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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtgtgcgttcgagcgttaattataccgcagtgtttaatgccttcgaacgttcacggatcgcattattcttgtcggcagCCCCCGCCACTGTCCAGCGACGAGGAGACGGTGCTCCGGCTCGGCAACTACGTCCCGGTCTTCGTCATGCTCCCA

Basic information

species Zea mays
transcript GRMZM5G803981_T01
intron # 1
splice site 3'
intron type U2

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|149107686|gb|EE189563.2|EE189563
EST:     CGCTTGGTCCTGTGGCCACCGAGCCCGCAGAAAGGTCTCCCGTGCCACAG                         CCCCCGCCACTGTCCAGCGACGAGGAGACGGTGCTCCGGCTCGGCAACTAC
genomic: CGCTTGGTCCTGTGGCCACCGAGCCCGCAGAAAGGTCTCCCGTGCCACAGgtacgtgtgc ... ttgtcggcagCCCCCGCCACTGTCCAGCGACGAGGAGACGGTGCTCCGGCTCGGCAACTAC
EST: gi|149105248|gb|EE290739.2|EE290739
EST:     CGCTTGGTCCTGTGGCCACCGAGCCCGCAGAAAGGTCTCCCGTGCCACAG                         CCCCCGCCACTGTCCAGCGACGAGGAGACGGTGCTCCGGCTCGGCAACTAC
genomic: CGCTTGGTCCTGTGGCCACCGAGCCCGCAGAAAGGTCTCCCGTGCCACAGgtacgtgtgc ... ttgtcggcagCCCCCGCCACTGTCCAGCGACGAGGAGACGGTGCTCCGGCTCGGCAACTAC
EST: gi|148969543|gb|EE020371.2|EE020371
EST:     CGCTTGGTCCTGTGGCCACCGAGCCCGCAGAAAGGTCTCCCGTGCCACAG                         CCCCCGCCACTGTCCAGCGACGAGGAGACGGTGCTCCGGCTCGGCAACTAC
genomic: CGCTTGGTCCTGTGGCCACCGAGCCCGCAGAAAGGTCTCCCGTGCCACAGgtacgtgtgc ... ttgtcggcagCCCCCGCCACTGTCCAGCGACGAGGAGACGGTGCTCCGGCTCGGCAACTAC
EST: gi|149078052|gb|EE166793.2|EE166793
EST:     CGCTTGGTCCTGTGGCCACCGAGCCCGCAGAAAGGTCTCCCGTGCCACAG                         CCCCCGCCACTGTCCAGCGACGAGGAGACGGTGCTCCGGCTCGGCAACTAC
genomic: CGCTTGGTCCTGTGGCCACCGAGCCCGCAGAAAGGTCTCCCGTGCCACAGgtacgtgtgc ... ttgtcggcagCCCCCGCCACTGTCCAGCGACGAGGAGACGGTGCTCCGGCTCGGCAACTAC
EST: gi|149005187|gb|EE039728.2|EE039728
EST:     CGCTTGGTCCTGTGGCCACCGAGCCCGCAGAAAGGTCTCCCGTGCCACAG                         CCCCCGCCACTGTCCAGCGACGAGGAGACGGTGCTCCGGCTCGGCAACTAC
genomic: CGCTTGGTCCTGTGGCCACCGAGCCCGCAGAAAGGTCTCCCGTGCCACAGgtacgtgtgc ... ttgtcggcagCCCCCGCCACTGTCCAGCGACGAGGAGACGGTGCTCCGGCTCGGCAACTAC

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 1 RNA-Seqlibrary.


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 27

GCTTGTCGCCGTCGATACCAGGAGGAGGACGAGGACGGTTGCCTCCGCCGCGCTTGGTCCTGTGGCCACCGAGCCCGCAGAAAGGTCTCCCGTGCCACAGgtacgtgtgc ... ttgtcggcagCCCCCGCCACTGTCCAGCGACGAGGAGACGGTGCTCCGGCTCGGCAACTACGTCCCGGTCTTCGTCATGCTCCCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

accgcagtgtttaatgccttcgaacgttcacggatcgcattattcttgtcggcagCCCCCGCCACTGTCCAGCGACGAGGAGACGGTGCTCCGGCTCGGCAACTACGTCCCGGTCTTCGTCATGCTCCCA
        gtttaat  putative branch site (score: 27)
 ttattctt  putative PPT
 attattctt  TA-rich tract