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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cattagttacgaagggtacggtacggatgaaacgttaaatctgagggatactcataaccgatttgtgaccatgacattttttttttgttccatgttgcagACCTACTCAAATCCATTACAAGATAACCCGGCATACTCTGTTGTGAA

Basic information

species Zea mays
transcript GRMZM2G443985_T04
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G443985_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os06g05860.1 (Oryza sativa), 3'ss of exon 1
-cattagttacgaagggtacggtacggatgaaacgttaaat-ctgagggatactcataaccgatttgtgaccatgacattttttttttgttccatgttgcagACCTACTCAAATCCATTACAAGATAACCCGGCATACTCTGTTGTGAA
  ||  || | ||   ||     |  |       | |||||  ||||   |       |      |||||  ||||      || | ||||   || ||||||| |||||||||||| | |||||||||||||||||||| ||||||||
tgatacgtgatgattagtc--acattggccttgtgataaatgttgagtcttcgattctatttcgctgtgattatgatggccattgtctgttgtttgatgcagACATACTCAAATCCACTGCAAGATAACCCGGCATACTCGGTTGTGAA
















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|148972520|gb|EE023481.2|EE023481
EST:     ACGTCTTAGAAGACGTGCCGCACGTGTCGGACTACCTCCCCGATCTCCCG                         ACCTACTCAAATCCATTACAAGATAACCCGGCATACTCTGTTGTGAA
genomic: ACGTCTTAGAAGACGTGCCGCACGTGTCGGACTACCTCCCCGATCTCCCGgtgagtgccg ... catgttgcagACCTACTCAAATCCATTACAAGATAACCCGGCATACTCTGTTGTGAA
EST: gi|211132977|gb|FL170882.1|FL170882
EST:     ACGTCTTAGAAGACGTGCCGCACGTGTCGGACTACCTCCCCGATCTCCCG                         ACCTACTCAAATCCATTACAAGATAACCCGGCATACTCTGTTGTAAA
genomic: ACGTCTTAGAAGACGTGCCGCACGTGTCGGACTACCTCCCCGATCTCCCGgtgagtgccg ... catgttgcagACCTACTCAAATCCATTACAAGATAACCCGGCATACTCTGTTGTGAA
EST: gi|211132967|gb|FL170872.1|FL170872
EST:     ACGTCTTAGAAGACGTGCCGCACGTGTCGGACTACCTCCCCGATCTCCCG                         ACCTACTCAAATCCATTACAAGATAACCCGGCATACTCTGTTGTGAA
genomic: ACGTCTTAGAAGACGTGCCGCACGTGTCGGACTACCTCCCCGATCTCCCGgtgagtgccg ... catgttgcagACCTACTCAAATCCATTACAAGATAACCCGGCATACTCTGTTGTGAA

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), 47 (downstream exon)
Score: 96

GGCGATGGACGGTGCTGCAGCGGTCAAGCTGGTACCCGGTGAGGCCGGGTACGTCTTAGAAGACGTGCCGCACGTGTCGGACTACCTCCCCGATCTCCCGgtgagtgccg ... catgttgcagACCTACTCAAATCCATTACAAGATAACCCGGCATACTCTGTTGTGAA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 157

GGCGATGGACGGTGCTGCAGCGGTCAAGCTGGTACCCGGTGAGGCCGGGTACGTCTTAGAAGACGTGCCGCACGTGTCGGACTACCTCCCCGATCTCCCGgtgagtgccg ... catgttgcagACCTACTCAAATCCATTACAAGATAACCCGGCATACTCTGTTGTGAA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 135

GGCGATGGACGGTGCTGCAGCGGTCAAGCTGGTACCCGGTGAGGCCGGGTACGTCTTAGAAGACGTGCCGCACGTGTCGGACTACCTCCCCGATCTCCCGgtgagtgccg ... catgttgcagACCTACTCAAATCCATTACAAGATAACCCGGCATACTCTGTTGTGAA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 110

GGCGATGGACGGTGCTGCAGCGGTCAAGCTGGTACCCGGTGAGGCCGGGTACGTCTTAGAAGACGTGCCGCACGTGTCGGACTACCTCCCCGATCTCCCGgtgagtgccg ... catgttgcagACCTACTCAAATCCATTACAAGATAACCCGGCATACTCTGTTGTGAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggatactcataaccgatttgtgaccatgacattttttttttgttccatgttgcagACCTACTCAAATCCATTACAAGATAACCCGGCATACTCTGTTGTGAA
      tcataac  putative branch site (score: 110)
                             cattttttttttgttc  putative PPT
                         atgacatttttttttt  TA-rich tract