Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatctgattcattttgagcaacaaaagtagttactaagaaaggtccatagagtttgcgcggtgaaggtttcttaactgatatgctttgtgctgtcttcagGAGTTGAACACCTTTTAAGGGACGTAAAGGACACAACCATAAGCACACTTGCTACAGAG

Basic information

species Zea mays
transcript GRMZM2G368908_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G368908_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os04g56646.1 (Oryza sativa), 3'ss of exon 5
--aatctgattcattt--tgagcaacaaaagtagttactaagaaaggtccatagagtttgcgcggtgaaggtttcttaactgatatgc-tttgtgctgtcttcagGAGTTGAACACCTTTTAAGGGACGTAAAGGACACAACCATAAGCACACTTGCTACAGAG
  | |  | ||  ||     ||    || | || ||     |  | |||  |     || |      |||| || || |||||| |   ||  | ||   |  ||||||||| || ||| | ||||| || ||||||||||| |||||||| ||||| ||||||
ctagtgaggtttcttcaccaagaggaaagaatatttttgtggtgaagtcttt-----ttccttcagaaaggattgttgactgatgtatgttcatcctacttatagGAGTTGAGCATCTTCTGAGGGATGTCAAGGACACAACAATAAGCACGCTTGCGACAGAG
















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|149042715|gb|EE047230.2|EE047230
EST:     ATTTGTCCATGTTCCTTCAGAAATTGCTGCTCATGAAGTTGAGGAAATTG                         GAGTTGAACACCTTTTTAGGGACGTAAAGGACACAACCATAAGCACACTTG
genomic: ATTTGTCCATGTTCCTTCAGAAATTGCTGCTCATGAAGTTGAGGAAATTGgtaagacttg ... ctgtcttcagGAGTTGAACACCTTTTAAGGGACGTAAAGGACACAACCATAAGCACACTTG
EST: gi|32930134|gb|CF034946.1|CF034946
EST:     ATTTGTCCATGTTCCTTCAGAAATTGCTGCTCATGAAGTTGAGGAAATTG                         GAGTTGAACACCTTTTAAGGGACGTAAAGGACACAACCATAAGCACACTTG
genomic: ATTTGTCCATGTTCCTTCAGAAATTGCTGCTCATGAAGTTGAGGAAATTGgtaagacttg ... ctgtcttcagGAGTTGAACACCTTTTAAGGGACGTAAAGGACACAACCATAAGCACACTTG
EST: gi|148973687|gb|EE024808.2|EE024808
EST:     ATTTGTCCATGTTCCTTCAGAAATTGCTGCTCATGAAGTTGAGGAAATTG                         GAGTTGAACACCTTTTAAGGGACGTAAAGGACACAACCATAAGCACACTTG
genomic: ATTTGTCCATGTTCCTTCAGAAATTGCTGCTCATGAAGTTGAGGAAATTGgtaagacttg ... ctgtcttcagGAGTTGAACACCTTTTAAGGGACGTAAAGGACACAACCATAAGCACACTTG

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), 48 (downstream exon)
Score: 248

AATGCTACACAGAAAAGTCAGAAGGTATTTGTCCATGTTCCTTCAGAAATTGCTGCTCATGAAGTTGAGGAAATTGgtaagacttg ... ctgtcttcagGAGTTGAACACCTTTTAAGGGACGTAAAGGACACAACCATAAGCACACTTGCTACAGAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 210

AATGCTACACAGAAAAGTCAGAAGGTATTTGTCCATGTTCCTTCAGAAATTGCTGCTCATGAAGTTGAGGAAATTGgtaagacttg ... ctgtcttcagGAGTTGAACACCTTTTAAGGGACGTAAAGGACACAACCATAAGCACACTTGCTACAGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 203

AATGCTACACAGAAAAGTCAGAAGGTATTTGTCCATGTTCCTTCAGAAATTGCTGCTCATGAAGTTGAGGAAATTGgtaagacttg ... ctgtcttcagGAGTTGAACACCTTTTAAGGGACGTAAAGGACACAACCATAAGCACACTTGCTACAGAG


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 146

AATGCTACACAGAAAAGTCAGAAGGTATTTGTCCATGTTCCTTCAGAAATTGCTGCTCATGAAGTTGAGGAAATTGgtaagacttg ... ctgtcttcagGAGTTGAACACCTTTTAAGGGACGTAAAGGACACAACCATAAGCACACTTGCTACAGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catagagtttgcgcggtgaaggtttcttaactgatatgctttgtgctgtcttcagGAGTTGAACACCTTTTAAGGGACGTAAAGGACACAACCATAAGCACACTTGCTACAGAG
                                             ctgtcttc  CT-rich tract
                      tttcttaa  TA-rich tract