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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactttgagttgcttttacttggctaatatgatttggtatcttttgctgtcctatttgatactgctcctttgttgtcacagGTGTATTCTGGAAATCCTATGGCCATAGATGGATGTGCTACTTTTTTTCGTAGAGACAAGTTTTCACATGTTAAAAAATACGAG

Basic information

species Zea mays
transcript GRMZM2G118467_T04
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G118467_T03 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA03G36550.1 (Glycine max), 3'ss of exon 3
--------gtaactttgagttgcttttacttggctaatatgatttggtatcttttgctgtcctatttgatactgctcctttgttgtcacagGTGTATTCTGGAAATCCTATGGCCATAGATGGATGTGCTACTTTTTTTCGTAGAGACAAGTTTTCACATGTTAAAAAATACGAG
           | |  || ||  | |   ||   |   || ||||  ||  | ||  | |  |  || |      |    ||   |||||||| ||   ||||||   ||   | || ||||| ||||| || ||||| ||||||||||  ||||||||||| |||||||| |||
gttgttacagtattcagatttattatagttttagtctcataatttt-taaatgttattttttttgttaagcggtttatggtgggttcacagGTATACAATGGAAACATTAATACAATTGATGGGTGTGCAACATTTTTCCGTAGAGACAGATTTTCACATGTGAAAAAATATGAG

upper sequence: GRMZM2G118467_T03 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA09G15980.2 (Glycine max), 3'ss of exon 3
gtaactttgagttgcttttacttggctaatatgatttggtatcttttgc-tgtcctatttgata--ctgctcctt-tgttgtcacagGTGTATTCTGGAAATCCTATGGCCATAGATGGATGTGCTACTTTTTTTCGTAGAGACAAGTTTTCACATGTTAAAAAATACGAG
          |||||  |    |||    | ||||     |  |||    | |  ||  || ||  ||| |  || ||   | |||||||||   ||| ||  | |   | || ||||| ||||| || ||||| ||||||||||  |||||||||||||| |||||||||
-------gttgttgcaatattctggtccttgtgatcataaacttttaaagtattttagatgctaacctgtttattatgggtttacagGTGTACAGTGGCAACACAAATACAATTGATGGGTGTGCAACATTTTTCCGTAGAGACAGATTTTCACATGTTAAGAAATACGAG

upper sequence: GRMZM2G118467_T03 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA02G26620.1 (Glycine max), 3'ss of exon 3
gtaactttgagttgcttttacttg-gctaatatgatttggtatcttttgctgtcctatttgatactgctcctttgttgtcacagGTGTATTCTGGAAATCCTATGGCCATAGATGGATGTGCTACTTTTTTTCGTAGAGACAAGTTTTCACATGTTAAAAAATACGAG
||   |   |  | ||  | |||| | | |||   |||   |   ||     |  ||     |  |  |      ||   |||||||||   ||| ||  | |   | || ||||| ||||| || ||||| ||||||||||  |||||||||||||| ||||| |||
gttgttgcaatattctggttcttgtgatcataaactttaaaaatattctagatggtaacctgt-ttattgtgggtttacaacagGTGTACAGTGGCAACACAAATACAATTGATGGGTGTGCAACATTTTTCCGTAGAGACAGATTTTCACATGTTAAGAAATATGAG

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: 228

GTACAAGTAAACCATTTCGAAGATTTTTTTTCACCTGAGCTTGACAAACATGGATATCAGGCGCTTTACAAGAAAAGGACAACAGAGgtaactttga ... gttgtcacagGTGTATTCTGGAAATCCTATGGCCATAGATGGATGTGCTACTTTTTTTCGTAGAGACAAGTTTTCACATGTTAAAAAATACGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 150

GTACAAGTAAACCATTTCGAAGATTTTTTTTCACCTGAGCTTGACAAACATGGATATCAGGCGCTTTACAAGAAAAGGACAACAGAGgtaactttga ... gttgtcacagGTGTATTCTGGAAATCCTATGGCCATAGATGGATGTGCTACTTTTTTTCGTAGAGACAAGTTTTCACATGTTAAAAAATACGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 197

GTACAAGTAAACCATTTCGAAGATTTTTTTTCACCTGAGCTTGACAAACATGGATATCAGGCGCTTTACAAGAAAAGGACAACAGAGgtaactttga ... gttgtcacagGTGTATTCTGGAAATCCTATGGCCATAGATGGATGTGCTACTTTTTTTCGTAGAGACAAGTTTTCACATGTTAAAAAATACGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 119

GTACAAGTAAACCATTTCGAAGATTTTTTTTCACCTGAGCTTGACAAACATGGATATCAGGCGCTTTACAAGAAAAGGACAACAGAGgtaactttga ... gttgtcacagGTGTATTCTGGAAATCCTATGGCCATAGATGGATGTGCTACTTTTTTTCGTAGAGACAAGTTTTCACATGTTAAAAAATACGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatgatttggtatcttttgctgtcctatttgatactgctcctttgttgtcacagGTGTATTCTGGAAATCCTATGGCCATAGATGGATGTGCTACTTTTTTTCGTAGAGACAAGTTTTCACATGTTAAAAAATACGAG
                                      ctcctttgtt  CT-rich tract
                          tatttgata  TA-rich tract