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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattttccctctcaactgttaccacacatttatcattgctgtattcatggtaaagaatgggagtgtcggttattgttttagtgcttcttaattgtttatctccaacatactgcagAGTGATGAATCTGTCTATGAGCGTGAATGTGCGAACAAACCTGGTTTTGCAGTGTACTTCAGATACCCAAACAGCCAGCGTGTGTCCTACAGTCAGTTTG

Basic information

species Zea mays
transcript GRMZM2G461356_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G461356_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g68810.1 (Oryza sativa), 3'ss of exon 26
gtattttccctctcaactgttaccacacatttatcattgctgtattcatggtaaagaatgggagtgtcggtta-ttgttttagtgcttcttaattgtttatctcca----acatactgcagAGTGATGAATCTGTCTATGAGCGTGAATGTGCGAACAAACCTGGTTTTGCAGTGTACTTCAGATACCCAAACAGCCAGCGTGTGTCCTACAGTCAGTTTG
                             | | |  ||||   |||| |  | ||  || |   | | || || || ||||  || || || | || || | | ||    || |  ||||||| ||||||||| | ||||||||||||||||  || || || ||||| || |||||| ||||||| ||||| ||||||||||| || || || |||||||
----------------------------gtatttggttgccacattctt--tcaaccatagttttattggatagtttttttgctggttttttaatgcttctattcacgtcaccttttgcagAGCGATGAATCTTTATATGAGCGTGAATGTGGAAATAAGCCAGGTTTCGCTGTGTACATCAGATATCCAAATAGCCAGCGTGTATCTTATAGCCAGTTTG
















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: 157

TAAAACCCTACAGCCAATGATATGCTGTTGCACAGAATTTGAAGCTGGCAGGCTTGGAAGATTTTTTCATGATACGTTGAAGATGGCCTACTATTGGAAGgtattttccc ... catactgcagAGTGATGAATCTGTCTATGAGCGTGAATGTGCGAACAAACCTGGTTTTGCAGTGTACTTCAGATACCCAAACAGCCAGCGTGTGTCCTACAGTCAGTTTG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 106

TAAAACCCTACAGCCAATGATATGCTGTTGCACAGAATTTGAAGCTGGCAGGCTTGGAAGATTTTTTCATGATACGTTGAAGATGGCCTACTATTGGAAGgtattttccc ... catactgcagAGTGATGAATCTGTCTATGAGCGTGAATGTGCGAACAAACCTGGTTTTGCAGTGTACTTCAGATACCCAAACAGCCAGCGTGTGTCCTACAGTCAGTTTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 108

TAAAACCCTACAGCCAATGATATGCTGTTGCACAGAATTTGAAGCTGGCAGGCTTGGAAGATTTTTTCATGATACGTTGAAGATGGCCTACTATTGGAAGgtattttccc ... catactgcagAGTGATGAATCTGTCTATGAGCGTGAATGTGCGAACAAACCTGGTTTTGCAGTGTACTTCAGATACCCAAACAGCCAGCGTGTGTCCTACAGTCAGTTTG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 67

TAAAACCCTACAGCCAATGATATGCTGTTGCACAGAATTTGAAGCTGGCAGGCTTGGAAGATTTTTTCATGATACGTTGAAGATGGCCTACTATTGGAAGgtattttccc ... catactgcagAGTGATGAATCTGTCTATGAGCGTGAATGTGCGAACAAACCTGGTTTTGCAGTGTACTTCAGATACCCAAACAGCCAGCGTGTGTCCTACAGTCAGTTTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagtgtcggttattgttttagtgcttcttaattgtttatctccaacatactgcagAGTGATGAATCTGTCTATGAGCGTGAATGTGCGAACAAACCTGGTTTTGCAGTGTACTTCAGATACCCAAACAGCCAGCGTGTGTCCTACAGTCAGTTTG
                         tcttaat  putative branch site (score: 67)
                        ttcttaattgtttat  TA-rich tract