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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctcttaaatttggtgacatatttttttctttatttcaataaatatagtgttctcttgtctcccaatactgaatttctttagtctgtggatccttacacagCATGGCCGTGGAGAAGTATCCAAACAACAGAATGCTTGGCCATCGTGAGATTGTTGATGGGAAG

Basic information

species Zea mays
transcript GRMZM2G002614_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G002614_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g46750.2 (Oryza sativa), 3'ss of exon 1
-----------ctcttaaatttggtgacatatttttt------tctttatttcaataaatatagtgttctcttg----tctcccaatactgaatttctttagtctgtggatccttacacagCATGGCCGTGGAGAAGTATCCAAACAACAGAATGCTTGGCCATCGTGAGATTGTTGATGGGAAG
              ||  | ||| || | |   || |      |||| | || ||| |   |  | | ||  ||    ||||  | | ||  |||||   | | | ||  | |||   ||| ||||||||||||||||  ||| |||||||||||||||| || |||||||||||||| ||||||
gtttgtcctttgcattctagttgctggcctgaattctgtcaattcttcaatttaatgacccttttctcctactgagcttctctaatttcttgatttcgacaatgtctg--ttcttgtgcagAATGGCCGTGGAGAAGTTCCCAGACAACAGAATGCTTGGTCACCGTGAGATTGTTGACGGGAAG

upper sequence: GRMZM2G002614_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g46750.3 (Oryza sativa), 3'ss of exon 1
ctcttaaatttggtgacatatttttttctttatttcaataaatatagtgttctcttg----tctcccaatactgaatttctttagtctgtggatccttacacagCATGGCCGTGGAGAAGTATCCAAACAACAGAATGCTTGGCCATCGTGAGATTGTTGATGGGAAG
 |        ||   |     |   ||||| | || ||| |   |  | | ||  ||    ||||  | | ||  |||||   | | | ||  | |||   ||| ||||||||||||||||  ||| |||||||||||||||| || |||||||||||||| ||||||
gttgctggcctga--attctgtcaattcttcaatttaatgacccttttctcctactgagcttctctaatttcttgatttcgacaatgtctg--ttcttgtgcagAATGGCCGTGGAGAAGTTCCCAGACAACAGAATGCTTGGTCACCGTGAGATTGTTGACGGGAAG
















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: 181

ATGGCCGGCCATCCGTGGGGCCCACCTACCGGAGCGCCTTCGCCCGCGACGGATTCCCGCCGCCCGTCCCCGGGATGGACAGCTGCTACGACATCTTCCGgtgagctctc ... ccttacacagCATGGCCGTGGAGAAGTATCCAAACAACAGAATGCTTGGCCATCGTGAGATTGTTGATGGGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 333

ATGGCCGGCCATCCGTGGGGCCCACCTACCGGAGCGCCTTCGCCCGCGACGGATTCCCGCCGCCCGTCCCCGGGATGGACAGCTGCTACGACATCTTCCGgtgagctctc ... ccttacacagCATGGCCGTGGAGAAGTATCCAAACAACAGAATGCTTGGCCATCGTGAGATTGTTGATGGGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 453

ATGGCCGGCCATCCGTGGGGCCCACCTACCGGAGCGCCTTCGCCCGCGACGGATTCCCGCCGCCCGTCCCCGGGATGGACAGCTGCTACGACATCTTCCGgtgagctctc ... ccttacacagCATGGCCGTGGAGAAGTATCCAAACAACAGAATGCTTGGCCATCGTGAGATTGTTGATGGGAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 110

ATGGCCGGCCATCCGTGGGGCCCACCTACCGGAGCGCCTTCGCCCGCGACGGATTCCCGCCGCCCGTCCCCGGGATGGACAGCTGCTACGACATCTTCCGgtgagctctc ... ccttacacagCATGGCCGTGGAGAAGTATCCAAACAACAGAATGCTTGGCCATCGTGAGATTGTTGATGGGAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtgttctcttgtctcccaatactgaatttctttagtctgtggatccttacacagCATGGCCGTGGAGAAGTATCCAAACAACAGAATGCTTGGCCATCGTGAGATTGTTGATGGGAAG
                                            tccttac  putative branch site (score: 110)
                                            tccttac  CT-rich tract
                         aatttcttta  TA-rich tract