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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttttccctccttgttttctttcattagtttctgcatcaattgcagagctagatatatgtctatatacagattgaaattttacacgtgcgccggtatactgaacattttttcagGTTCAAGTGAAATGCTCATTGGTTTATATGGACTTTGAAGGTCGCTCTGATGGGCGTTCTGTAAAATCAATTATTGCTCACGTGGCTCCACTGAAACTT

Basic information

species Zea mays
transcript GRMZM2G036050_T03
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G036050_T03 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os09g39590.1 (Oryza sativa), 3'ss of exon 12
gtaagtttttccctccttgttttctttcattagtttctgcatcaattgcagagctagatatatgtctatatacagattgaaattttacacgtgcgccggtatactgaacattttttcagGTTCAAGTGAAATGCTCATTGGTTTATATGGACTTTGAAGGTCGCTCTGATGGGCGTTCTGTAAAATCAATTATTGCTCACGTGGCTCCACTGAAACTT
                |   ||| |||    | || || |||   |||     ||   ||| | | | || | | ||      |||||   |       |||  | |||||||||  |||| ||||| || || ||||| |  |||||||||||||||||||| ||||||||||| |||||||||||  |||||||||| ||||| ||| | ||||||
---------------gtaagttttttttcccatttacttcatt--ttgtctgtctgtttatttatttctagaaaaatc-----tttacttctatttaattatgatcaacattttt--agGTGCAAGTCAAGTGTTCATTAGCATATATGGACTTTGAAGGTCGGTCTGATGGGCGCTCTGTAAAATCTGTTATTGCTCATGTGGCCCCATTAAAACTT
















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|60348741|gb|DN215714.1|DN215714
EST:     GCCTGCTTCTTGATTCAACGCCCTCAAAAGTCATTTCCAACGAGATGACT                         GTTCAAGTGAAATGCTCATTGGTTTATATGGACTTTGAAGGTCGCTCTGAT
genomic: GCCTGCTTCTTGATTCAACGCCCTCAAAAGTCATTTCCAACGAGATGACTgtaagttttt ... attttttcagGTTCAAGTGAAATGCTCATTGGTTTATATGGACTTTGAAGGTCGCTCTGAT
EST: gi|5847327|gb|AW000406.1|AW000406
EST:     GCCTGCTTCTTGATTCAACGCCCTCAAAAGTCATTTCCAACGAGATGACT                         GTTCAAGTGAAATGCTCATTGGTTTATATGGACTTTGAAGGTCGCTCTGAT
genomic: GCCTGCTTCTTGATTCAACGCCCTCAAAAGTCATTTCCAACGAGATGACTgtaagttttt ... attttttcagGTTCAAGTGAAATGCTCATTGGTTTATATGGACTTTGAAGGTCGCTCTGAT
EST: gi|211178129|gb|FL062330.1|FL062330
EST:     GCCTGCTTCTTGATTCAACGCCCTCAAAAGTCATTTCCAACGAGATGACT                         GTTCAAGTGAAATGCTCATTGGTTTATATGGACTTTGAAGGTCGCTCTGAT
genomic: GCCTGCTTCTTGATTCAACGCCCTCAAAAGTCATTTCCAACGAGATGACTgtaagttttt ... attttttcagGTTCAAGTGAAATGCTCATTGGTTTATATGGACTTTGAAGGTCGCTCTGAT

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: 203

GGCCCTGGAGATGGATTAGATGGTAGGATCGATGATGGCTCAGCACGCCTGCTTCTTGATTCAACGCCCTCAAAAGTCATTTCCAACGAGATGACTgtaagttttt ... attttttcagGTTCAAGTGAAATGCTCATTGGTTTATATGGACTTTGAAGGTCGCTCTGATGGGCGTTCTGTAAAATCAATTATTGCTCACGTGGCTCCACTGAAACTT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 100

GGCCCTGGAGATGGATTAGATGGTAGGATCGATGATGGCTCAGCACGCCTGCTTCTTGATTCAACGCCCTCAAAAGTCATTTCCAACGAGATGACTgtaagttttt ... attttttcagGTTCAAGTGAAATGCTCATTGGTTTATATGGACTTTGAAGGTCGCTCTGATGGGCGTTCTGTAAAATCAATTATTGCTCACGTGGCTCCACTGAAACTT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 107

GGCCCTGGAGATGGATTAGATGGTAGGATCGATGATGGCTCAGCACGCCTGCTTCTTGATTCAACGCCCTCAAAAGTCATTTCCAACGAGATGACTgtaagttttt ... attttttcagGTTCAAGTGAAATGCTCATTGGTTTATATGGACTTTGAAGGTCGCTCTGATGGGCGTTCTGTAAAATCAATTATTGCTCACGTGGCTCCACTGAAACTT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 66

GGCCCTGGAGATGGATTAGATGGTAGGATCGATGATGGCTCAGCACGCCTGCTTCTTGATTCAACGCCCTCAAAAGTCATTTCCAACGAGATGACTgtaagttttt ... attttttcagGTTCAAGTGAAATGCTCATTGGTTTATATGGACTTTGAAGGTCGCTCTGATGGGCGTTCTGTAAAATCAATTATTGCTCACGTGGCTCCACTGAAACTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctatatacagattgaaattttacacgtgcgccggtatactgaacattttttcagGTTCAAGTGAAATGCTCATTGGTTTATATGGACTTTGAAGGTCGCTCTGATGGGCGTTCTGTAAAATCAATTATTGCTCACGTGGCTCCACTGAAACTT
                                            cattttttc  CT-rich tract
         agattgaaatttta  TA-rich tract