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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctagttgctattatagtttctacacaggtttggtaaaatgtgagtgctacttttttttctattcaaacttacattgttgaaaatgacacctgcttgcagGGTAAATTAGCTGATGGAAGGGTGGTGGCTGTAAAACAGTTATCTGAAACATCTCATCAGGGAAAACAGCAATTTGCAGCCGAAATAGAAACTATTTCTC

Basic information

species Zea mays
transcript GRMZM2G155837_T01
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G155837_T01 (Zea mays), 3'ss of exon 16
lower sequence: LOC_Os04g52600.1 (Oryza sativa), 3'ss of exon 20
-------tctagttgctattatagtttctacacaggtttggtaaaatgtgagtgctacttttttttctattcaaacttacattgttgaaaatgacacctgcttgcagGGTAAATTAGCTGATGGAAGGGTGGTGGCTGTAAAACAGTTATCTGAAACATCTCATCAGGGAAAACAGCAATTTGCAGCCGAAATAGAAACTATTTCTC
        | ||     | |||| |  | |   |    |   | ||  ||   |  | |    |   |    || ||| |||| | |  |||  ||| |   |||||||||| |||  |||||||||||| ||||| || || ||| ||||| ||||||||||||| |||||| ||||||||||| | |||||||||||||| || |
tgaataaaccagaaaaaaatata-tgccaatgtatccattacagaagatgtccggcattgcaatacttg---aatcttgcattttggtgaattccactt---tgcagGGTAAGTTAAATGATGGAAGGGTAGTGGCAGTGAAGCAGCTATCTCAAACATCTCATCAAGGAAAAAAGCAATTTGCAACGGAAATAGAAACTATATCCC

upper sequence: GRMZM2G155837_T01 (Zea mays), 3'ss of exon 16
lower sequence: LOC_Os04g52606.1 (Oryza sativa), 3'ss of exon 6
------tctagttgctattatagtttctacacaggtttggtaaaatgtgagtgctacttttttttctattcaaacttacattgttgaaaatgacacctgcttgcagGGTAAATTAGCTGATGGAAGGGTGGTGGCTGTAAAACAGTTATCTGAAACATCTCATCAGGGAAAACAGCAATTTGCAGCCGAAATAGAAACTATTTCTC
      || | || | |     |||  |  | |    |   ||||   |  ||  | |    |  ||    |||||| |||| |||   |  |  ||  |||||||||||| ||| ||||||||||||| ||||| || || ||| ||||| ||||||||||||| || |||  |||||||||||| |||||| ||||||| || |
accgtatcca-ttacaaaagatgttcttttagaaacattacaaaagacgtttgacattgcagtacctg---aaacttgcatttttggtga--atgccaccttgcagGGTAAGTTAACTGATGGAAGGGTAGTGGCAGTGAAGCAGCTATCTCAAACATCTCATCAAGGGAAAGTGCAATTTGCAGCTGAAATACAAACTATATCCC

upper sequence: GRMZM2G155837_T01 (Zea mays), 3'ss of exon 16
lower sequence: LOC_Os04g52630.1 (Oryza sativa), 3'ss of exon 18
-------tctagttgctattatagtttctacacaggtttggtaaaatgtgagtgctacttttttttctattcaaacttacattgttgaaaatgacacctgcttgcagGGTAAATTAGCTGATGGAAGGGTGGTGGCTGTAAAACAGTTATCTGAAACATCTCATCAGGGAAAACAGCAATTTGCAGCCGAAATAGAAACTATTTCTC
       |  | | |  | |||| || | |   |    |   ||||  ||     ||||       ||    |||||| |||| | |  |||   |||    |||||||||| ||| ||||||||||||| ||||| ||||||||| ||||| | |||||| |||| || ||||| ||||||||  | |||||||||||||| ||||
ttattaataaattggaaaatata-ttccaatgaatccattacaaaagatgttcagtactgcaaaacctg---aaacttgcattttggtgaattctacca---tgcagGGTAAGTTAACTGATGGAAGGGTAGTGGCAGTAAAACAGCTATCTCAGACATCTAATCAAGGGAAACAACAATTTGCGACTGAAATAGAAACTATATCTC

upper sequence: GRMZM2G155837_T01 (Zea mays), 3'ss of exon 16
lower sequence: LOC_Os04g52614.1 (Oryza sativa), 3'ss of exon 16
tctagttgctattatagtttctacacaggtttggtaaaatgtgagtgctacttttttttctattc---aaacttacattgttgaaaatgacacctgcttgcagGGTAAATTAGCTGATGGAAGGGTGGTGGCTGTAAAACAGTTATCTGAAACATCTCATCAGGGAAAACAGCAATTTGCAGCCGAAATAGAAACTATTTCTC
||        |  |   || | |   |    |    |||| ||   |    |    || | || |    ||||| |  | | |  |||| |||||   ||||||| || ||| ||||||||||||| ||||| || || ||| ||||| ||||||||||||| || ||| | ||||||||  | || ||||||||||| || |
tcagaaaaaaaaaaacattccaatgtatccattaccaaatatgttcggctttgacattgcgatcccttgaacttgctgtttggtgaatgccacct---tgcagGGCAAGTTAACTGATGGAAGGGTAGTGGCAGTGAAGCAGCTATCTCAAACATCTCATCAAGGGAAAAAACAATTTGCGACGGAGATAGAAACTATATCCC

upper sequence: GRMZM2G155837_T01 (Zea mays), 3'ss of exon 16
lower sequence: LOC_Os04g52640.2 (Oryza sativa), 3'ss of exon 19
-tctagttgctattatagtttctacacaggtttggtaaaatgtgagtgctacttttttttcta-----ttcaaacttacattgttgaaaatgacacctgcttgcagGGTAAATTAGCTGATGGAAGGGTGGTGGCTGTAAAACAGTTATCTGAAACATCTCATCAGGGAAAACAGCAATTTGCAGCCGAAATAGAAACTATTTCTC
  | |  |  ||    || || ||   |  |||  | ||||   |  | || |     ||  |     || || ||  |||| | |  ||||  ||||   ||||||||||  ||   ||||||||| | ||||| || || ||| ||||| ||||||||||||| || ||| | ||||| ||| | |||||||||||||| || |
gacca--taataggtgaggttttatg-aaatttactcaaataaaaaagatattcagcattgcaaatacttgaagctggcattttggtgaatgcaacct---tgcagGGTAAGCTAATGGATGGAAGGATAGTGGCAGTGAAGCAGCTATCTCAAACATCTCATCAAGGGAAAAAACAATTCGCAACTGAAATAGAAACTATATCCC

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), 47 (downstream exon)
Score: 16

AAGACCCAATGTATTTGTTTATGGTGAGCTAAGGACCGCTACTGAAAATTTTAGTTCCAATAACCTTCTTGGTGAAGGAGGATATGGGTCAGTTTATAAGgttagtttat ... ctgcttgcagGGTAAATTAGCTGATGGAAGGGTGGTGGCTGTAAAACAGTTATCTGAAACATCTCATCAGGGAAAACAGCAATTTGCAGCCGAAATAGAAACTATTTCTC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 53

AAGACCCAATGTATTTGTTTATGGTGAGCTAAGGACCGCTACTGAAAATTTTAGTTCCAATAACCTTCTTGGTGAAGGAGGATATGGGTCAGTTTATAAGgttagtttat ... ctgcttgcagGGTAAATTAGCTGATGGAAGGGTGGTGGCTGTAAAACAGTTATCTGAAACATCTCATCAGGGAAAACAGCAATTTGCAGCCGAAATAGAAACTATTTCTC


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 22

AAGACCCAATGTATTTGTTTATGGTGAGCTAAGGACCGCTACTGAAAATTTTAGTTCCAATAACCTTCTTGGTGAAGGAGGATATGGGTCAGTTTATAAGgttagtttat ... ctgcttgcagGGTAAATTAGCTGATGGAAGGGTGGTGGCTGTAAAACAGTTATCTGAAACATCTCATCAGGGAAAACAGCAATTTGCAGCCGAAATAGAAACTATTTCTC


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 55

AAGACCCAATGTATTTGTTTATGGTGAGCTAAGGACCGCTACTGAAAATTTTAGTTCCAATAACCTTCTTGGTGAAGGAGGATATGGGTCAGTTTATAAGgttagtttat ... ctgcttgcagGGTAAATTAGCTGATGGAAGGGTGGTGGCTGTAAAACAGTTATCTGAAACATCTCATCAGGGAAAACAGCAATTTGCAGCCGAAATAGAAACTATTTCTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgctacttttttttctattcaaacttacattgttgaaaatgacacctgcttgcagGGTAAATTAGCTGATGGAAGGGTGGTGGCTGTAAAACAGTTATCTGAAACATCTCATCAGGGAAAACAGCAATTTGCAGCCGAAATAGAAACTATTTCTC
                     aacttac  putative branch site (score: 55)
                                            cctgctt  putative PPT
      ttttttttctattcaa  TA-rich tract