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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgatatctgaaacctctgctcacgtgccaagtcaagcttgagaagagtgtaacattgtgaatgcctaattttttcagCTAACTATTGTTTCTGCACATCGTACACCAGAGCGGATGTATGATTATGCGAAGTCTGCTAAAGACAGGGGTTTCGAGGTCATAATTGCAGGTGCAGGCG

Basic information

species Zea mays
transcript GRMZM2G036123_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G036123_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g10280.3 (Oryza sativa), 3'ss of exon 12
gtttgatatctgaaacctct--------------------gctcacgtgccaagtcaag-cttgagaagagtgtaacattgtgaatgcctaattttttcagCTAACTATTGTTTCTGCACATCGTACACCAGAGCGGATGTATGATTATGCGAAGTCTGCTAAAGACAGGGGTTTCGAGGTCATAATTGCAGGTGCAGGCG
||||||| |||||||||  |                    | | || ||| |||||||   ||   |||  || || ||  |  |      | ||||  |||| || |||||||| || ||||||||||||||| |||||||  |||||||    ||| ||||||| || || || ||||||||||||||||||||||| |
gtttgatctctgaaacccttccattgacaagttatgaaatgtttacatgctaagtcaaaattttctaaggatgcaaaatgattgactgtcgaattttgtagCTTACAATTGTTTCGGCTCATCGTACACCAGAGAGGATGTACCATTATGCATTATCTACTAAAGAAAGAGGCTTAGAGGTCATAATTGCAGGTGCAGGTG
















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), 49 (downstream exon)
Score: 128

TTAGCCCTCGTGTTGCTATTATAATGGGGTCCCAATCTGATCTTCCTGTGATGAAAGATGCTGAGAGGGTTTTGAAAGAGTTCGACATACCTTGTGAGgtttgatatc ... attttttcagCTAACTATTGTTTCTGCACATCGTACACCAGAGCGGATGTATGATTATGCGAAGTCTGCTAAAGACAGGGGTTTCGAGGTCATAATTGCAGGTGCAGGCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 103

TTAGCCCTCGTGTTGCTATTATAATGGGGTCCCAATCTGATCTTCCTGTGATGAAAGATGCTGAGAGGGTTTTGAAAGAGTTCGACATACCTTGTGAGgtttgatatc ... attttttcagCTAACTATTGTTTCTGCACATCGTACACCAGAGCGGATGTATGATTATGCGAAGTCTGCTAAAGACAGGGGTTTCGAGGTCATAATTGCAGGTGCAGGCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 151

TTAGCCCTCGTGTTGCTATTATAATGGGGTCCCAATCTGATCTTCCTGTGATGAAAGATGCTGAGAGGGTTTTGAAAGAGTTCGACATACCTTGTGAGgtttgatatc ... attttttcagCTAACTATTGTTTCTGCACATCGTACACCAGAGCGGATGTATGATTATGCGAAGTCTGCTAAAGACAGGGGTTTCGAGGTCATAATTGCAGGTGCAGGCG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 94

TTAGCCCTCGTGTTGCTATTATAATGGGGTCCCAATCTGATCTTCCTGTGATGAAAGATGCTGAGAGGGTTTTGAAAGAGTTCGACATACCTTGTGAGgtttgatatc ... attttttcagCTAACTATTGTTTCTGCACATCGTACACCAGAGCGGATGTATGATTATGCGAAGTCTGCTAAAGACAGGGGTTTCGAGGTCATAATTGCAGGTGCAGGCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgtgccaagtcaagcttgagaagagtgtaacattgtgaatgcctaattttttcagCTAACTATTGTTTCTGCACATCGTACACCAGAGCGGATGTATGATTATGCGAAGTCTGCTAAAGACAGGGGTTTCGAGGTCATAATTGCAGGTGCAGGCG
                                        gcctaat  putative branch site (score: 94)
                                              ttttttc  CT-rich tract
                                           taattttttca  TA-rich tract