgtggctgaaagaactgaactcatagcgcatacacttcatggtgcacggatcacgg

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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaaagaac