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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtatgcaaggatcctccagcactgtatttttcataatctctgaaacaaaaacaaattggtcatggaagactgaacaggttgatgtcatgaacccctcagcttatatctttttcgcgtctgtcgtgctttcagAGATTCCTGCAGACTATGAGGGCCGTACAAGGTTCACTGATTGTATCCTCAAGCATCCAAATAATTCTTGGATATAGCCAGTTGTGGGCTATATGTTCTA

Basic information

species Zea mays
transcript GRMZM2G100484_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G100484_T03 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os09g15170.1 (Oryza sativa), 3'ss of exon 4
gtaagtatgcaaggatcctccagcactgtatttttcataatctctgaaacaaaaacaaattggtcatggaag-actgaacaggttgatgtcatgaacccctcagcttatatctttttcgcgtctgtcgtgctttcagAGATTCCTGCAGACTATGAGGGCCGTACAAGGTTCACTGATTGTATCCTCAAGCATCCAAATAATTCTTGGATATAGCCAGTTGTGGGCTATATGTTCTA
|||||||||||| |||| || |||    |||||   |||  || |        ||  |  ||| |||    | |||| | |  ||   ||  |     ||| |     ||||| ||| |  ||        || ||||||||  ||||||| ||||| ||  ||||||| || ||||| || ||||| ||||| || ||||||||||| |||||||| |||||||| || || || |
gtaagtatgcaatgatcttcaagct---tatttcaaataggctat----tgttaatta--tggccattttggtactgga-aaattttcgttgtatttacctaaa---gtatctgttttggttc------atttgcagAGATTTGTGCAGACAATGAGAGCAATACAAGGCTCCCTGATAGTCTCCTCGAGCATTCAGATAATTCTTGGCTATAGCCAATTGTGGGCAATTTGCTCCA
















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|76283310|gb|DV022878.1|DV022878
EST:     TCTCCATAGTCCGTGACCCCTCGTTCGCGCGTATAGCTGATGGCCACACT                         AGATTCCTGCAGACTATGAGGGCCGTACAAGGTTCACTGATTGTATCCTCA
genomic: TCTCCATAGTCCGTGACCCCTCGTTCGCGCGTATAGCTGATGGCCACACTgtaagtatgc ... gtgctttcagAGATTCCTGCAGACTATGAGGGCCGTACAAGGTTCACTGATTGTATCCTCA
EST: gi|78086985|gb|DV515378.1|DV515378
EST:     TCTCCATAGTCCGTGACCCCTCGTTCGCGCGTATAGCTGATGGCCACACT                         AGATTCCTGCAGACTATGAGGGCCGTACAAGGTTCACTGATTGTATCCTCA
genomic: TCTCCATAGTCCGTGACCCCTCGTTCGCGCGTATAGCTGATGGCCACACTgtaagtatgc ... gtgctttcagAGATTCCTGCAGACTATGAGGGCCGTACAAGGTTCACTGATTGTATCCTCA

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: 48 (upstream exon), 49 (downstream exon)
Score: 112

TCGTCTTCCCACAGTCATGGGAGGTTCATACGCTTACGTGGTTCCAATCCTCTCCATAGTCCGTGACCCCTCGTTCGCGCGTATAGCTGATGGCCACACTgtaagtatgc ... gtgctttcagAGATTCCTGCAGACTATGAGGGCCGTACAAGGTTCACTGATTGTATCCTCAAGCATCCAAATAATTCTTGGATATAGCCAGTTGTGGGCTATATGTTCTA


Block sizes: 46 (upstream exon), 45 (downstream exon)
Score: 18

TCGTCTTCCCACAGTCATGGGAGGTTCATACGCTTACGTGGTTCCAATCCTCTCCATAGTCCGTGACCCCTCGTTCGCGCGTATAGCTGATGGCCACACTgtaagtatgc ... gtgctttcagAGATTCCTGCAGACTATGAGGGCCGTACAAGGTTCACTGATTGTATCCTCAAGCATCCAAATAATTCTTGGATATAGCCAGTTGTGGGCTATATGTTCTA


Block sizes: 48 (upstream exon), 35 (downstream exon)
Score: 28

TCGTCTTCCCACAGTCATGGGAGGTTCATACGCTTACGTGGTTCCAATCCTCTCCATAGTCCGTGACCCCTCGTTCGCGCGTATAGCTGATGGCCACACTgtaagtatgc ... gtgctttcagAGATTCCTGCAGACTATGAGGGCCGTACAAGGTTCACTGATTGTATCCTCAAGCATCCAAATAATTCTTGGATATAGCCAGTTGTGGGCTATATGTTCTA


Block sizes: 49 (upstream exon), 43 (downstream exon)
Score: 22

TCGTCTTCCCACAGTCATGGGAGGTTCATACGCTTACGTGGTTCCAATCCTCTCCATAGTCCGTGACCCCTCGTTCGCGCGTATAGCTGATGGCCACACTgtaagtatgc ... gtgctttcagAGATTCCTGCAGACTATGAGGGCCGTACAAGGTTCACTGATTGTATCCTCAAGCATCCAAATAATTCTTGGATATAGCCAGTTGTGGGCTATATGTTCTA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttgatgtcatgaacccctcagcttatatctttttcgcgtctgtcgtgctttcagAGATTCCTGCAGACTATGAGGGCCGTACAAGGTTCACTGATTGTATCCTCAAGCATCCAAATAATTCTTGGATATAGCCAGTTGTGGGCTATATGTTCTA
 ggttgat  putative branch site (score: 22)
                                              tgctttc  putative PPT
                       ttatatcttttt  TA-rich tract