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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatttcacctttttttcttttccaaatagtttttagttggtttaacaataacaataactaagtctgttatgtcttatttgctagCTGTGCACACTTGAGTTTGACATACGTCGCCCTTCATACTACTGGCTACTTGTTGCCTTGGGCCTTTATCAACCATATGTGTGGGAATATTCGAGGCTAA

Basic information

species Zea mays
transcript GRMZM2G032049_T01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G032049_T01 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os01g09000.1 (Oryza sativa), 3'ss of exon 13
gtaatttcacctttttttcttttccaaatagtttttagttggtttaacaataacaataactaagtctgttatgtcttatttgctagCTGTGCACACTTGAGTTTGACATACGTCGCCCTTCATACTACTGGCTACTTGTTGCCTTGGGCCTTTATCAACCATATGTGTGGGAATATTCGAGGCTAA
             |||  ||||||  |||    || |||| |||  |  ||  ||  |  |        | ||  |||||   ||||||||||| || |||||||||||||||||||| |||||||||||||||||||||||||||||||| || || |||||||| ||||| |||||||||||||
---------gtactttgccttttctcaattagattgagttagttgcattatggcatgatgtggactaagtgtgg-ttattcattagCTGTGCACGCTCGAGTTTGACATACGTCGCCCGTCATACTACTGGCTACTTGTTGCCTTGGGCCTGTACCAGCCATATGTTTGGGAGTATTCGAGGCTAA
















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|32933496|gb|CF038308.1|CF038308
EST:     ATGACTACGCTCATTGCATGGTGGATTCTCTTGAAAACATCACACATTCG                         CTGTGCACACTTGAGTTTGACATACGTCGCCCTTCATACTACTGGCTACTT
genomic: ATGACTACGCTCATTGCATGGTGGATTCTCTTGAAAACATCACACATTCGgtaatttcac ... tatttgctagCTGTGCACACTTGAGTTTGACATACGTCGCCCTTCATACTACTGGCTACTT
EST: gi|32934107|gb|CF038919.1|CF038919
EST:     ATGACTACGCTCATTGCATGGTGGATTCTCTTGAAAACATCACACATTCG                         CTGTGCACACTTGAGTTTGACATACGTCGCCCTTCATACTACTGGCTACTT
genomic: ATGACTACGCTCATTGCATGGTGGATTCTCTTGAAAACATCACACATTCGgtaatttcac ... tatttgctagCTGTGCACACTTGAGTTTGACATACGTCGCCCTTCATACTACTGGCTACTT
EST: gi|32933499|gb|CF038311.1|CF038311
EST:     ATGACTACGCTCATTGCATGGTGGATTCTCTTGAAAACATCACACATTCG                         CTGTGCACACTTGAGTTTGACATACGTCGCCCTTCATACTACTGGCTACTT
genomic: ATGACTACGCTCATTGCATGGTGGATTCTCTTGAAAACATCACACATTCGgtaatttcac ... tatttgctagCTGTGCACACTTGAGTTTGACATACGTCGCCCTTCATACTACTGGCTACTT

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: 217

TTCACCCCCCATCCACATGCTGGCGACAAGTGGTGTGTCTATCCGAGCTATGACTACGCTCATTGCATGGTGGATTCTCTTGAAAACATCACACATTCGgtaatttcac ... tatttgctagCTGTGCACACTTGAGTTTGACATACGTCGCCCTTCATACTACTGGCTACTTGTTGCCTTGGGCCTTTATCAACCATATGTGTGGGAATATTCGAGGCTAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 229

TTCACCCCCCATCCACATGCTGGCGACAAGTGGTGTGTCTATCCGAGCTATGACTACGCTCATTGCATGGTGGATTCTCTTGAAAACATCACACATTCGgtaatttcac ... tatttgctagCTGTGCACACTTGAGTTTGACATACGTCGCCCTTCATACTACTGGCTACTTGTTGCCTTGGGCCTTTATCAACCATATGTGTGGGAATATTCGAGGCTAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 299

TTCACCCCCCATCCACATGCTGGCGACAAGTGGTGTGTCTATCCGAGCTATGACTACGCTCATTGCATGGTGGATTCTCTTGAAAACATCACACATTCGgtaatttcac ... tatttgctagCTGTGCACACTTGAGTTTGACATACGTCGCCCTTCATACTACTGGCTACTTGTTGCCTTGGGCCTTTATCAACCATATGTGTGGGAATATTCGAGGCTAA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 231

TTCACCCCCCATCCACATGCTGGCGACAAGTGGTGTGTCTATCCGAGCTATGACTACGCTCATTGCATGGTGGATTCTCTTGAAAACATCACACATTCGgtaatttcac ... tatttgctagCTGTGCACACTTGAGTTTGACATACGTCGCCCTTCATACTACTGGCTACTTGTTGCCTTGGGCCTTTATCAACCATATGTGTGGGAATATTCGAGGCTAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttagttggtttaacaataacaataactaagtctgttatgtcttatttgctagCTGTGCACACTTGAGTTTGACATACGTCGCCCTTCATACTACTGGCTACTTGTTGCCTTGGGCCTTTATCAACCATATGTGTGGGAATATTCGAGGCTAA
                      caataac  putative branch site (score: 231)
                                          tcttattt  putative PPT
           tttaacaataacaata  TA-rich tract