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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtcaaactgcaacttttgacattgagaattggttgctttaaacacttggtttcttacattttctctacacttcttcagATCAAACTTAGAGCATTGCTCACACATCTGCAACAACTCCGGATTGGCTATTGGGGGGTTGCTACAGGGAAAAGCCAACCATTGCAGTCATATGGCATGG

Basic information

species Zea mays
transcript GRMZM2G074466_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G074466_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g39380.2 (Oryza sativa), 3'ss of exon 21
gtaagtcaaactgcaac-----ttttgacattgagaatt-ggttgctttaaacacttggtttcttacattttctctacacttcttcagATCAAACTTAGAGCATTGCTCACACATCTGCAACAACTCCGGATTGGCTATTGGGGGGTTGCTACAGGGAAAAGCCAACCATTGCAGTCATATGGCATGG
|| ||||||||  || |     ||||    |||| |||| | ||| ||| || || |  |||||||    ||||  |  | || |||||||||||||||||||||||||||||||||||||||||| || |||||||||||||| || |||||||||||| | |||| |  ||  |||||||||||||
gtgagtcaaacaacaccagattttttttttttgaaaatttgattgttttgaatacct--tttcttaaccattcttaaaccctcctcagATCAAACTTAGAGCATTGCTCACACATCTGCAACAACTGCGCATTGGCTATTGGGGAGTCGCTACAGGGAAAGGACAACAACCGCCATCATATGGCATGG
















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: 48 (upstream exon), 39 (downstream exon)
Score: 253

GCTGGATTGGGATTACCTGACATTGACTCTTGGAATATGATTGAGAAAATAGCCGAGAGAAACAACTTGGGTTATAAACAGCTTgtaagtcaaa ... acttcttcagATCAAACTTAGAGCATTGCTCACACATCTGCAACAACTCCGGATTGGCTATTGGGGGGTTGCTACAGGGAAAAGCCAACCATTGCAGTCATATGGCATGG


Block sizes: 49 (upstream exon), 39 (downstream exon)
Score: 216

GCTGGATTGGGATTACCTGACATTGACTCTTGGAATATGATTGAGAAAATAGCCGAGAGAAACAACTTGGGTTATAAACAGCTTgtaagtcaaa ... acttcttcagATCAAACTTAGAGCATTGCTCACACATCTGCAACAACTCCGGATTGGCTATTGGGGGGTTGCTACAGGGAAAAGCCAACCATTGCAGTCATATGGCATGG


Block sizes: 49 (upstream exon), 39 (downstream exon)
Score: 228

GCTGGATTGGGATTACCTGACATTGACTCTTGGAATATGATTGAGAAAATAGCCGAGAGAAACAACTTGGGTTATAAACAGCTTgtaagtcaaa ... acttcttcagATCAAACTTAGAGCATTGCTCACACATCTGCAACAACTCCGGATTGGCTATTGGGGGGTTGCTACAGGGAAAAGCCAACCATTGCAGTCATATGGCATGG


Block sizes: 47 (upstream exon), 39 (downstream exon)
Score: 204

GCTGGATTGGGATTACCTGACATTGACTCTTGGAATATGATTGAGAAAATAGCCGAGAGAAACAACTTGGGTTATAAACAGCTTgtaagtcaaa ... acttcttcagATCAAACTTAGAGCATTGCTCACACATCTGCAACAACTCCGGATTGGCTATTGGGGGGTTGCTACAGGGAAAAGCCAACCATTGCAGTCATATGGCATGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagaattggttgctttaaacacttggtttcttacattttctctacacttcttcagATCAAACTTAGAGCATTGCTCACACATCTGCAACAACTCCGGATTGGCTATTGGGGGGTTGCTACAGGGAAAAGCCAACCATTGCAGTCATATGGCATGG
                           ttcttac  putative branch site (score: 204)
                          tttcttacattttctc  CT-rich tract
                              ttacatttt  TA-rich tract