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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttcagtgtatttgaactttgaaacaaagcggtataaaagagttcttatcatttttgttcaattatcataccattttagcgtctttgtctcagGAAGAGTGCCAAAGGGTATCGACAGAGGGACAGAACATGCGTACGGAATTGTCTGAAAAATTTGATCATGCCATAAAG

Basic information

species Zea mays
transcript GRMZM2G107731_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G107731_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os03g17930.1 (Oryza sativa), 3'ss of exon 4
gtatg--ttcagtgtatttgaactttgaaacaaagcggtataaaagagttcttatcatttttgttcaattatcataccattttagcgtctttgtctcagGAAGAGTGCCAAAGGGTATCGACAGAGGGACAGAACATGCGTACGGAATTGTCTGAAAAATTTGATCATGCCATAAAG
|||||     |||||||  ||  ||||||      | || ||         || ||| |||||||||| ||| ||| | |||||||||   || ||||||||||||||| |||||| || |||||||| ||||| ||||| | ||| || || || |||||  || |||| ||||||
gtatggaacaagtgtatc-gagttttgaagtgt--ctgttta---------ttttcacttttgttcaactataatatc-ttttagcgttgatgactcagGAAGAGTGCCGAAGGGTGTCAACAGAGGGGCAGAATATGCGGATGGAGTTATCCGACAAATTCAATAATGCTATAAAG
















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|211002685|gb|FL029004.1|FL029004
EST:     ACTAGAATCTNCTTTGTAGGGAATTTCAGCGTCAAAACAAA-TGCTAAAA                         GAAGAGTGCCAAAGG-TATCGACAGAGGGACAGAACATGCGTACGGAAATG
genomic: ACTAGAATCT-CTTTGTAGGGAATTTCAGCGTCAAAACAAAATGCTAAAGgtatgttcag ... tttgtctcagGAAGAGTGCCAAAGGGTATCGACAGAGGGACAGAACATGCGTACGGAATTG
EST: gi|148994670|gb|EE034191.2|EE034191
EST:     GACTAGAATCTCTTTGTAGGGAATTTCAGCGTCAAAACAAAATGCTAAAG                         GAAGAGTGCCAAAGGGTATCGACAGAGGGACAGAACATGCGTACGGAATTG
genomic: GACTAGAATCTCTTTGTAGGGAATTTCAGCGTCAAAACAAAATGCTAAAGgtatgttcag ... tttgtctcagGAAGAGTGCCAAAGGGTATCGACAGAGGGACAGAACATGCGTACGGAATTG
EST: gi|71436912|gb|DR817962.1|DR817962
EST:     GACTAGAATCTCTTTGTAGGGAATTTCAGCGTCAAAACAAAATGCTAAAG                         GAAGAGTGCCAAAGGGTATCGACAGAGGGACAGAACATGCGTACGGAAATG
genomic: GACTAGAATCTCTTTGTAGGGAATTTCAGCGTCAAAACAAAATGCTAAAGgtatgttcag ... tttgtctcagGAAGAGTGCCAAAGGGTATCGACAGAGGGACAGAACATGCGTACGGAATTG
EST: gi|31354731|gb|CD439088.1|CD439088
EST:     GACTAGAATCTCTTTGTAGGGAATTTCAGCGTCAAAACAAAATGCTAAAG                         GAAGAGTGCCAAAGGGTATCGACAGAGGGACAGAACATGCGTACGGAATTG
genomic: GACTAGAATCTCTTTGTAGGGAATTTCAGCGTCAAAACAAAATGCTAAAGgtatgttcag ... tttgtctcagGAAGAGTGCCAAAGGGTATCGACAGAGGGACAGAACATGCGTACGGAATTG
EST: gi|60358220|gb|DN225193.1|DN225193
EST:     GACTAGAATCTCTTTGTAGGGAATTTCAGCGTCAAAACAAAATGCTAAAG                         GAAGAGTGCCAAAGGGTATCGACAGAGGGACAGAACATGCGTACGGAATTG
genomic: GACTAGAATCTCTTTGTAGGGAATTTCAGCGTCAAAACAAAATGCTAAAGgtatgttcag ... tttgtctcagGAAGAGTGCCAAAGGGTATCGACAGAGGGACAGAACATGCGTACGGAATTG
EST: gi|91055771|gb|EB166189.1|EB166189
EST:     ACTAGAATCTCTTTGTAGGGAATTTCAGCGTCAAAACAAAATGGCTAA-G                         GAAGAGTGCCAAAGGGTATCGACAGAGGGACAGAACATGCGTACGGAATT
genomic: ACTAGAATCTCTTTGTAGGGAATTTCAGCGTCAAAACAAAATG-CTAAAGgtatgttcag ... tttgtctcagGAAGAGTGCCAAAGGGTATCGACAGAGGGACAGAACATGCGTACGGAATT
EST: gi|149081200|gb|EE170309.2|EE170309
EST:     GACTAGAATCTCTTTGTAGGGAATTTCAGCGTCAAAACAAAATGCTAAAG                         GAAGAGTGCCAAAGGGTATCGACAGAGGGACAGAACATGCGTACGGAATTG
genomic: GACTAGAATCTCTTTGTAGGGAATTTCAGCGTCAAAACAAAATGCTAAAGgtatgttcag ... tttgtctcagGAAGAGTGCCAAAGGGTATCGACAGAGGGACAGAACATGCGTACGGAATTG
EST: gi|149027108|gb|EE046399.2|EE046399
EST:     GACTAGAATCTCTTTGTAGGGAATTTCAGCGTCAAAACAAAATGCTAAAG                         GAAGAGTGCCAAAGGGTATCGACAGAGGGACAGAACATGCGTACGGAATTG
genomic: GACTAGAATCTCTTTGTAGGGAATTTCAGCGTCAAAACAAAATGCTAAAGgtatgttcag ... tttgtctcagGAAGAGTGCCAAAGGGTATCGACAGAGGGACAGAACATGCGTACGGAATTG
EST: gi|148961119|gb|EE011825.2|EE011825
EST:     GACTAGAATCTCTTTGTAGGGAATTTCAGCGTCAAAACAAAATGCTAAGG                         GAAGAGTGCCAAA
genomic: GACTAGAATCTCTTTGTAGGGAATTTCAGCGTCAAAACAAAATGCTAAAGgtatgttcag ... tttgtctcagGAAGAGTGCCAAA

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: 252

CCATTGCAGTCAAAGATAGACTAGAATCTCTTTGTAGGGAATTTCAGCGTCAAAACAAAATGCTAAAGgtatgttcag ... tttgtctcagGAAGAGTGCCAAAGGGTATCGACAGAGGGACAGAACATGCGTACGGAATTGTCTGAAAAATTTGATCATGCCATAAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 180

CCATTGCAGTCAAAGATAGACTAGAATCTCTTTGTAGGGAATTTCAGCGTCAAAACAAAATGCTAAAGgtatgttcag ... tttgtctcagGAAGAGTGCCAAAGGGTATCGACAGAGGGACAGAACATGCGTACGGAATTGTCTGAAAAATTTGATCATGCCATAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 149

CCATTGCAGTCAAAGATAGACTAGAATCTCTTTGTAGGGAATTTCAGCGTCAAAACAAAATGCTAAAGgtatgttcag ... tttgtctcagGAAGAGTGCCAAAGGGTATCGACAGAGGGACAGAACATGCGTACGGAATTGTCTGAAAAATTTGATCATGCCATAAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 224

CCATTGCAGTCAAAGATAGACTAGAATCTCTTTGTAGGGAATTTCAGCGTCAAAACAAAATGCTAAAGgtatgttcag ... tttgtctcagGAAGAGTGCCAAAGGGTATCGACAGAGGGACAGAACATGCGTACGGAATTGTCTGAAAAATTTGATCATGCCATAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agagttcttatcatttttgttcaattatcataccattttagcgtctttgtctcagGAAGAGTGCCAAAGGGTATCGACAGAGGGACAGAACATGCGTACGGAATTGTCTGAAAAATTTGATCATGCCATAAAG
                                           tctttgtctc  CT-rich tract
       ttatcatttttgttca  TA-rich tract