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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagagcagctccctcgatcatccctcgtcaccattttttccggccatcaatcaagtaaaaaaatggaaacgcaacgcagGACGACGCGTACCAGGAGACGGGCTGCTACAACCTCCACTGCTCGGGCTTCGTGCAGACCAGCAGCCGCGTGGCCATCGGCGCCGCCATCTCGCCCGTCT

Basic information

species Zea mays
transcript GRMZM2G131650_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G131650_T04 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os05g07764.1 (Oryza sativa), 3'ss of exon 5
--------------------gtaagagcagctccctcgatcatccctcgtc--------accattttttccggccatcaatcaagtaa--aaaaatggaaacgcaacgcagGACGACGCGTACCAGGAGACGGGCTGCTACAACCTCCACTGCTCGGGCTTCGTGCAGACCAGCAGCCGCGTGGCCATCGGCGCCGCCATCTCGCCCGTCT
                    |||  |     | ||| |    ||  |  |         |    |   || |  ||   | ||||| |   || |  ||  |     |||| | || ||||||||||||||||| ||||||||||| |||||||| || ||||| ||||||| ||||||  | ||||| |||||||||||||| ||| |||
gtaagttctttgctagtaaagtagtaatctgttcctagtgtttcagtattagaagagagatagatcagtcagttcaaagaacaagttactgaagaatgatgcattgtgcagAATGATGCGTACCAGGAGACGGGTTGCTACAACCTGCACTGCTCAGGGTTCGTCCAGACCAACAGCCGGATCGCCATGGGCGCCGCCATCTCCCCCATCT
















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|76010479|gb|DT937649.1|DT937649
EST:     GCCTTCAGCTGTACGGCGACAACAGCCCCAGGTTCTTCACCTACTGGACA                         GACGACGCGTACCAGGAGACGGGCTGCTACAACCTCCACTGCTCGGGCTTC
genomic: GCCCTCAGCTGTACGGCGACAACAGCCCCAGGTTCTTCACCTACTGGACAgtaagagcag ... cgcaacgcagGACGACGCGTACCAGGAGACGGGCTGCTACAACCTCCACTGCTCGGGCTTC
EST: gi|12046190|gb|BF728329.1|BF728329
EST:     GCCCTCAGCTGTACGGCGACAACAGCCCCAGGTTCTTCACCTACTGGACA                         GACGACGCGTACCAGGAGACGGGCTGCTACAACCTCCACTGCTCGGGCTTC
genomic: GCCCTCAGCTGTACGGCGACAACAGCCCCAGGTTCTTCACCTACTGGACAgtaagagcag ... cgcaacgcagGACGACGCGTACCAGGAGACGGGCTGCTACAACCTCCACTGCTCGGGCTTC
EST: gi|86474297|gb|DY240667.1|DY240667
EST:     GCCCTCAGCTGTACGGCGACAACAGCCCCAGGTTCTTCACCTACTGGACA                         GACGACGCGTACCAGGAGACGGGCTGCTACAACCTCCACTGCTCGGGCTTC
genomic: GCCCTCAGCTGTACGGCGACAACAGCCCCAGGTTCTTCACCTACTGGACAgtaagagcag ... cgcaacgcagGACGACGCGTACCAGGAGACGGGCTGCTACAACCTCCACTGCTCGGGCTTC
EST: gi|78180215|gb|DV550588.1|DV550588
EST:     GCCCTCAGCTGTACGGCGACAACAGCCCCAGGTTCTTCACCTACTGGACA                         GACGACGCGTACCAGGAGACGGGCTGCTACAACCTCCACTGCTCGGGCTTC
genomic: GCCCTCAGCTGTACGGCGACAACAGCCCCAGGTTCTTCACCTACTGGACAgtaagagcag ... cgcaacgcagGACGACGCGTACCAGGAGACGGGCTGCTACAACCTCCACTGCTCGGGCTTC
EST: gi|6827523|gb|AW331166.1|AW331166
EST:     GCCCTCAGCTGGACGGCGACAACAGCCCCAGGTTCTTCACCTACTGGACA                         GACGACGCGTACCAGGAGACGGGCTGCTACAACCTCCACTGCTCGGCCTTC
genomic: GCCCTCAGCTGTACGGCGACAACAGCCCCAGGTTCTTCACCTACTGGACAgtaagagcag ... cgcaacgcagGACGACGCGTACCAGGAGACGGGCTGCTACAACCTCCACTGCTCGGGCTTC
EST: gi|149076068|gb|EE164645.2|EE164645
EST:     GCCCTCAGCTGTACGGCGACAACAGCCCCAGGTTCTTCACCTACTGGACA                         GACGACGCGTACCAGGAGACGGGCTGCTACAACCTCCACTGCTCGGGCTTC
genomic: GCCCTCAGCTGTACGGCGACAACAGCCCCAGGTTCTTCACCTACTGGACAgtaagagcag ... cgcaacgcagGACGACGCGTACCAGGAGACGGGCTGCTACAACCTCCACTGCTCGGGCTTC

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 3 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 21

CGGCGCCTTCGGCAACGACCTCAACACCATCGAGGCCGGCTGGCAGGTCAGCCCTCAGCTGTACGGCGACAACAGCCCCAGGTTCTTCACCTACTGGACAgtaagagcag ... cgcaacgcagGACGACGCGTACCAGGAGACGGGCTGCTACAACCTCCACTGCTCGGGCTTCGTGCAGACCAGCAGCCGCGTGGCCATCGGCGCCGCCATCTCGCCCGTCT


Block sizes: 49 (upstream exon), 9 (downstream exon)
Score: 4

CGGCGCCTTCGGCAACGACCTCAACACCATCGAGGCCGGCTGGCAGGTCAGCCCTCAGCTGTACGGCGACAACAGCCCCAGGTTCTTCACCTACTGGACAgtaagagcag ... cgcaacgcagGACGACGCGTACCAGGAGACGGGCTGCTACAACCTCCACTGCTCGGGCTTCGTGCAGACCAGCAGCCGCGTGGCCATCGGCGCCGCCATCTCGCCCGTCT


Block sizes: 47 (upstream exon), 23 (downstream exon)
Score: 2

CGGCGCCTTCGGCAACGACCTCAACACCATCGAGGCCGGCTGGCAGGTCAGCCCTCAGCTGTACGGCGACAACAGCCCCAGGTTCTTCACCTACTGGACAgtaagagcag ... cgcaacgcagGACGACGCGTACCAGGAGACGGGCTGCTACAACCTCCACTGCTCGGGCTTCGTGCAGACCAGCAGCCGCGTGGCCATCGGCGCCGCCATCTCGCCCGTCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcgtcaccattttttccggccatcaatcaagtaaaaaaatggaaacgcaacgcagGACGACGCGTACCAGGAGACGGGCTGCTACAACCTCCACTGCTCGGGCTTCGTGCAGACCAGCAGCCGCGTGGCCATCGGCGCCGCCATCTCGCCCGTCT
                        aatcaagtaaaaaaat  TA-rich tract