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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaatgatatgctagattgctaggctaacgcaatccttaaactcagcaaataggttttttcttacaaactaacagtatgtggtgtttgcagAGCTCTACAATATTGTTCGAATACCTAATGTATTCTGTTACACTTATGGTGAACTAAGGACCGCTACTGAAAATTTTAGTTCTGCTAATCTTCTTGGTGA

Basic information

species Zea mays
transcript GRMZM2G126858_T01
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G126858_T02 (Zea mays), 3'ss of exon 17
lower sequence: LOC_Os04g52640.2 (Oryza sativa), 3'ss of exon 18
gtaaaatgatatgctagattgctaggctaacgcaat-ccttaaactcagcaaataggttttttcttacaaactaac--agtatgtggtgtttgcagAGCTCTACAATATTGTTCGAATACCTAATGTATTCTGTTACACTTATGGTGAACTAAGGACCGCTACTGAAAATTTTAGTTCTGCTAATCTTCTTGGTGA------
         ||   | |    |||||| |||   ||  ||| |||  |||||| |||      || | ||| | |   |   | | |||||||||||||| |||| ||||||| ||| ||||||| ||||| ||||      ||||||||||||| |||| |||||||||||||||||    || | |||||||||      
--------gtaca-tggcacactaggccaacaatatatctttaaccgagcaaacaggaag---ctaataaattgatgtaccttttcgtgtttgcagAGCTGTACAGTATTGTTGGAAGACCTAATATATTCAGTTA------TGGTGAACTAAGGTCCGCAACTGAAAATTTTAGTTCCAGCAACCGTCTTGGTGAAGGAGG

upper sequence: GRMZM2G126858_T02 (Zea mays), 3'ss of exon 17
lower sequence: LOC_Os04g52614.1 (Oryza sativa), 3'ss of exon 15
gtaaaatgatatgctagattgctaggctaacgcaat-ccttaaactcagcaaataggttttttcttacaaactaaca-gtatgtg-gtgtttgcagAGCTCTACAATATTGTTCGAATACCTAATGTATTCTGTTACACTTATGGTGAACTAAGGACCGCTACTGAAAATTTTAGTTCTGCTAATCTTCTTGGTGA------
         ||   | |    ||||||| ||   ||  | |  |||  |||||   |   ||    | ||| | |    ||| |   ||||||||||||| |||| ||||||  ||| ||||||||||||| |||| |      ||||||||||| | || |||||||||||||||||    || |  ||||||||      
--------gtaca-tggcacactaggctcacaatatatccttgactaggcaaactagaagtta---ataaattgatgtatatttttatgtttgcagAGCTATACAGTATTGTCGGAAGACCTAATGTATTCAGTTATA------GTGAACTAAGGTCTGCAACTGAAAATTTTAGTTCCAGCAACCGCCTTGGTGAAGGAGG

upper sequence: GRMZM2G126858_T02 (Zea mays), 3'ss of exon 17
lower sequence: LOC_Os04g52600.1 (Oryza sativa), 3'ss of exon 19
gtaaaatgatatgctagattgctaggctaacgcaat-ccttaaactcagcaaataggttttttcttacaaactaacagt--atgtggtgtttgcagAGCTCTACAATATTGTTCGAATACCTAATGTATTCTGTTACACTTATGGTGAACTAAGGACCGCTACTGAAAATTTTAGTTCTGCTAATCTTCTTGGTGA------
         ||   | |    ||| ||| ||    |  | |  ||   ||||| | |   ||    | ||| | |   |   | |  |||| |||||||| |||| ||||||| ||| ||||||||||||| |||| |      ||||||||||| | || |||||||||||||||||    || | |||||||||      
--------gtaca-tggcacactatgctcacattgtatccttgaccaggcaaacaagaagtta---ataaattgatgttcctttttatgttcgcagAGCTATACAGTATTGTTGGAAGACCTAATGTATTCAGTTATA------GTGAACTAAGGTCTGCAACTGAAAATTTTAGTTCCAGCAACCGTCTTGGTGAAGGAGG

upper sequence: GRMZM2G126858_T02 (Zea mays), 3'ss of exon 17
lower sequence: LOC_Os04g52606.1 (Oryza sativa), 3'ss of exon 5
gtaaaatgatatgctagattgctaggctaacgcaatccttaaactcagcaaataggttttttcttacaaactaac--agtatgtggtgtttgcagAGCTCTACAATATTGTTCGAATACCTAATGTATTCTGTTACACTTATGGTGAACTAAGGACCGCTACTGAAAATTTTAGTTCTGCTAATCTTCTTGGTGA------
           | |  ||   |||||            || |||  || |||| ||      || | ||| | |   |   | |  ||||||||||| | |||| ||||||| ||| ||| |||||| || ||||      |||||| |||||| |||| |||||||||||||||||    || |||||||||||      
----------gtacaggaccactagg------------ttcaaccgagtaaatgggaag---ctcataaagtgatgtatctttttatgtttgcagAGTTGTACAGTATTGTTGGAAGACCCAATGTAATCAGTTA------TGGTGAGCTAAGGTCCGCAACTGAAAATTTTAGTTCCAGCAACCTTCTTGGTGAAGGAGG

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), 48 (downstream exon)
Score: 54

ATTGGAGTCGTGATTGGTGCAACAGTTTTAGGACTAGCAATACTTGCTACACTCTGTGTGTGGAGGCACAAAAGGAGAAAAGTATCACTAGAGCAGCAAGgtaaaatgat ... gtgtttgcagAGCTCTACAATATTGTTCGAATACCTAATGTATTCTGTTACACTTATGGTGAACTAAGGACCGCTACTGAAAATTTTAGTTCTGCTAATCTTCTTGGTGA


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 25

ATTGGAGTCGTGATTGGTGCAACAGTTTTAGGACTAGCAATACTTGCTACACTCTGTGTGTGGAGGCACAAAAGGAGAAAAGTATCACTAGAGCAGCAAGgtaaaatgat ... gtgtttgcagAGCTCTACAATATTGTTCGAATACCTAATGTATTCTGTTACACTTATGGTGAACTAAGGACCGCTACTGAAAATTTTAGTTCTGCTAATCTTCTTGGTGA


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 13

ATTGGAGTCGTGATTGGTGCAACAGTTTTAGGACTAGCAATACTTGCTACACTCTGTGTGTGGAGGCACAAAAGGAGAAAAGTATCACTAGAGCAGCAAGgtaaaatgat ... gtgtttgcagAGCTCTACAATATTGTTCGAATACCTAATGTATTCTGTTACACTTATGGTGAACTAAGGACCGCTACTGAAAATTTTAGTTCTGCTAATCTTCTTGGTGA


Block sizes: 40 (upstream exon), 48 (downstream exon)
Score: 15

ATTGGAGTCGTGATTGGTGCAACAGTTTTAGGACTAGCAATACTTGCTACACTCTGTGTGTGGAGGCACAAAAGGAGAAAAGTATCACTAGAGCAGCAAGgtaaaatgat ... gtgtttgcagAGCTCTACAATATTGTTCGAATACCTAATGTATTCTGTTACACTTATGGTGAACTAAGGACCGCTACTGAAAATTTTAGTTCTGCTAATCTTCTTGGTGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaaactcagcaaataggttttttcttacaaactaacagtatgtggtgtttgcagAGCTCTACAATATTGTTCGAATACCTAATGTATTCTGTTACACTTATGGTGAACTAAGGACCGCTACTGAAAATTTTAGTTCTGCTAATCTTCTTGGTGA
                              aactaac  putative branch site (score: 15)
                  ttttttcttacaaa  TA-rich tract