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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaatagttttaatcctttttactagtttatttatgtttgatttaattaaacattctttcgctaaaactgctcttaactatttgcagCCCCAGGTAGCACAGTGCAAATTCACTGGTATATAATGACGAGTCCTTTTACCGATGAAGTGACCCGAAAGTTCTTTGAAACCCACAGATATTTTGGTTT

Basic information

species Zea mays
transcript GRMZM2G155729_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G155729_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os08g10600.1 (Oryza sativa), 3'ss of exon 5
gtaaaatagttttaatcctttttactagtttatttatgtttgatttaattaaacattctttcgctaaaactgctcttaactatttgcagCCCCAGGTAGCACAGTGCAAATTCACTGGTATATAATGACGAGTCCTTTTACCGATGAAGTGACCCGAAAGTTCTTTGAAACCCACAGATATTTTGGTTT---------
||||  ||||           ||| | |||| ||||   ||   ||||  || ||    |||   |       | |||||| | |||| |||||||||   ||   ||||| ||||||||||||||||| || || ||||| ||||||| ||| ||||| || ||||||| ||||||||||||||| ||         
gtaatttagtcaagcatgccattaatggtttctttactcttt-cttaaaaaatcacatgttcaaca-------tgttaactttgtgcaaccccagGTACTCCA---CAAATACACTGGTATATAATGACTAGCCCCTTTACTGATGAAGCGACTCGAAAATTTTTTGAAAGCCACAGATATTTTGGCTTAGAGCCTGA
















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|71439643|gb|DR820693.1|DR820693
EST:     AGCTGAACGGATTTTATGTATTCAGAAGCTGGCTGCACAGTGCACTGATG                         CCCCAGGTAGCACAGTGCAAATTCACTGGTATATAATGACGAGTCCTTTTA
genomic: AGCTGAACGGATTTTATGTATTCAGAAGCTGGCTGCACAGTGCACTGATGgtaaaatagt ... ctatttgcagCCCCAGGTAGCACAGTGCAAATTCACTGGTATATAATGACGAGTCCTTTTA
EST: gi|74243750|gb|DT651664.1|DT651664
EST:     AGCTGAACGGATTTTATGTATTCAGAAGCTGGCTGCACAGTGCACTGATG                         CCCCAGGTAGCACAGTGCAAATTCACTGGTATATAATGACGAGTCCTTTTA
genomic: AGCTGAACGGATTTTATGTATTCAGAAGCTGGCTGCACAGTGCACTGATGgtaaaatagt ... ctatttgcagCCCCAGGTAGCACAGTGCAAATTCACTGGTATATAATGACGAGTCCTTTTA
EST: gi|33468149|gb|CF245198.1|CF245198
EST:     AGCTGAACGGATTTTATGTATTCAGAAGCTGGCTGCACAGTGCACTGATG                         CCCCAGGTAGCACAGTGCAAATTCACTG
genomic: AGCTGAACGGATTTTATGTATTCAGAAGCTGGCTGCACAGTGCACTGATGgtaaaatagt ... ctatttgcagCCCCAGGTAGCACAGTGCAAATTCACTG
EST: gi|148942820|gb|EC887853.2|EC887853
EST:     AGCTGAACGGATTTTATGTATTCAGAAGCTGGCTGCACAGTGCACTGATG                         CCCCAGGTAGCACAGTGCAAATTCACTGGTATATAATGACGAGTCCTTTTA
genomic: AGCTGAACGGATTTTATGTATTCAGAAGCTGGCTGCACAGTGCACTGATGgtaaaatagt ... ctatttgcagCCCCAGGTAGCACAGTGCAAATTCACTGGTATATAATGACGAGTCCTTTTA

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), 46 (downstream exon)
Score: 84

GTATCGGGCTCCCATCTAGGAAGTCACTTTTCCAACTACAAGCTGAACGGATTTTATGTATTCAGAAGCTGGCTGCACAGTGCACTGATGgtaaaatagt ... ctatttgcagCCCCAGGTAGCACAGTGCAAATTCACTGGTATATAATGACGAGTCCTTTTACCGATGAAGTGACCCGAAAGTTCTTTGAAACCCACAGATATTTTGGTTT


Block sizes: 47 (upstream exon), 46 (downstream exon)
Score: 34

GTATCGGGCTCCCATCTAGGAAGTCACTTTTCCAACTACAAGCTGAACGGATTTTATGTATTCAGAAGCTGGCTGCACAGTGCACTGATGgtaaaatagt ... ctatttgcagCCCCAGGTAGCACAGTGCAAATTCACTGGTATATAATGACGAGTCCTTTTACCGATGAAGTGACCCGAAAGTTCTTTGAAACCCACAGATATTTTGGTTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 56

GTATCGGGCTCCCATCTAGGAAGTCACTTTTCCAACTACAAGCTGAACGGATTTTATGTATTCAGAAGCTGGCTGCACAGTGCACTGATGgtaaaatagt ... ctatttgcagCCCCAGGTAGCACAGTGCAAATTCACTGGTATATAATGACGAGTCCTTTTACCGATGAAGTGACCCGAAAGTTCTTTGAAACCCACAGATATTTTGGTTT


Block sizes: 49 (upstream exon), 39 (downstream exon)
Score: 77

GTATCGGGCTCCCATCTAGGAAGTCACTTTTCCAACTACAAGCTGAACGGATTTTATGTATTCAGAAGCTGGCTGCACAGTGCACTGATGgtaaaatagt ... ctatttgcagCCCCAGGTAGCACAGTGCAAATTCACTGGTATATAATGACGAGTCCTTTTACCGATGAAGTGACCCGAAAGTTCTTTGAAACCCACAGATATTTTGGTTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgtttgatttaattaaacattctttcgctaaaactgctcttaactatttgcagCCCCAGGTAGCACAGTGCAAATTCACTGGTATATAATGACGAGTCCTTTTACCGATGAAGTGACCCGAAAGTTCTTTGAAACCCACAGATATTTTGGTTT
                                       tcttaac  putative branch site (score: 77)
     ttgatttaattaaaca  TA-rich tract