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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAATCTTCATATATTGGTGGTTTGAAGTCCATTGAGGAGTTCCATCATATTGAGATTCCTCCTAATGCTCCACCGGCGATCGATGAAGAGATGCTAGAGgtaataaactagtagtcttaatgctagctgttttctgtgaattaagtggatttaatatggcagccactgtagattctgtgtcatcttgctacctgttagt...

Basic information

species Zea mays
transcript GRMZM2G403149_T01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G403149_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os01g27730.1 (Oryza sativa), 5'ss of exon 8
TGAATCTTCATATATTGGTGGTTTGAAGTCCATTGAGGAGTTCCATCATATTGAGATTCCTCCTAATGCTCCACCGGCGATCGATGAAGAGATGCTAGAGgtaataaactagtagtcttaatgct--agctgttttctgtgaatta--agtggatttaatatggcagccactgtagattctgtgtcatcttgctacctgttagt-----------------------------------------------------
||| || ||||||||||||||| |||| ||  | |||||||||| ||| |||||||||||  ||||||| ||||||  ||| || |||||||||||||||||| ||   | ||  || |     |  |  |  | ||| |   |||   |||   ||   ||| ||       |||     |  |   | |  |     | |                                                       
TGAGTCATCATATATTGGTGGTCTGAAATCACTGGAGGAGTTCCGTCACATTGAGATTCCATCTAATGCCCCACCGCAGATTGACGAAGAGATGCTAGAGgtattactatggttttcgtcccattgaaaataatctctattctttatgggtgtgatttgcatgacatttgtgctaggaataggattgccatagttggcatcatcgatgagtcatgacactgcaattagataatgtacttgtcttgtgcttgatatag
















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|71432455|gb|DR813505.1|DR813505
EST:     TTGAGATTCCTCCTAATGCTCCACCGGCGATCGATGAAGAGATGCTAGAG                         GATGGTGGCAAGAAACCAAGCGAAGCCATCCAGGAAAGCCGGGACAGGGAG
genomic: TTGAGATTCCTCCTAATGCTCCACCGGCGATCGATGAAGAGATGCTAGAGgtaataaact ... cttaaaccagGATGGTGGCAAGAAACCAAGCGAAGCCATCCAGGAAAGCCGGGACAGGGAG
EST: gi|60343046|gb|DN210019.1|DN210019
EST:     TTGAGATTCCTCCTAATGCTCCACCGGCGATCGATGAAGAGATGCTAGAG                         GATGGTGGCAAGAAACCAAGCGAAGCCATCCAGGAAAGCCGGGACAGGGAG
genomic: TTGAGATTCCTCCTAATGCTCCACCGGCGATCGATGAAGAGATGCTAGAGgtaataaact ... cttaaaccagGATGGTGGCAAGAAACCAAGCGAAGCCATCCAGGAAAGCCGGGACAGGGAG
EST: gi|60399377|gb|DN232191.1|DN232191
EST:     TTGAGATTCCTCCTAATGCTCCACTGGCGATCGATGAAGAGATGCTAGAG                         GATGGTGGCAAGAAACCAAGCGAAGCCATCCAGGAAAGCCGGGACAGGGAG
genomic: TTGAGATTCCTCCTAATGCTCCACCGGCGATCGATGAAGAGATGCTAGAGgtaataaact ... cttaaaccagGATGGTGGCAAGAAACCAAGCGAAGCCATCCAGGAAAGCCGGGACAGGGAG
EST: gi|6012306|gb|AW061662.1|AW061662
EST:     ACCGGCGATCGATGAAGAGATGCTAGAG                         GATGGTGGCAAGAAACCAAGCGAAGCCATCCAGGAAAGCCGGGACAGGGAG
genomic: ACCGGCGATCGATGAAGAGATGCTAGAGgtaataaact ... cttaaaccagGATGGTGGCAAGAAACCAAGCGAAGCCATCCAGGAAAGCCGGGACAGGGAG
EST: gi|113674501|gb|DW828662.1|DW828662
EST:     TTGAGATTCCTCCTAATGCTCCACCGGCGATCGATGAAGAGATGCTAGAG                         GATGGTGGCAAGAAACCAAGCG
genomic: TTGAGATTCCTCCTAATGCTCCACCGGCGATCGATGAAGAGATGCTAGAGgtaataaact ... cttaaaccagGATGGTGGCAAGAAACCAAGCG

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), 48 (downstream exon)
Score: 122

TGAATCTTCATATATTGGTGGTTTGAAGTCCATTGAGGAGTTCCATCATATTGAGATTCCTCCTAATGCTCCACCGGCGATCGATGAAGAGATGCTAGAGgtaataaact ... cttaaaccagGATGGTGGCAAGAAACCAAGCGAAGCCATCCAGGAAAGCCGGGACAGGGAGGAGCAAATGCCCGACGTGAAGGACTCAGGAGGAAGCAAGGCAGCCAGCG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 85

TGAATCTTCATATATTGGTGGTTTGAAGTCCATTGAGGAGTTCCATCATATTGAGATTCCTCCTAATGCTCCACCGGCGATCGATGAAGAGATGCTAGAGgtaataaact ... cttaaaccagGATGGTGGCAAGAAACCAAGCGAAGCCATCCAGGAAAGCCGGGACAGGGAGGAGCAAATGCCCGACGTGAAGGACTCAGGAGGAAGCAAGGCAGCCAGCG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 112

TGAATCTTCATATATTGGTGGTTTGAAGTCCATTGAGGAGTTCCATCATATTGAGATTCCTCCTAATGCTCCACCGGCGATCGATGAAGAGATGCTAGAGgtaataaact ... cttaaaccagGATGGTGGCAAGAAACCAAGCGAAGCCATCCAGGAAAGCCGGGACAGGGAGGAGCAAATGCCCGACGTGAAGGACTCAGGAGGAAGCAAGGCAGCCAGCG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 90

TGAATCTTCATATATTGGTGGTTTGAAGTCCATTGAGGAGTTCCATCATATTGAGATTCCTCCTAATGCTCCACCGGCGATCGATGAAGAGATGCTAGAGgtaataaact ... cttaaaccagGATGGTGGCAAGAAACCAAGCGAAGCCATCCAGGAAAGCCGGGACAGGGAGGAGCAAATGCCCGACGTGAAGGACTCAGGAGGAAGCAAGGCAGCCAGCG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGAATCTTCATATATTGGTGGTTTGAAGTCCATTGAGGAGTTCCATCATATTGAGATTCCTCCTAATGCTCCACCGGCGATCGATGAAGAGATGCTAGAGgtaataaactagtagtcttaatgctagctgttttctgtgaattaagtggatttaatatggcagccactgtagattctgtgtcatcttgctacctgttagt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG