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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggtttcctcgttttcttcttattttgtttcctcgtcgtcgcagcctgcaaattggtggtttcttggttcttatcagtggagctcgctttggaatttgcagGCACCGTTCTGAGCTGCGCTGGTGCTCCTGGAAAGGTACTGGTGCCTGGAGGTGGCAGTGATGACTTGCTTTCCTCCGCAGAGCCGGTCGTGGACACTCA

Basic information

species Zea mays
transcript GRMZM2G073054_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G073054_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os04g33460.1 (Oryza sativa), 3'ss of exon 1
ggtttcctcgttttcttcttatt-ttgtttcctcgtcgtcgcagcctgcaaattgg--tggtttcttggt-tcttatcagtggagctcgctttggaatttgcagGCACCGTTCTGAGCTGCGCTGGTGCTCCTGGAAAGGTACTGGTGCCTGGAGGTGGCAGTGATGACTTGCTTTCCTCCGCAGAGCCGGTCGTGGACACTCA
   ||    |  |  | |  ||  |   ||  |  | || ||| | ||||| | ||  |||| |   | |  || |  ||| |||   |||||| | ||||||||   |||| |||||||||| ||||||||||| ||||| ||||||||||| ||||| || || |||||||| ||||| || || || | |||||| |||||
---ttttgaggctgatgcagatgatctcttatttattgttgcaacttgcaagtgggggtggtatggcgttgcctgactagtagagtcggctttgca-tttgcagGTGGCGTTGTGAGCTGCGCGGGTGCTCCTGGGAAGGTGCTGGTGCCTGGCGGTGGGAGCGACGACTTGCTGTCCTCTGCGGAACCAGACGTGGAAACTCA
















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|149040593|gb|EE046834.2|EE046834
EST:     TGCGGTGGACTTGCCGTCGGTGCTCTTCAGGAGGAAGGACGCTTTCTCTC                         GCACCGTTCTGAGCTGCGCTGGTGCTCCTGGAAAGGTACTGGTGCCTGGAG
genomic: TGCGGTGGACTTGCCGTCGGTGCTCTTCAGGAGGAAGGACGCTTTCTCTCgtacggctct ... gaatttgcagGCACCGTTCTGAGCTGCGCTGGTGCTCCTGGAAAGGTACTGGTGCCTGGAG
EST: gi|101383106|gb|EB813605.1|EB813605
EST:     TGCGGTGGACTTGCCGTCGGTGCTCTTCAGGAGGAAGGACGCTTTCTCTC                         GCACCGTTCTGAGCTGCGCTGGTGCTCCTGGAAAGGTACTGGTGCCTGGAG
genomic: TGCGGTGGACTTGCCGTCGGTGCTCTTCAGGAGGAAGGACGCTTTCTCTCgtacggctct ... gaatttgcagGCACCGTTCTGAGCTGCGCTGGTGCTCCTGGAAAGGTACTGGTGCCTGGAG
EST: gi|89253055|gb|DY624841.1|DY624841
EST:     TGCGGTGGACTTGCCGTCGGTGCTCTTCAGGAGGAAGGACGCTTTCTCTC                         GCACCGTTCTGAGCTGCGCTGGTGCTCCTGGAAAGGTACTGGTGCCTGGAG
genomic: TGCGGTGGACTTGCCGTCGGTGCTCTTCAGGAGGAAGGACGCTTTCTCTCgtacggctct ... gaatttgcagGCACCGTTCTGAGCTGCGCTGGTGCTCCTGGAAAGGTACTGGTGCCTGGAG

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: 966

GGGGTCGTGCGGCCCGGCGGCTCGGCGCGATCTGGTGGGGAGCGGAGGAGTGCGGTGGACTTGCCGTCGGTGCTCTTCAGGAGGAAGGACGCTTTCTCTCgtacggctct ... gaatttgcagGCACCGTTCTGAGCTGCGCTGGTGCTCCTGGAAAGGTACTGGTGCCTGGAGGTGGCAGTGATGACTTGCTTTCCTCCGCAGAGCCGGTCGTGGACACTCA


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 158

GGGGTCGTGCGGCCCGGCGGCTCGGCGCGATCTGGTGGGGAGCGGAGGAGTGCGGTGGACTTGCCGTCGGTGCTCTTCAGGAGGAAGGACGCTTTCTCTCgtacggctct ... gaatttgcagGCACCGTTCTGAGCTGCGCTGGTGCTCCTGGAAAGGTACTGGTGCCTGGAGGTGGCAGTGATGACTTGCTTTCCTCCGCAGAGCCGGTCGTGGACACTCA


Block sizes: 48 (upstream exon), 42 (downstream exon)
Score: 12

GGGGTCGTGCGGCCCGGCGGCTCGGCGCGATCTGGTGGGGAGCGGAGGAGTGCGGTGGACTTGCCGTCGGTGCTCTTCAGGAGGAAGGACGCTTTCTCTCgtacggctct ... gaatttgcagGCACCGTTCTGAGCTGCGCTGGTGCTCCTGGAAAGGTACTGGTGCCTGGAGGTGGCAGTGATGACTTGCTTTCCTCCGCAGAGCCGGTCGTGGACACTCA


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 354

GGGGTCGTGCGGCCCGGCGGCTCGGCGCGATCTGGTGGGGAGCGGAGGAGTGCGGTGGACTTGCCGTCGGTGCTCTTCAGGAGGAAGGACGCTTTCTCTCgtacggctct ... gaatttgcagGCACCGTTCTGAGCTGCGCTGGTGCTCCTGGAAAGGTACTGGTGCCTGGAGGTGGCAGTGATGACTTGCTTTCCTCCGCAGAGCCGGTCGTGGACACTCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcaaattggtggtttcttggttcttatcagtggagctcgctttggaatttgcagGCACCGTTCTGAGCTGCGCTGGTGCTCCTGGAAAGGTACTGGTGCCTGGAGGTGGCAGTGATGACTTGCTTTCCTCCGCAGAGCCGGTCGTGGACACTCA
                     ttcttat  TA-rich tract