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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatgcatatgttctatcttcatatacttatggctccaggacgcggcattatgtctgtatcgtgtttgtttagggactaataatgatgtttattttgtgctcacagAGAAGCGCCTTGGGCTTCAACCAGCATGCACCGCCGCCTGAAGGGCAAACTCTCTAAGTTGTACAGCTAACAGTTGCTAGGTTTGCCTCATGTTTTTTTC

Basic information

species Zea mays
transcript GRMZM2G012964_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G012964_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os05g01910.1 (Oryza sativa), 3'ss of exon 8
gtatatgcata-tgttctatcttcatatacttatggctccaggacgcggcattatgtctgtatcgtgtttgtttagggactaataatgatgtttattttgtgctcacagAGAAGCGCCTTGGGCTTCAACCAGCATGCACC---GCCGCCTGAAGGGCAAACTCTCTAAGTTGTACAGCTAACAGTTGCTAGGTTTGCCTCATGTTTTTTTC-
||||     || |||  |||  ||||  |   || | | |  |  ||  |||   | ||  |   |||||           |||| |  |  ||     |      |||||||||| || |||||||||||||||||||||   |||||||||||||||| |  |    | ||||||||||||||| ||||||||||  |     |    |  
gtatgattgtactgtcttattgtcattcagccattgtttcttgctgc--catagggacta-acaatgttt-----------aatattcgttgttgcgacgcaaatgcagAGAAGCGACTAGGGCTTCAACCAGCATGCACCAGTGCCGCCTGAAGGGCAAGCAAT----GCTGTACAGCTAACAGTGGCTAGGTTTGGTTTGCACTCACGTTT

upper sequence: GRMZM2G012964_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os01g74030.1 (Oryza sativa), 3'ss of exon 8
gtatatgcatatgttctatcttcatatacttatggctccaggacgcggcattatgtctgtatcgtgtttgtttagggacta-ataatgatgtttattttgtgctcacagAGAAGCGCCTTGGGCTTCAACCAGCATGCACCGCCGCCTGAAGGGCAAACTCT-CTAAGTTGTACAGCTAACAGTTGCTAGGTTTGC-CTCATGTTTTTTTC-
      | |   |   || |  || | |   ||   |   |   |    | || |    |||  || ||  |||   |  | | || | ||||| || ||||  | |||| ||||| ||||||||||||||| ||   || || || |||||   || | ||    |||||||||||||||||| ||||||||||| ||   ||  | ||  
------gtacgggacataaca-caaagagagataagttttgtgtg----actagg---atatgatgatttgttatatataacacaaagctgttt-ttgtgtgtgcgcagAAAAGCGGCTTGGGCTTCAACCATCA---ACTGCAGCTTGAAGAATAAGCGCTATCTAGTTGTACAGCTAACAGTGGCTAGGTTTGCACTGGCGTCATGTTTT
















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: 224

ATGATCTTAACAAGGATAAAGACACACTTGAACACACTCAAGAAGTACACATACGGGAAGCACATAGTAGCGCGTGTAGAGAAGCTTGTTGCTGCTGGAGgtatatgcat ... gtgctcacagAGAAGCGCCTTGGGCTTCAACCAGCATGCACCGCCGCCTGAAGGGCAAACTCTCTAAGTTGTACAGCTAACAGTTGCTAGGTTTGCCTCATGTTTTTTTC


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 82

ATGATCTTAACAAGGATAAAGACACACTTGAACACACTCAAGAAGTACACATACGGGAAGCACATAGTAGCGCGTGTAGAGAAGCTTGTTGCTGCTGGAGgtatatgcat ... gtgctcacagAGAAGCGCCTTGGGCTTCAACCAGCATGCACCGCCGCCTGAAGGGCAAACTCTCTAAGTTGTACAGCTAACAGTTGCTAGGTTTGCCTCATGTTTTTTTC


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 148

ATGATCTTAACAAGGATAAAGACACACTTGAACACACTCAAGAAGTACACATACGGGAAGCACATAGTAGCGCGTGTAGAGAAGCTTGTTGCTGCTGGAGgtatatgcat ... gtgctcacagAGAAGCGCCTTGGGCTTCAACCAGCATGCACCGCCGCCTGAAGGGCAAACTCTCTAAGTTGTACAGCTAACAGTTGCTAGGTTTGCCTCATGTTTTTTTC


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 93

ATGATCTTAACAAGGATAAAGACACACTTGAACACACTCAAGAAGTACACATACGGGAAGCACATAGTAGCGCGTGTAGAGAAGCTTGTTGCTGCTGGAGgtatatgcat ... gtgctcacagAGAAGCGCCTTGGGCTTCAACCAGCATGCACCGCCGCCTGAAGGGCAAACTCTCTAAGTTGTACAGCTAACAGTTGCTAGGTTTGCCTCATGTTTTTTTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtctgtatcgtgtttgtttagggactaataatgatgtttattttgtgctcacagAGAAGCGCCTTGGGCTTCAACCAGCATGCACCGCCGCCTGAAGGGCAAACTCTCTAAGTTGTACAGCTAACAGTTGCTAGGTTTGCCTCATGTTTTTTTC
                       gactaat  putative branch site (score: 93)
                        actaataatgatgttt  TA-rich tract