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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacaaatttatgggacagttgtaaatcctcttacatgtatttagttccccatttgattttgatccgactgtgcataatcttggatatgctctctgaagGTTGTGGACTGTCGCATGCGTGGGGACCCAAATTCAGTCCTTAGGTTTGCTTTCGTAGAGTTCACTGATGAGG

Basic information

species Zea mays
transcript GRMZM2G456149_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G456149_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os08g02330.1 (Oryza sativa), 3'ss of exon 3
gtacaaatttatgggacagttgtaaatcctcttacatgtatttagttccccatttgattt-tgatccgactgtgcataat---cttgga--tatgctctctgaagGTTGTGGACTGTCGCATGCGTGGGGACCCAAATTCAGTCCTTAGGTTTGCTTTCGTAGAGTTCACTGATGAGG
                                ||||| | | | | ||| || ||| ||| ||     | ||||||||||   |||| |  | | || ||||||||||||||||||||| ||| ||||||| || ||||| || ||| | ||||||||| ||||||||||||||||||
-------------------------------gtacatttttctggctccacacttgctttctgtgataattgtgcataataatcttgaaatttttctttctgaagGTTGTGGACTGTCGTATGTGTGGGGATCCGAATTCTGTTCTTCGTTTTGCTTTCATAGAGTTCACTGATGAGG

upper sequence: GRMZM2G456149_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT4G10610.2 (Arabidopsis thaliana), 3'ss of exon 3
gtacaaatttatgggacagttgtaaatcctcttacatgtatttagttccccatttgattttgatccgactgtgcataatcttggatatgctctctgaagGTTGTGGACTGTCGCATGCGTGGGGACCCAAATTCAGTCCTTAGGTTTGCTTTCGTAGAGTTCACTGATGAGG
                   ||    | | ||||| |    || |  ||    ||||  ||   |     |||  |   | || | | || |      ||||||| |||||||| ||  |||| || || || ||||| ||||||||||||||| | |||||||||||||| |
-----------------gtttaagcaacttcttaaa---gttca--tctttgtttgtgttgtgttatggtgttgactgtatttggt-tgttt-----agGTTGTTGACTGTCGTATATGTGGTGATCCCAACTCAGTACTTAGGTTTGCTTTCATCGAGTTCACTGATGAAG

upper sequence: GRMZM2G456149_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT1G32790.2 (Arabidopsis thaliana), 3'ss of exon 3
gtacaaatttatgggacagttgtaaatcctcttac-atgtatttagttccccatttgattttgatcc--gactgtgcataatcttggatatgctctctgaagGTTGTGGACTGTCGCATGCGTGGGGACCCAAATTCAGTCCTTAGGTTTGCTTTCGTAGAGTTCACTGATGAGG
                  |||| ||||  | |    | |   | |  |    | |  ||  |  | |  |  ||||  |  |  ||  | || | |    ||||||| |||||||||||  | || |||||||| || |||||| ||||||| ||| |||||||||||||||| |
------------------gttgaaaatattttcttgaagctctcatctatgaactccatcattgtgcttggttgtgtgtcttactgtgtttggttttaacagGTTGTTGACTGTCGCATATGCGGTGACCCAAACTCGGTCCTTCGGTTTGCATTCATAGAGTTCACTGATGAAG

upper sequence: GRMZM2G456149_T01 (Zea mays), 3'ss of exon 5
lower sequence: PP1S196_50V6.1 (Physcomitrella patens), 3'ss of exon 4
gtacaaatttatgggacagttgtaaatcctcttacatgtatttagttccccatttgattttgatccgactgtgcataatcttg-gatatgctct---ctgaagGTTGTGGACTGTCGCATGCGTGGGGACCCAAATTCAGTCCTTAGGTTTGCTTTCGTAGAGTTCACTGATGAGG
  ||   ||  ||       ||| |||   |   |||   |||    |||  |        | | |   || |  | |||||  ||  |||| |    |  ||||||| || || ||  |  | ||||||||||| || || ||| ||||||||||||| ||||||||||| || |
cgactccttcctgaatttcgtgttaatgaac---cattggttttagacccagtacctacgcgttgccgatgggggttatcttacgaattgctgtggattacagGTTGTAGATTGCCGTGTTTGCGGGGACCCAAACTCTGTGCTTCGGTTTGCTTTCGTGGAGTTCACTGACGAAG

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 3 RNA-Seq libraries.


Block sizes: 43 (upstream exon), 14 (downstream exon)
Score: 7

GTTACTGAAGAAAACCTCGCAACACTATTTATAAATTGCGGTCAGgtacaaattt ... ctctctgaagGTTGTGGACTGTCGCATGCGTGGGGACCCAAATTCAGTCCTTAGGTTTGCTTTCGTAGAGTTCACTGATGAGG


Block sizes: 38 (upstream exon), 14 (downstream exon)
Score: 6

GTTACTGAAGAAAACCTCGCAACACTATTTATAAATTGCGGTCAGgtacaaattt ... ctctctgaagGTTGTGGACTGTCGCATGCGTGGGGACCCAAATTCAGTCCTTAGGTTTGCTTTCGTAGAGTTCACTGATGAGG


Block sizes: 36 (upstream exon), 15 (downstream exon)
Score: 2

GTTACTGAAGAAAACCTCGCAACACTATTTATAAATTGCGGTCAGgtacaaattt ... ctctctgaagGTTGTGGACTGTCGCATGCGTGGGGACCCAAATTCAGTCCTTAGGTTTGCTTTCGTAGAGTTCACTGATGAGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttccccatttgattttgatccgactgtgcataatcttggatatgctctctgaagGTTGTGGACTGTCGCATGCGTGGGGACCCAAATTCAGTCCTTAGGTTTGCTTTCGTAGAGTTCACTGATGAGG
             ttttgat  putative branch site (score: 2)
                                           tgctctct  putative PPT
       atttgatttt  TA-rich tract