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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actttcaaaaactcaatcatctgtcttttcttcaacaaatattaaagcgccaataaatgatctatgctggaagctgatgtaatttgtattactcttgcagACAGATTGGGATCTAAGATTAGCATGTCTTCTTCTATATGCATTTGATATAGAAGACAACTTTTGGCAGTTATATTCTGATTTTTTGCCAAGTGTTGATG

Basic information

species Zea mays
transcript GRMZM5G807767_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G807767_T03 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os05g50980.1 (Oryza sativa), 3'ss of exon 3
-act-ttcaaaaactcaatcatctgtcttttcttcaacaaatattaaagcgccaataaatgatctatgctggaagctgatgtaatttgtattactcttgcagACAGATTGGGATCTAAGATTAGCATGTCTTCTTCTATATGCATTTGATATAGAAGACAACTTTTGGCAGTTATATTCTGATTTTTTGCCAAGTGTTGATG
 | |  |||| |  |  | | | | |  || |||||     | | |||||  || ||| |||| ||  ||| |  || | | ||| ||||   |||||||||||||||||||||||||| ||||| || |||||||| |||||||||||| |||||||||||||||||||| |||||  |||||||||||| ||||||||||
tattactcaacacttgcaacctgttttcttccttcatgcggtgtcaaagcttca-taagtgatgtagactgcatcctaacgcaatctgtacc-ctcttgcagACAGATTGGGATCTAAGGTTAGCTTGCCTTCTTCTCTATGCATTTGATGTAGAAGACAACTTTTGGCAGCTATATGGTGATTTTTTGCCTAGTGTTGATG

upper sequence: GRMZM5G807767_T03 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA15G16830.1 (Glycine max), 3'ss of exon 4
-----------------------------------------------------------------------------------acttt-caaaaactcaatcatctgtcttttcttcaacaaa--tattaaagcgccaataaatgatctatgctggaagctgatgtaatt---tgtattactcttgcagACAGATTGGGATCTAAGATTAGCATGTCTTCTTCTATATGCATTTGATATAGAAGACAACTTTTGGCAGTTATATTCTGATTTTTTGCCAAGTGTTGATG
                                                                                   || || | ||      | | | ||| ||  ||       |  |  || |     || ||||| |||           | ||||||||      ||   | | ||||||||||||||| ||||| |||||||| |||||  |||||||||||||    |||| |||||||||||| || |||   || || || || ||||  ||||
gtaattactattctcttctaagttcatttgttcataataagatataaccaattggttgttttcgcttttcatgataaatacatacgttaccaatgtgtcaccctttgttttaactgtgttgtacctgctacaaaagtaaaaaatgttctggttatctgcttaatgtaattgtgcaaatctttgtggcagACAGATTGGGACCTAAGGTTAGCATGCCTTCTCTTATATGCATTTGACTGTGAAGGCAACTTTTGGCAATTGTATGGCGACTTCTTACCGAGTGCAGATG

upper sequence: GRMZM5G807767_T03 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA09G05510.1 (Glycine max), 3'ss of exon 4
------------------------------------------------------------------------------------acttt-caaaaactcaatcatctgtcttttcttcaacaaatattaaagcgccaataaatgatctatgctggaagctgatgtaatt---tgtattactcttgcagACAGATTGGGATCTAAGATTAGCATGTCTTCTTCTATATGCATTTGATATAGAAGACAACTTTTGGCAGTTATATTCTGATTTTTTGCCAAGTGTTGATG
                                                                                    || || | ||      | | | ||| ||  ||     |  |  || |     || ||||| |||           | ||||||||      ||   | | ||||||||||||||| ||||| |||||||| |||||  |||| |||||||||   |||| |||||||||||| || |||   || || || || ||||  ||||
gtaattacaatctcttctaagttcatttcataataagatataaccaatttgcttggttgttttcacttttcatgataaatacatacattaccaatgtatcaccctttgttttaactattgtacctgctacaaaagtaaaaaatgttctggttatctgcttaatgtaattgtgcaaatctttgtggcagACAGATTGGGACCTAAGGTTAGCATGCCTTCTCTTATACGCATTTGATTGCGAAGGCAACTTTTGGCAATTGTATGGCGACTTCTTACCGAGTGCAGATG

upper sequence: GRMZM5G807767_T03 (Zea mays), 3'ss of exon 3
lower sequence: Vv01s0011g01080.t01 (Vitis vinifera), 3'ss of exon 4
---actttcaaaaactcaa--tcatctgtcttttcttcaacaaatattaaagcgccaataaatgatctatgctggaagctgatgtaatttgtattactcttgcagACAGATTGGGATCTAAGATTAGCATGTCTTCTTCTATATGCATTTGATATAGAAGACAACTTTTGGCAGTTATATTCTGATTTTTTGCCAAGTGTTGATG
     |       || |||  | ||   | |  |  | ||   |  || | |   |  |   ||      | |   | ||   ||| ||||    ||| | ||||||||||||||||||  | |||||||| |||||| | | ||||||||||  ||| || ||||| |||||| |||||  ||||||||| || ||||  |  |
ttggttgatgggtacacaaagttataaatataattctgaaatgaagttgatggctctttttgtgtcactggttcttaacttcggta-tttg----actgtggcagACAGATTGGGATCTGCGGTTAGCATGCCTTCTTTTGTTTGCATTTGATCAAGAGGATAACTTCTGGCAGCTATATGGTGATTTTTTACCTAGTGAAGGAG

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: 47 (upstream exon), 49 (downstream exon)
Score: 37

GATGCTGACTATAACTCAAAAGAAACCTTGGATGTTTTTCCCTGACATTATTCCACTAGGCCATCCTATATTTGATGTTATCGAGTCAACAGATCCAGAGgtaggtggat ... actcttgcagACAGATTGGGATCTAAGATTAGCATGTCTTCTTCTATATGCATTTGATATAGAAGACAACTTTTGGCAGTTATATTCTGATTTTTTGCCAAGTGTTGATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 83

GATGCTGACTATAACTCAAAAGAAACCTTGGATGTTTTTCCCTGACATTATTCCACTAGGCCATCCTATATTTGATGTTATCGAGTCAACAGATCCAGAGgtaggtggat ... actcttgcagACAGATTGGGATCTAAGATTAGCATGTCTTCTTCTATATGCATTTGATATAGAAGACAACTTTTGGCAGTTATATTCTGATTTTTTGCCAAGTGTTGATG


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

GATGCTGACTATAACTCAAAAGAAACCTTGGATGTTTTTCCCTGACATTATTCCACTAGGCCATCCTATATTTGATGTTATCGAGTCAACAGATCCAGAGgtaggtggat ... actcttgcagACAGATTGGGATCTAAGATTAGCATGTCTTCTTCTATATGCATTTGATATAGAAGACAACTTTTGGCAGTTATATTCTGATTTTTTGCCAAGTGTTGATG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 46

GATGCTGACTATAACTCAAAAGAAACCTTGGATGTTTTTCCCTGACATTATTCCACTAGGCCATCCTATATTTGATGTTATCGAGTCAACAGATCCAGAGgtaggtggat ... actcttgcagACAGATTGGGATCTAAGATTAGCATGTCTTCTTCTATATGCATTTGATATAGAAGACAACTTTTGGCAGTTATATTCTGATTTTTTGCCAAGTGTTGATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agcgccaataaatgatctatgctggaagctgatgtaatttgtattactcttgcagACAGATTGGGATCTAAGATTAGCATGTCTTCTTCTATATGCATTTGATATAGAAGACAACTTTTGGCAGTTATATTCTGATTTTTTGCCAAGTGTTGATG
                          agctgat  putative branch site (score: 46)
                                           ttactctt  putative PPT
                               atgtaatttgtatta  TA-rich tract