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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttttttttcctttgttctgtctttcttattttgctagcatgcccaaccatacacacttaacttggtgttccacagCCTGTGATGTTCCGGGTATCAAAAGATTACTTCCATCAGAATGGAGGGAATGGGAAATGTTTGACAATATCTACAAGTTAGATGGTGTCCCTGTTGTCAC

Basic information

species Zea mays
transcript GRMZM2G454952_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G454952_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os07g10490.1 (Oryza sativa), 3'ss of exon 9
gttttttttcctttgttctgtctttcttattttgctagcatgcccaaccatacacacttaacttggtgtt-----ccacagCCTGTGATGTTCCGGGTATCAAAAGATTACTTCCATCAGAATGGAGGGAATGGGAAATGTTTGACAATATCTACAAGTTAGATGGTGTCCCTGTTGTCAC
||| ||| || |   || |||||||         ||| || | || ||||| ||   |||| ||||  ||         ||| |||||||| ||||| ||||||||| |  | || || ||||||||| ||||||| |  |||||||| |||||||||||||||||||| ||||| |||||
gttctttctcttccattttgtctttg-------actaccacgtcctaccatgcaagattaaattggaattgttgattgtagCTTGTGATGTCCCGGGGATCAAAAGACTTTTACCTTCTGAATGGAGGCAATGGGATACATTTGACAACATCTACAAGTTAGATGGTGTTCCTGTAGTCAC

upper sequence: GRMZM2G454952_T01 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA10G30220.1 (Glycine max), 3'ss of exon 9
--------gtt-ttttttcctttgttctgtctttcttattttgctagcatgcccaaccatacacacttaacttggtgttccacagCCTGTGATGTTCCGGGTATCAAAAGATTACTTCCATCAGAATGGAGGGAATGGGAAATGTTTGACAATATCTACAAGTTAGATGGTGTCCCTGTTGTCAC
        |||  | ||| ||||  | | | || |||||| || || ||  |   |  |        | | ||         |||| |||||||| || || || || ||||||||||||||||| |||||||||  |||  | ||  | ||||||||  |  ||| ||| || ||||| |||||
gttagtaggttactctttgcttttgtatttattccttattgtgttaacaatcttcaataccttagtgtcatttacgcaatgccagCTTGTGATGTCCCTGGAATTAAGAGATTACTTCCATCAGAGTGGAGGGAACAGGAGTTTTTCAATAATATCTATGAACTAGTTGGAGTTCCTGTAGTCAC

upper sequence: GRMZM2G454952_T01 (Zea mays), 3'ss of exon 9
lower sequence: AT3G04870.2 (Arabidopsis thaliana), 3'ss of exon 9
--------------------------------------------------------------------------------------------------------------------gttttttttcctttgttctgtctttcttattttgctagcatgcccaaccatacacacttaacttggtgttccacagCCTGTGATGTTCCGGGTATCAAAAGATTACTTCCATCAGAATGGAGGGAATGGGAAATGTTTGACAATATCTACAAGTTAGATGGTGTCCCTGTTGTCAC
                                                                                                                    |  ||||||  ||| ||   |   | | |   | | | || |    |   |  |  || |  |   ||||   |||| |||||||| ||||| |||||||| |||||||||  ||||||||||||||                                                 
gtgaaatttagcttcagacgtaggattttagtggactgcgaaaatgtatacatacattctgaaggttgcagcttctgggtagagaaaaagcacaaaactttgatatgaaagtaaaggactttttttgttttttggtttgctttcagGCTACGAACAAGAA-GATTGTGAAAGCTGATGTATATGTT--GCAGCATGTGATGTGCCGGGAATCAAAAGGTTACTTCCAAAAGAATGGAGGGAATCTCGGT-------------------------------------------

upper sequence: GRMZM2G454952_T01 (Zea mays), 3'ss of exon 9
lower sequence: Vv14s0030g01740.t01 (Vitis vinifera), 3'ss of exon 9
------------------gttttttttcctttgttctgtctttcttattttgctagcatgcccaaccatacacac-ttaacttggtgtt--ccacagCCTGTGATGTTCCGGGTATCAAAAGATTACTTCCATCAGAATGGAGGGAATGGGAAATGTTTGACAATATCTACAAGTTAGATGGTGTCCCTGTTGTCAC
                   |   || | ||||||||  | |  |    |||   ||  |||  ||||    |  | |||||||    ||  | ||||| ||||||||||| || |||||||||||| ||||  || |||||||||| |||||| | ||||| ||||| || ||  ||| ||| || || ||||||||
gtttgttaataacgtttcttcaattcttctttgttccttttccccccctttttaaggttgcttaacctctaatgcattaacttccatttgactacagCTTGTGATGTTCCTGGAATCAAAAGATTAGTTCCGGCACAATGGAGGGACTGGGAATTTTTTGATAATATTTATAAACTAGTTGGGGTGCCAGTTGTCAC

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: 42 (upstream exon), 49 (downstream exon)
Score: 67

GCTACAAGTAGAGAGATAATCAAAGCTGATGCATACGTCGCAGgttttttttc ... tgttccacagCCTGTGATGTTCCGGGTATCAAAAGATTACTTCCATCAGAATGGAGGGAATGGGAAATGTTTGACAATATCTACAAGTTAGATGGTGTCCCTGTTGTCAC


Block sizes: 43 (upstream exon), 48 (downstream exon)
Score: 102

GCTACAAGTAGAGAGATAATCAAAGCTGATGCATACGTCGCAGgttttttttc ... tgttccacagCCTGTGATGTTCCGGGTATCAAAAGATTACTTCCATCAGAATGGAGGGAATGGGAAATGTTTGACAATATCTACAAGTTAGATGGTGTCCCTGTTGTCAC


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 59

GCTACAAGTAGAGAGATAATCAAAGCTGATGCATACGTCGCAGgttttttttc ... tgttccacagCCTGTGATGTTCCGGGTATCAAAAGATTACTTCCATCAGAATGGAGGGAATGGGAAATGTTTGACAATATCTACAAGTTAGATGGTGTCCCTGTTGTCAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 277

GCTACAAGTAGAGAGATAATCAAAGCTGATGCATACGTCGCAGgttttttttc ... tgttccacagCCTGTGATGTTCCGGGTATCAAAAGATTACTTCCATCAGAATGGAGGGAATGGGAAATGTTTGACAATATCTACAAGTTAGATGGTGTCCCTGTTGTCAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttcttattttgctagcatgcccaaccatacacacttaacttggtgttccacagCCTGTGATGTTCCGGGTATCAAAAGATTACTTCCATCAGAATGGAGGGAATGGGAAATGTTTGACAATATCTACAAGTTAGATGGTGTCCCTGTTGTCAC
                                  acttaac  putative branch site (score: 277)
     ttatttt  TA-rich tract