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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgattagtccaaaagtgcatattggatgtgttatcatatttcatattacaatcatgaccaaattcctgttctgcagTCTGGTCATAACATTGAAAAAGTCAGGGAAAAAATGGGGGATCTGATAAAGCAAATGGTCAACATTTATTCTCTTCCCAAATTACTTCCCTATATTCTTG

Basic information

species Zea mays
transcript GRMZM2G009849_T03
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G009849_T01 (Zea mays), 3'ss of exon 18
lower sequence: LOC_Os01g60040.2 (Oryza sativa), 3'ss of exon 36
-------------------------------------------------------------------------------------------gtatgattagtccaaaagtgcatattggatgtgt---tatcatatttcatattacaatcatgaccaaat---tcctgttctgcagTCTGGTCATAACATTGAAAAAGTCAGGGAAAAAATGGGGGATCTGATAAAGCAAATGGTCAACATTTATTCTCTTCCCAAATTACTTCCCTATATTCTTG
                                                                                             ||  ||| |    |  |||   |   || | |   ||| || ||  || ||  | ||||  | |||    | ||||  |||||||||| || ||||| ||||||||||| ||||||||||| || ||||||||||||||||||||||| ||||||||||| ||| | || || || ||| | |
gtacatagagtgcacaaatattgattagtgtaatcctgaatcttcccatcagaaacacaggctggagaagtatattcttcagattgatcgaacatatttatttgttatatgccattgcaatctttgcctataattttaaattttcgattcattcctaaacaactgctgtattgcagTCTGGCCACAACATCGAAAAAGTCAGAGAAAAAATGGGAGAGCTGATAAAGCAAATGGTCAACATCTATTCTCTTCCAAAACTTCTCCCATACATTTTGG

upper sequence: GRMZM2G009849_T01 (Zea mays), 3'ss of exon 18
lower sequence: AT2G35630.1 (Arabidopsis thaliana), 3'ss of exon 37
------------------------------------------------gtatgatta--gtccaaaagtgcatattggatgtgttatcatatttcatattacaatcatgaccaaattcctgttct----gcagTCTGGTCATAACATTGAAAAAGTCAGGGAAAAAATGGGGGATCTGATAAAGCAAATGGTCAACATTTATTCTCTTCCCAAATTACTTCCCTATATTCTTG
                                                  || |||   ||  |    |   | || ||       |  |  ||||   |    | ||    || | | ||| ||    |||||  || ||||||||||||||||| || ||||||||| |||| ||||| ||||| ||  |  |    |||||| |    ||      |||||||||| | |
gttaggcatctgatattaatccaatttcctatggtgttggcctctttctaatcattcccgtttatctttctgttttagaaaaagattggtgcttcag--tgtctttatatttaactccttgtccttggtgcagTTGGGGCATAACATTGAAAAAGTAAGAGAAAAAATGCGGGAGCTGATGAAGCAGATCATTCAGGCATATTCTGTAGGAAAGACGTATCCCTATATTTTGG

upper sequence: GRMZM2G009849_T01 (Zea mays), 3'ss of exon 18
lower sequence: EFJ11209 (Selaginella moellendorffii), 3'ss of exon 35
gtatgattagtccaaaagtgcatattggatgtgttatcatatttcata-ttacaatcatgaccaaattcctgttctgcagTCTGGTCATAACATTGAAAAAGTCAGGGAAAAAATGGGGGATCTGATAAAGCAAATGGTCAACATTTATTCTCTTCCCAAATTACTTCCCTATATTCTTG
                                || ||     || ||  || | |   |  |  |     | | ||||||||||||||||| |||||||| ||  ||||||| ||| |||| ||||| |  |  ||      ||| ||  ||    | ||  || || | || |||   |
--------------------------------gtaattgacatttatgcttgcgagtttagctgagcatgtttcctgcagTCTGGTCATAATATTGAAAAGGTTCGGGAAAAGATGCGGGAGCTGATGAGACTCATCTGTTGCATCTACCCTGCATCAAAGCTATTTACGTACATTTGCG

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|28909669|gb|CB331043.1|CB331043
EST:     TGTTGACAGAAGCTGAAGCTGCAATTTTTCTTCCTTGCCTCATAGAGAAG                         TCTGG-CATAAC-TTGAAAAAGTCAGGGAAAAAATGGGGGATCTGATAAAG
genomic: TGTTGACAGAAGCTGAAGCTGCAATTTTTCTTCCTTGCCTCATAGAGAAGgtatgattag ... tgttctgcagTCTGGTCATAACATTGAAAAAGTCAGGGAAAAAATGGGGGATCTGATAAAG




















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), 49 (downstream exon)
Score: 319

TCTTGACTTTCTACCTGAGCTTTTTGATATTTTAAAAGACCAGTCTTACATGTTGACAGAAGCTGAAGCTGCAATTTTTCTTCCTTGCCTCATAGAGAAGgtatgattag ... tgttctgcagTCTGGTCATAACATTGAAAAAGTCAGGGAAAAAATGGGGGATCTGATAAAGCAAATGGTCAACATTTATTCTCTTCCCAAATTACTTCCCTATATTCTTG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 97

TCTTGACTTTCTACCTGAGCTTTTTGATATTTTAAAAGACCAGTCTTACATGTTGACAGAAGCTGAAGCTGCAATTTTTCTTCCTTGCCTCATAGAGAAGgtatgattag ... tgttctgcagTCTGGTCATAACATTGAAAAAGTCAGGGAAAAAATGGGGGATCTGATAAAGCAAATGGTCAACATTTATTCTCTTCCCAAATTACTTCCCTATATTCTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 136

TCTTGACTTTCTACCTGAGCTTTTTGATATTTTAAAAGACCAGTCTTACATGTTGACAGAAGCTGAAGCTGCAATTTTTCTTCCTTGCCTCATAGAGAAGgtatgattag ... tgttctgcagTCTGGTCATAACATTGAAAAAGTCAGGGAAAAAATGGGGGATCTGATAAAGCAAATGGTCAACATTTATTCTCTTCCCAAATTACTTCCCTATATTCTTG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 207

TCTTGACTTTCTACCTGAGCTTTTTGATATTTTAAAAGACCAGTCTTACATGTTGACAGAAGCTGAAGCTGCAATTTTTCTTCCTTGCCTCATAGAGAAGgtatgattag ... tgttctgcagTCTGGTCATAACATTGAAAAAGTCAGGGAAAAAATGGGGGATCTGATAAAGCAAATGGTCAACATTTATTCTCTTCCCAAATTACTTCCCTATATTCTTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggatgtgttatcatatttcatattacaatcatgaccaaattcctgttctgcagTCTGGTCATAACATTGAAAAAGTCAGGGAAAAAATGGGGGATCTGATAAAGCAAATGGTCAACATTTATTCTCTTCCCAAATTACTTCCCTATATTCTTG
                                         ttcctgttct  CT-rich tract
         ttatcatatttcatat  TA-rich tract