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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttccaagtcttacttcacttttgtatggaaattgtcaatgctgggttttaatggctttctgtaaatgcaatcgcagACTTGAAGGAAACTCATTTGCCAATGGACCTGCTCCCCCGCCGCCACCTTTTATGCCACCACCCCCTCAAAGGCCACGGAATCGTCCTAAGCATCCTCAG

Basic information

species Zea mays
transcript GRMZM2G103070_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G103070_T02 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os02g09740.1 (Oryza sativa), 3'ss of exon 9
gtatgttccaagtcttacttcacttt-tgtatggaaattgtcaatgctgggttttaatggctttctgtaaatgcaatcgcagACTTGAAGGAAACTCATTTGCCAATGGACCTGCTCCCCCGCCGCCACCTTTTATGCCACCACCCCCTCAAAGGCCACGGAATCGTCCTAAGCATCCTCAG
|||||    |  | ||||| | |||| | | |||||||  ||  ||      | ||||| | |  || || | ||| |  ||||||| ||||||||||||  | |||||||||||||| || || ||||||||||||||||||||||||  ||| ||||| ||||| || |  ||||||| |
gtatgagatac-ttttactgccctttctctttggaaatcatctttgacacactctaatgacctgttgcaattacaaccatagACTTGGAGGAAACTCATTCACAAATGGACCTGCTCCACCACCACCACCTTTTATGCCACCACCCCCTAGAAGACCACGTAATCGGCCCAGCCATCCTCGG
















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|91868538|gb|EB400066.1|EB400066
EST:     AATTTCAGTGGTTGGATACCAAAAGAATTCAGCTCCATTCCAGATGTAAC                         ACTTGAAGGAAACTCATTTGCCAATGGACCTGCTCCCCCGCCGCCACCTTT
genomic: AATTTCAGTGGTTGGATACCAAAAGAATTCAGCTCCATTCCAGATGTAACgtatgttcca ... gcaatcgcagACTTGAAGGAAACTCATTTGCCAATGGACCTGCTCCCCCGCCGCCACCTTT
EST: gi|148960881|gb|EE011562.2|EE011562
EST:     AATTTCAGTGGCTGGATACCAAAAGAATTCAGCTCCATTCCAGATGTAAC                         ACTTGAAGGAAACTCATTTGCCAATGGACCTGCTCCCCCGCCGCCACCTTT
genomic: AATTTCAGTGGTTGGATACCAAAAGAATTCAGCTCCATTCCAGATGTAACgtatgttcca ... gcaatcgcagACTTGAAGGAAACTCATTTGCCAATGGACCTGCTCCCCCGCCGCCACCTTT

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), 46 (downstream exon)
Score: 100

AAACATAGCAAACAACAATTTCAGTGGTTGGATACCAAAAGAATTCAGCTCCATTCCAGATGTAACgtatgttcca ... gcaatcgcagACTTGAAGGAAACTCATTTGCCAATGGACCTGCTCCCCCGCCGCCACCTTTTATGCCACCACCCCCTCAAAGGCCACGGAATCGTCCTAAGCATCCTCAG


Block sizes: 43 (upstream exon), 46 (downstream exon)
Score: 28

AAACATAGCAAACAACAATTTCAGTGGTTGGATACCAAAAGAATTCAGCTCCATTCCAGATGTAACgtatgttcca ... gcaatcgcagACTTGAAGGAAACTCATTTGCCAATGGACCTGCTCCCCCGCCGCCACCTTTTATGCCACCACCCCCTCAAAGGCCACGGAATCGTCCTAAGCATCCTCAG


Block sizes: 39 (upstream exon), 43 (downstream exon)
Score: 21

AAACATAGCAAACAACAATTTCAGTGGTTGGATACCAAAAGAATTCAGCTCCATTCCAGATGTAACgtatgttcca ... gcaatcgcagACTTGAAGGAAACTCATTTGCCAATGGACCTGCTCCCCCGCCGCCACCTTTTATGCCACCACCCCCTCAAAGGCCACGGAATCGTCCTAAGCATCCTCAG


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 167

AAACATAGCAAACAACAATTTCAGTGGTTGGATACCAAAAGAATTCAGCTCCATTCCAGATGTAACgtatgttcca ... gcaatcgcagACTTGAAGGAAACTCATTTGCCAATGGACCTGCTCCCCCGCCGCCACCTTTTATGCCACCACCCCCTCAAAGGCCACGGAATCGTCCTAAGCATCCTCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtatggaaattgtcaatgctgggttttaatggctttctgtaaatgcaatcgcagACTTGAAGGAAACTCATTTGCCAATGGACCTGCTCCCCCGCCGCCACCTTTTATGCCACCACCCCCTCAAAGGCCACGGAATCGTCCTAAGCATCCTCAG
                        ttttaat  putative branch site (score: 167)
                        ttttaat  TA-rich tract