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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtactattctactattgattagttaactttctgtcctagaggtgtttcaatgtgtttccttttcagGTTGAGAGTGGTGATCTAATAGCTTATGGACTTATCCCAGAATTTATTGGACGTTTCCCTATCCTTGTGAGCCTCACCGCTCTAAATGAGGACCAGCTTG

Basic information

species Zea mays
transcript GRMZM2G101791_T02
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G101791_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os02g35630.1 (Oryza sativa), 3'ss of exon 10
-----------------------------------------------------------------gttagtactattctactattgattagttaactttctgtcctagaggtgtttcaatgtgtttccttttcagGTTGAGAGTGGTGATCTAATAGCTTATGGACTTATCCCAGAATTTATTGGACGTTTCCCTATCCTTGTGAGCCTCACCGCTCTAAATGAGGACCAGCTTG
                                                                 || | | |  |   | || ||  ||   ||| ||   ||    |||||||| ||  ||||   || | ||||||||||||| || |||||||| ||||||||||| || |||||||||||||| || ||||||||||| ||| |  | |||||||| |||||||||||||
gtaagcaccaaaattccgagtttaacattttttggaaatctcctttgtttaaggagaatgcatgtgtgaattcagtgaaattactgtgtaa--aaccttaaatct---aggtgtttaaac-tgttcatttcttagGTTGAGAGTGGCGACCTAATAGCATATGGACTTATTCCGGAATTTATTGGACGGTTTCCTATCCTTGTTAGCTTGGCAGCTCTAAACGAGGACCAGCTTG

upper sequence: GRMZM2G101791_T01 (Zea mays), 3'ss of exon 10
lower sequence: Vv18s0089g01240.t01 (Vitis vinifera), 3'ss of exon 10
-----------------------gttagtactattctactattgattagtta--actttctgtcctagaggtgtttcaatgtgtttcctt-----ttcagGTTGAGAGTGGTGATCTAATAGCTTATGGACTTATCCCAGAATTTATTGGACGTTTCCCTATCCTTGTGAGCCTCACCGCTCTAAATGAGGACCAGCTTG
                        || |     | | ||   |    | |    ||  ||| |||| |   | || |||  | | || ||     |||||||||| ||| ||||||| || || ||||| || || ||||| ||||||||||| || ||||| || || ||  |  | ||||| | |||||| || ||||
ataaaactcccatatattaagctttttgcttgctgccacccctccccactctccaccctctatcctggttcttttacaaattttctctttgcattttcagGTTGAAAGTAGTGATCTTATTGCATATGGCCTCATACCAGAGTTTATTGGACGCTTTCCTATTCTAGTTAGTTTGTCAGCTCTGACTGAGGATCAACTTG
















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|211127807|gb|FL448898.1|FL448898
EST:     GTGGGTGGCACTTCAAGTGCTNCAAGTGACATCGTCCTTGTT-GAATCGG                         GTTGAGAGTGGTGATCTAATAGCTTATGGAC-TATTCCCAGAATTTATTG
genomic: GTCGGTGGCACTTCAAGTGCT-CAAGTGACATCGTCCTTGTTGGAATC-Ggttagtacta ... tccttttcagGTTGAGAGTGGTGATCTAATAGCTTATGGACTTA-TCCCAGAATTTATTG




















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: 94

ACGGCAGGATTCTTCTATTGGCTTCGGCGCACCAGTTCGTGCAAACATGAGGGTCGGTGGCACTTCAAGTGCTCAAGTGACATCGTCCTTGTTGGAATCGgttagtacta ... tccttttcagGTTGAGAGTGGTGATCTAATAGCTTATGGACTTATCCCAGAATTTATTGGACGTTTCCCTATCCTTGTGAGCCTCACCGCTCTAAATGAGGACCAGCTTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 33

ACGGCAGGATTCTTCTATTGGCTTCGGCGCACCAGTTCGTGCAAACATGAGGGTCGGTGGCACTTCAAGTGCTCAAGTGACATCGTCCTTGTTGGAATCGgttagtacta ... tccttttcagGTTGAGAGTGGTGATCTAATAGCTTATGGACTTATCCCAGAATTTATTGGACGTTTCCCTATCCTTGTGAGCCTCACCGCTCTAAATGAGGACCAGCTTG


Block sizes: 48 (upstream exon), 40 (downstream exon)
Score: 39

ACGGCAGGATTCTTCTATTGGCTTCGGCGCACCAGTTCGTGCAAACATGAGGGTCGGTGGCACTTCAAGTGCTCAAGTGACATCGTCCTTGTTGGAATCGgttagtacta ... tccttttcagGTTGAGAGTGGTGATCTAATAGCTTATGGACTTATCCCAGAATTTATTGGACGTTTCCCTATCCTTGTGAGCCTCACCGCTCTAAATGAGGACCAGCTTG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 62

ACGGCAGGATTCTTCTATTGGCTTCGGCGCACCAGTTCGTGCAAACATGAGGGTCGGTGGCACTTCAAGTGCTCAAGTGACATCGTCCTTGTTGGAATCGgttagtacta ... tccttttcagGTTGAGAGTGGTGATCTAATAGCTTATGGACTTATCCCAGAATTTATTGGACGTTTCCCTATCCTTGTGAGCCTCACCGCTCTAAATGAGGACCAGCTTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctattgattagttaactttctgtcctagaggtgtttcaatgtgtttccttttcagGTTGAGAGTGGTGATCTAATAGCTTATGGACTTATCCCAGAATTTATTGGACGTTTCCCTATCCTTGTGAGCCTCACCGCTCTAAATGAGGACCAGCTTG
         agttaac  putative branch site (score: 62)
                                       tgtgtttccttttc  putative PPT
      attagttaa  TA-rich tract