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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGTTAGTTGGAACACAGTACAAGCCAATGGAGCTGTCAAAGTCAGATTGGGCTTCAATTAGAAAATCACCCCCATGGGCCATTGATTCTTGGGGACTAGgtgagcgtaaataactcttaatggttcctcctcatgcatgacatgcttgttatggttgtacttatatatttttttttgagtaaagtacatttccggtcct...

Basic information

species Zea mays
transcript AC218972.3_FGT001
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC218972.3_FGT001 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os01g60440.1 (Oryza sativa), 5'ss of exon 6
TGGTTAGTTGGAACACAGTACAAGCCAATGGAGCTGTCAAAGTCAGATTGGGCTTCAATTAGAAAATCACCCCCATGGGCCATTGATTCTTGGGGACTAGgtgagcgtaaataactcttaatggttcctcctcatgcatgacatgcttgtt--atggttgtacttatata-tttttttttgagtaaagtacatttccggtcct-------
||||||||||||||||| || ||||||||||||||  |||||||||||||||  |||||||| |||||||| |||||||| |||||||| |||||||| ||| |||  |  ||||||          ||  || | ||| |||| ||||||  || ||| |  ||  ||| ||||    |  | ||| |      | | ||||       
TGGTTAGTTGGAACACAATATAAGCCAATGGAGCTAACAAAGTCAGATTGGGTGTCAATTAGGAAATCACCTCCATGGGCAATTGATTCCTGGGGACTGGgtaagcagagctaactc----------cttttccttcattacattcttgtttgattgttctgtttccataattttacaattcggaaactgttcaacagttccttgtcgga

upper sequence: AC218972.3_FGT001 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA20G36180.1 (Glycine max), 5'ss of exon 6
TGGTTAGTTGGAACACAGTACAAGCCAATGGAGCTGTCAAAGTCAGATTGGGCTTCAATTAGAAAATCACCCCCATGGGCCATTGATTCTTGGGGACTAGgtgagcgtaaataactcttaatggttcctcctcatgcatgacatgcttgttatggttgtacttat--atatttttttttgagtaaagtacatttccggtcct------
||| | |||||| |||| ||||| |||||||| ||| |||| || || |||||| ||||||  || || || |||||||||||||||||||||||  | |      |||  | | ||| | |  |     || ||   ||| ||  | |      | | ||  |   | ||| | || |   |  |||   | |    | ||      
TGGCTTGTTGGATCACAATACAAACCAATGGAACTGGCAAAATCTGACTGGGCTGCAATTAAGAAGTCTCCTCCATGGGCCATTGATTCTTGGGGCATGG-

upper sequence: AC218972.3_FGT001 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA09G38740.1 (Glycine max), 5'ss of exon 6
TGGTTAGTTGGAACACAGTACAAGCCAATGGAGCTGTCAAAGTCAGATTGGGCTTCAATTAGAAAATCACCCCCATGGGCCATTGATTCTTGGGGACTAGgtgagcg----taaataactcttaatggttcctcctcatgcatgacatgcttgttatggttgtacttatatatttttttttgagtaaagtac-atttccggtcct
||| | |||||| |||| ||||| ||||||||| || |||| ||||| |||| | ||||||  || || || |||||||||||||||||||||||  | |||  |      |   |  || || ||| |   || |  || ||  ||   | |||    | || |  ||| |         ||  ||  | | ||||  |   ||
TGGCTTGTTGGATCACAATACAAACCAATGGAGTTGGCAAAATCAGACTGGGATGCAATTAAGAAGTCTCCTCCATGGGCCATTGATTCTTGGGGCATGGgtatgttgttttctgttccttttgatgatagttcatagtg-atagcaaattggtttatatggtgca-atagaacac---gggaacaatctgctatttttgtgtct

upper sequence: AC218972.3_FGT001 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA18G47590.1 (Glycine max), 5'ss of exon 6
TGGTTAGTTGGAACACAGTACAAGCCAATGGAGCTGTCAAAGTCAGATTGGGCTTCAATTAGAAAATCACCCCCATGGGCCATTGATTCTTGGGGACTAGgtgagc-gtaaataactcttaatggttcctcctcatgcatgacatgcttgttatggttgtacttatatatttttttttgagtaaagtacatt--tccggtcct
||| | |||||| |||| ||||| ||||||||| || |||| ||||| |||| | ||||||  || || || ||||||||||| |||||||||||  | |||  |  ||       || |  || |      |||    ||| | ||   ||| | || || |  |  | |         | | | |   ||  |   ||   
TGGCTTGTTGGATCACAATACAAACCAATGGAGTTGGCAAAATCAGACTGGGATGCAATTAAGAAGTCTCCTCCATGGGCCATAGATTCTTGGGGCATGGgtatgttgttttctgttccttttgatgatagttcaca-gtgata-gcaaattaggtttata-tggtgcaatagaacacaggaacaatctgttatttttgtgtc

upper sequence: AC218972.3_FGT001 (Zea mays), 5'ss of exon 6
lower sequence: AT2G40730.1 (Arabidopsis thaliana), 5'ss of exon 6
TGGTTAGTTGGAACACAGTACAAGCCAATGGAGCTGTCAAAGTCAGATTGGGCTTCAATTAGAAAATCACCCCCATGGGCCATTGATTCTTGGGGACTAGgtgagcgtaaata--actcttaatggttcctcctcatgcatgacatgcttgtta----tggttgtacttatatatttttttttgagtaaagtacatttccggtcct-------
||| |||| |||||||||||||||||||||||  ||   ||||| ||||||| | | ||||| ||||| || ||||||||||||||||| |||||| ||||| |  |||  |   |  | | |    | |||       || | |||||  |      |   || ||||   |  | || ||| | |||||  | || |      |       
TGGCTAGTGGGAACACAGTACAAGCCAATGGAAATGGTCAAGTCTGATTGGGTTGCTATTAGGAAATCTCCACCATGGGCCATTGATTCGTGGGGATTAGgt-actgtagtttttatgccttactaattctcaatggagattatatgctcctcgacccttagtgcacttgagtgctattctttcactaaagccctttacttccttttttgaag

upper sequence: AC218972.3_FGT001 (Zea mays), 5'ss of exon 6
lower sequence: Vv13s0067g03110.t01 (Vitis vinifera), 5'ss of exon 6
TGGTTAGTTGGAACACAGTACAAGCCAATGGAGCTGTCAAAGTCAGATTGGGCTTCAATTAGAAAATCACCCCCATGGGCCATTGATTCTTGGGGACTAGgtgagcgtaaataactcttaatggttcctcct-catgcatgacatgcttgtt-atggttgtacttatatatttttttttgagtaaagtacatttccggtcct--------
||| | |||||  |||| ||||| ||||||||| ||  |||||| || |||||  |||| || ||||| || |||||||||||||||||||||||  | ||| ||         ||   | || |||||  |  | | ||   |     ||| || |||    ||| |||   |  ||| |  || |  |  || |  |  |        
TGGCTTGTTGGTTCACAATACAAACCAATGGAGTTGCTAAAGTCTGACTGGGCAGCAATCAGGAAATCTCCACCATGGGCCATTGATTCTTGGGGCTTGGgtaagt--------cttccactgtttccttttgtaggtatagtagatgcgttcatagtttg--ttacataaagtggtttaataaacgatctcttactattgtgcttcccc

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: 157

TGGTTAGTTGGAACACAGTACAAGCCAATGGAGCTGTCAAAGTCAGATTGGGCTTCAATTAGAAAATCACCCCCATGGGCCATTGATTCTTGGGGACTAGgtgagcgtaa ... ctcattgcagGGTGTTTAATTTATGAACTATTTTCTGGTGCAAAGCTGGCTAGAACAGAGGACCTTCGAAATACTGCTTCAATCCCAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 120

TGGTTAGTTGGAACACAGTACAAGCCAATGGAGCTGTCAAAGTCAGATTGGGCTTCAATTAGAAAATCACCCCCATGGGCCATTGATTCTTGGGGACTAGgtgagcgtaa ... ctcattgcagGGTGTTTAATTTATGAACTATTTTCTGGTGCAAAGCTGGCTAGAACAGAGGACCTTCGAAATACTGCTTCAATCCCAAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 131

TGGTTAGTTGGAACACAGTACAAGCCAATGGAGCTGTCAAAGTCAGATTGGGCTTCAATTAGAAAATCACCCCCATGGGCCATTGATTCTTGGGGACTAGgtgagcgtaa ... ctcattgcagGGTGTTTAATTTATGAACTATTTTCTGGTGCAAAGCTGGCTAGAACAGAGGACCTTCGAAATACTGCTTCAATCCCAAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 135

TGGTTAGTTGGAACACAGTACAAGCCAATGGAGCTGTCAAAGTCAGATTGGGCTTCAATTAGAAAATCACCCCCATGGGCCATTGATTCTTGGGGACTAGgtgagcgtaa ... ctcattgcagGGTGTTTAATTTATGAACTATTTTCTGGTGCAAAGCTGGCTAGAACAGAGGACCTTCGAAATACTGCTTCAATCCCAAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGTTAGTTGGAACACAGTACAAGCCAATGGAGCTGTCAAAGTCAGATTGGGCTTCAATTAGAAAATCACCCCCATGGGCCATTGATTCTTGGGGACTAGgtgagcgtaaataactcttaatggttcctcctcatgcatgacatgcttgttatggttgtacttatatatttttttttgagtaaagtacatttccggtcct

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cctcctca