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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atagttagcatgcttctaaaaagcagttattggctattcaatagttgcttagatattcctttttttcaagtactcactatgtctagaacttgacaatcagATCTCGCCACGACAAGGACTTCTCCGAGTCCGTGAATTCACATTGGCAGAGATTGAGCATTTTGTGGACCCAGAGGACAAATCACATCCAAAATTTGTTG

Basic information

species Zea mays
transcript GRMZM5G821551_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G821551_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os08g42560.1 (Oryza sativa), 3'ss of exon 3
------------------------------------------------------------------------------------atagttagc-atgcttctaaaaagcagttattggctattcaatagttgcttagatattcctttttttcaag---tactcactatgtctagaacttgacaatcagATCTCGCCACGACAAGGACTTCTCCGAGTCCGTGAATTCACATTGGCAGAGATTGAGCATTTTGTGGACCCAGAGGACAAATCACATCCAAAATTTGTTG
|||| || | |||||| | | | | | |||| | || ||| ||||| | |||| ||| | |||||||| | |||| | | || |||||||| || ||||||||||| ||||| || || |||||||||||||| || ||||||||||| |||||||| || ||||| ||||| || |||||||||||||
gtctgtgttttgatacattttgtctttgcgttctgcatttcgattatatgcttgaaggagtctagacttattgactataggtctatagctaactatgctt-----aggaaactctccactatgccatggttttttagagggttctttcttttgtgttatactcactgtttctataccatgcaaatcagATTTCTCCACGACAAGGTCTTCTACGTGTGCGTGAATTCACATTAGCCGAGATTGAGCACTTTGTGGATCCTGAGGATAAATCTCACCCAAAATTTGTTG

upper sequence: GRMZM5G821551_T02 (Zea mays), 3'ss of exon 3
lower sequence: AT1G29880.1 (Arabidopsis thaliana), 3'ss of exon 3
---atagttagcatgcttctaaaaagcagttattggctattcaatagttgcttagatattcctttttt--tcaagtactcact---atgtctagaacttgacaatcagATCTCGCCACGACAAGGACTTCTCCGAGTCCGTGAATTCACATTGGCAGAGATTGAGCATTTTGTGGACCCAGAGGACAAATCACATCCAAAATTTGTTG
|| | | | | | | | | | | ||||| | | ||| |||| ||| | | | || | || ||| | | || ||||| || || |||||||| ||||| |||| ||||||||||| |||||||||||||||| || || || || ||| | || |||||||| || || ||
gtaatgtattactttgcttgatgtatgggatgtcttcatctcaatcttctttaagaaattcttttctgcattatgtctgggttttaataagtagcatattactcgcagATATCTCCTCGACAAGGGCTTCTTAGAGTTCGTGAATTCACGCTGGCAGAGATTGAGCACTTCGTTGATCCTGAGAATAAGTCACATCCTAAGTTCTCTG
















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|31349469|gb|CD433826.1|CD433826
EST:     AAAAGCTCCCTTTTGCAGCTGCTCAAATTGGGCAAGCTTTTAGAAATTCG                         AACTCGCCACGACAAGGACTTCTCCGAGTCCGTGAATTCACATTGGCAGAG
genomic: AAAAGCTCCCTTTTGCAGCTGCTCAAATTGGGCAAGCTTTTAGAAATGAGgtttgtgttt ... tgacaatcagATCTCGCCACGACAAGGACTTCTCCGAGTCCGTGAATTCACATTGGCAGAG
EST: gi|31351285|gb|CD435642.1|CD435642
EST:     AAAAGCTCCCTTTTGCAGCTGCTCAAATTGGGCAAGCTTTTAGAAATGAG                         ATCTCGCCACGACAAGGACTTCTCCGAGTCCGTGAATTCACATTGGCAGAG
genomic: AAAAGCTCCCTTTTGCAGCTGCTCAAATTGGGCAAGCTTTTAGAAATGAGgtttgtgttt ... tgacaatcagATCTCGCCACGACAAGGACTTCTCCGAGTCCGTGAATTCACATTGGCAGAG
EST: gi|31349068|gb|CD433425.1|CD433425
EST:     AAAAGCTCCCTTTTGCAGCTGCTCAAATTGGGCAAGCTTTTAGATTTGAG                         ATCTCGCCACGACAAGGACTTCTCCGAGTCCGTGAATTCACATTGGCAGAG
genomic: AAAAGCTCCCTTTTGCAGCTGCTCAAATTGGGCAAGCTTTTAGAAATGAGgtttgtgttt ... tgacaatcagATCTCGCCACGACAAGGACTTCTCCGAGTCCGTGAATTCACATTGGCAGAG
EST: gi|31350288|gb|CD434645.1|CD434645
EST:     AAAAGCTCCCTTTTGCAGCTGCTCAAATTGGGCAAGCTTTTAGAAATGAG                         ATCTCGCCACGACAAGGACTTCTCCGAGTCCGTGAATTCACATTGGCAGAG
genomic: AAAAGCTCCCTTTTGCAGCTGCTCAAATTGGGCAAGCTTTTAGAAATGAGgtttgtgttt ... tgacaatcagATCTCGCCACGACAAGGACTTCTCCGAGTCCGTGAATTCACATTGGCAGAG

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: 102

CGCACAGGGTATTTTTGTAAACTTCAAGGATCTGTACTATTACAATGGCCAAAAGCTCCCTTTTGCAGCTGCTCAAATTGGGCAAGCTTTTAGAAATGAGgtttgtgttt ... tgacaatcagATCTCGCCACGACAAGGACTTCTCCGAGTCCGTGAATTCACATTGGCAGAGATTGAGCATTTTGTGGACCCAGAGGACAAATCACATCCAAAATTTGTTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 40

CGCACAGGGTATTTTTGTAAACTTCAAGGATCTGTACTATTACAATGGCCAAAAGCTCCCTTTTGCAGCTGCTCAAATTGGGCAAGCTTTTAGAAATGAGgtttgtgttt ... tgacaatcagATCTCGCCACGACAAGGACTTCTCCGAGTCCGTGAATTCACATTGGCAGAGATTGAGCATTTTGTGGACCCAGAGGACAAATCACATCCAAAATTTGTTG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 61

CGCACAGGGTATTTTTGTAAACTTCAAGGATCTGTACTATTACAATGGCCAAAAGCTCCCTTTTGCAGCTGCTCAAATTGGGCAAGCTTTTAGAAATGAGgtttgtgttt ... tgacaatcagATCTCGCCACGACAAGGACTTCTCCGAGTCCGTGAATTCACATTGGCAGAGATTGAGCATTTTGTGGACCCAGAGGACAAATCACATCCAAAATTTGTTG


Block sizes: 44 (upstream exon), 46 (downstream exon)
Score: 29

CGCACAGGGTATTTTTGTAAACTTCAAGGATCTGTACTATTACAATGGCCAAAAGCTCCCTTTTGCAGCTGCTCAAATTGGGCAAGCTTTTAGAAATGAGgtttgtgttt ... tgacaatcagATCTCGCCACGACAAGGACTTCTCCGAGTCCGTGAATTCACATTGGCAGAGATTGAGCATTTTGTGGACCCAGAGGACAAATCACATCCAAAATTTGTTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcttagatattcctttttttcaagtactcactatgtctagaacttgacaatcagATCTCGCCACGACAAGGACTTCTCCGAGTCCGTGAATTCACATTGGCAGAGATTGAGCATTTTGTGGACCCAGAGGACAAATCACATCCAAAATTTGTTG
       atattccttttttt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atagttagcatgcttctaaaaagcagttattggctattcaatagttgcttagatattcctttttttcaagtactcactatgtctagaacttgacaatcagATCTCGCCACGACAAGGACTTCTCCGAGTCCGTGAATTCACATTGGCAGAGATTGAGCATTTTGTGGACCCAGAGGACAAATCACATCCAAAATTTGTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - agcatgc
- - - - - - - -ctaaaaag
- - - - - - - - - - - - - - - - - - - - - agttgct