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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactatataatgcttacaaataggctcccaaaaaatttctttcgttttctgagtgctagaggctaatataacacctaaatttgttgcgcagGTGGGATGAAGCTTTATATTTCAGACAACAAAGTGATCTTGACAGAAGGTTTTGATGGCGTCGTCCCGGTGAAATACTTTGAAAGAGTCGAAACATGGCC

Basic information

species Zea mays
transcript GRMZM2G061783_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G061783_T04 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os06g04300.1 (Oryza sativa), 3'ss of exon 6
gtactatataatgcttacaaataggctcccaaaaaatttctttcgttttctgagtgctagaggctaatat--aacacctaaatttgttgcgcagGTGGGATGAAGCTTTATATTTCAGACAACAAAGTGATCTTGACAGAAGGTTTTGATGGCGTCGTCCCGGTGAAATACTTTGAAAGAGTCGAAACATGGCC
|||  ||    |   |  | |    |   |||   |||| ||   || ||    |||||| ||||  | |   | | || ||| |||| | ||| ||| |||||||| || |||||||||||||| |||||  ||||||| ||||| |||||||| || || ||||| ||||| || | | | |||||||||||
gtatgatgctgtttgtttatagccacaagcaatctatttattctcttatcaacttgctaggggctggtttctgatagctgaatctgtttctcagATGGAATGAAGCTGTACATTTCAGACAACAAGGTGATTCTGACAGAGGGTTTCGATGGCGTTGTTCCTGTGAAGTACTTCGAGAAAATTGAAACATGGCC

upper sequence: GRMZM2G061783_T04 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA17G29450.1 (Glycine max), 3'ss of exon 7
-------gtactatataatgcttacaaataggctcccaaa---aaatttctttcgttttctgagtgctagaggctaatataacacctaaatttgttgcgcagGTGGGATGAAGCTTTATATTTCAGACAACAAAGTGATCTTGACAGAAGGTTTTGATGGCGTCGTCCCGGTGAAATACTTTGAAAGAGTCGAAACATGGCC
       | | | | |  || ||    ||||      |||   | |     |  | || ||||  ||||       |||||     | |   | || |  ||   | || |||||||| ||||| |||||||| ||||||||||| |||||||||||||| || || ||   ||| || ||||||||  | ||| |||||||
aaatgttggattttttgttgtttgttgatagtgagtaaaatctacaacaaataagattactgatcgctacttctctatatattttttcatcctatttc--agAAAGTATAAAGCTTTACATTTCTGACAACAAGGTGATCTTGACGGAAGGTTTTGATGGTGTTGTTCCTCCGAAGTATTTTGAAAGGATAGAATCATGGCC

upper sequence: GRMZM2G061783_T04 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA17G37310.1 (Glycine max), 3'ss of exon 9
-----------------------------------------------------------------gtactatataatgcttacaaataggctcccaaa---aaatttctttcgttttctgagtgctagaggctaatataacacctaaatttgttgcgcagGTGGGATGAAGCTTTATATTTCAGACAACAAAGTGATCTTGACAGAAGGTTTTGATGGCGTCGTCCCGGTGAAATACTTTGAAAGAGTCGAAACATGGCC
                                                                 | | | | |  ||  ||   ||||      |||   | |     |  |  | ||||  ||||       |||||     | |   | || |  ||  || ||||||||||| ||||| |||||||| ||||||||||| |||||||||||||| || || || |  || || |||||||   | ||| |||||||
gtatgatatgacaatattccaaacatgttctgaactgaatgtctacaagttcatcttgaaatgttggattttttgttgtctattgatagtgagtaaaatctacaacaaataagactactgatagctacttctctatatattttttcatcctatttc--agAAGGTATGAAGCTTTACATTTCTGACAACAAGGTGATCTTGACGGAAGGTTTTGATGGTGTTGTTCCTGCCAAGTATTTTGAAAAGATAGAATCATGGCC

upper sequence: GRMZM2G061783_T04 (Zea mays), 3'ss of exon 4
lower sequence: Vv15s0048g00300.t01 (Vitis vinifera), 3'ss of exon 7
--------------------gtactatataatgcttacaaataggctcccaaaaaatttctttcgttt---tctgagtgctagaggctaata-taacaccta-------------aatttgttgcgcagGTGGGATGAAGCTTTATATTTCAGACAACAAAGTGATCTTGACAGAAGGTTTTGATGGCGTCGTCCCGGTGAAATACTTTGAAAGAGTCGAAACATGGCC
                      | |   |    ||   | |   | ||  ||  |||    || ||     | |||| | |  ||   | || |||  | |              ||||   |  | || ||| |||||||| || |||||||||||||| || |||||||| |||||||||||||| || || || || || ||||||||||   | ||| | |||||
gtatacccttaaattcaaaatgagttggtccaactcctataggagttcagaatgaatcctatttgtaacagtatgagagatgtagaacactactaatgcttttttccccgtctctaattcaat-tgtagATGGAATGAAGCTCTACATTTCAGACAACAAGGTCATCTTGACCGAAGGTTTTGATGGTGTTGTGCCTGTCAAGTACTTTGAAAAGATAGAATCTTGGCC

upper sequence: GRMZM2G061783_T04 (Zea mays), 3'ss of exon 4
lower sequence: Vv15s0048g00280.t01 (Vitis vinifera), 3'ss of exon 7
---------------------------------gtactatataatgcttacaaataggctcccaaaaaatttctttcgttttctgagtgcta--gaggctaatataacacctaaatttgttgcgcagGTGGGATGAAGCTTTATATTTCAGACAACAAAGTGATCTTGACAGAAGGTTTTGATGGCGTCGTCCCGGTGAAATACTTTGAAAGAGTCGAAACATGGCC
                                  | |||||  |       |   |  ||  |   ||   | |      |   ||   |||   | |||  |    |  ||  | ||     | || ||| |||||||| || |||||||||||||| || |||||||| |||||||||||||| || || || || || ||||||||||   | ||| | |||||
gtatacctttaaattcaaaatgaattggtccaactcctataggagttcagaatgaatcctatctgtaacagtataagagatgtagaacactactaatgctttttccccgtctctaattcaattgtagATGGAATGAAGCTCTACATTTCAGACAACAAGGTCATCTTGACCGAAGGTTTTGATGGTGTTGTGCCTGTCAAGTACTTTGAAAAGATAGAATCTTGGCC

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: 109

GTGTACGGCAGAATGTAAACATCTTGATACATCTGGACGTTAGTAAAGCACTTAAAGgtactatata ... tgttgcgcagGTGGGATGAAGCTTTATATTTCAGACAACAAAGTGATCTTGACAGAAGGTTTTGATGGCGTCGTCCCGGTGAAATACTTTGAAAGAGTCGAAACATGGCC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 85

GTGTACGGCAGAATGTAAACATCTTGATACATCTGGACGTTAGTAAAGCACTTAAAGgtactatata ... tgttgcgcagGTGGGATGAAGCTTTATATTTCAGACAACAAAGTGATCTTGACAGAAGGTTTTGATGGCGTCGTCCCGGTGAAATACTTTGAAAGAGTCGAAACATGGCC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 113

GTGTACGGCAGAATGTAAACATCTTGATACATCTGGACGTTAGTAAAGCACTTAAAGgtactatata ... tgttgcgcagGTGGGATGAAGCTTTATATTTCAGACAACAAAGTGATCTTGACAGAAGGTTTTGATGGCGTCGTCCCGGTGAAATACTTTGAAAGAGTCGAAACATGGCC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 119

GTGTACGGCAGAATGTAAACATCTTGATACATCTGGACGTTAGTAAAGCACTTAAAGgtactatata ... tgttgcgcagGTGGGATGAAGCTTTATATTTCAGACAACAAAGTGATCTTGACAGAAGGTTTTGATGGCGTCGTCCCGGTGAAATACTTTGAAAGAGTCGAAACATGGCC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctttcgttttctgagtgctagaggctaatataacacctaaatttgttgcgcagGTGGGATGAAGCTTTATATTTCAGACAACAAAGTGATCTTGACAGAAGGTTTTGATGGCGTCGTCCCGGTGAAATACTTTGAAAGAGTCGAAACATGGCC
                                    acctaaa  putative branch site (score: 119)
                           taatataaca  TA-rich tract