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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gccttctttgaaacagacatttcacattctggttggaacacttttgctttgatactccacttgtttttcaacactcaggagtcttctctgtccattttagGTGTTAAACAAAATGGAAGTGTATCACATTTCTTCCACAGAACATTTAAGGCTTACAACACTGGGACTAGGAAGCGTCGAAGGATAAACACTGACGATGC

Basic information

species Zea mays
transcript GRMZM2G379608_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G379608_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os06g15690.1 (Oryza sativa), 3'ss of exon 3
gccttctttgaaacagacatttcacattctggttggaacacttttgctttg-atactccacttgtttttc-------aacactcaggagtcttctctgtccattttagGTGTTAAACAAAATGGAAGTGTATCACATTTCTTCCACAGAACATTTAAGGCTTACAACACTGGGACTAGGAAGCGTCGAAGGATAAACACTGACGATGC
        ||| | ||  || |||  ||||   ||||| | | ||| |||   |||  |  |||| || |       |    |||   | ||| | | ||  ||| |||||| || ||| ||||||| |||||||| || ||||| |||||||||||||| || || ||||| |  || ||||| || | |||||||||||  |||  
--------tgacataggaatctcagtttctaactggaaaattgttgttttttgtacctctgttgtattgcttgtggtattcttcaactgacttttttttctttttcagGTGTCAAGCAAGATGGAAGCGTATCACACTTTTTCCATAGAACATTTAAGGCCTATAATACTGGAATAAGAAAGCGCCGGAAGATAAACACTGGTGATCT
















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: 44 (upstream exon), 48 (downstream exon)
Score: 131

GGAAAATCTGGAATAAAACCTCATCCGTTCATTGATGAATTCATTCCAACAGTTGAGGAAGATGAAGGCATCTGTTACACTCATCCACAGAAACTTCCAGgtacttatat ... tccattttagGTGTTAAACAAAATGGAAGTGTATCACATTTCTTCCACAGAACATTTAAGGCTTACAACACTGGGACTAGGAAGCGTCGAAGGATAAACACTGACGATGC


Block sizes: 49 (upstream exon), 41 (downstream exon)
Score: 11

GGAAAATCTGGAATAAAACCTCATCCGTTCATTGATGAATTCATTCCAACAGTTGAGGAAGATGAAGGCATCTGTTACACTCATCCACAGAAACTTCCAGgtacttatat ... tccattttagGTGTTAAACAAAATGGAAGTGTATCACATTTCTTCCACAGAACATTTAAGGCTTACAACACTGGGACTAGGAAGCGTCGAAGGATAAACACTGACGATGC


Block sizes: 46 (upstream exon), 47 (downstream exon)
Score: 35

GGAAAATCTGGAATAAAACCTCATCCGTTCATTGATGAATTCATTCCAACAGTTGAGGAAGATGAAGGCATCTGTTACACTCATCCACAGAAACTTCCAGgtacttatat ... tccattttagGTGTTAAACAAAATGGAAGTGTATCACATTTCTTCCACAGAACATTTAAGGCTTACAACACTGGGACTAGGAAGCGTCGAAGGATAAACACTGACGATGC


Block sizes: 44 (upstream exon), 43 (downstream exon)
Score: 10

GGAAAATCTGGAATAAAACCTCATCCGTTCATTGATGAATTCATTCCAACAGTTGAGGAAGATGAAGGCATCTGTTACACTCATCCACAGAAACTTCCAGgtacttatat ... tccattttagGTGTTAAACAAAATGGAAGTGTATCACATTTCTTCCACAGAACATTTAAGGCTTACAACACTGGGACTAGGAAGCGTCGAAGGATAAACACTGACGATGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctttgatactccacttgtttttcaacactcaggagtcttctctgtccattttagGTGTTAAACAAAATGGAAGTGTATCACATTTCTTCCACAGAACATTTAAGGCTTACAACACTGGGACTAGGAAGCGTCGAAGGATAAACACTGACGATGC
 ctttgat  putative branch site (score: 10)
                                    tcttctctgtccattt  putative PPT
               ttgttttt  TA-rich tract