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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcatttgtcaatttttttatccaagtgtttactattccatgccacctttgtttctttgaaacttcatagattttcttagtgttattttcccaattatctcccccttctttgttgttgttgatatgtggcacccaaaattgtacaaCATCCAAGTGGAGAGAGAATAATGGTCATCATGTTGATTATGATCAACGGCCTGATATCTTTAG

Basic information

species Zea mays
transcript GRMZM2G082099_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G082099_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os07g07560.1 (Oryza sativa), 3'ss of exon 8
gtatgcatttgtcaattt-ttttatccaagtgt-ttactattccatgccacctttgttt--ctttgaaacttcatagattt-----tcttagtgttattttcccaattatctcccccttctttgttgttgttgatatgtggcacccaaaattgtacaaCATCCAAGTGGAGAGAGAATAATGGTCATCATGTTGATTATGATCAACGGCCTGATATCTTTAG
||| || || | ||| ||| || | || || ||| | || | | | | ||| ||| | || || | |||| || ||| |||| | | | ||| |||| ||||||| | |||||||||| |||| || ||||| ||| || || |||||||||||||| ||| ||||||||||||||||
gtaagctattaatagtttgtttcatttcaccacattttcatggcatac-actaggactaaaatcttatgctttatacacttgtatttccaattgttgttgcccctattagttttcaagtattttttgta--tgatatggcattgtccaaattgtacagCATCGAAATGGAGGGAGTCATCAGGGCAACATGTTGATTATGACCAAAGGCCTGATATCTTTAG
















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|61118494|gb|DN559455.1|DN559455
EST:     GCCTGGATCGCCTGAAGATAAGAAGCTTTACCTTATAGATCTTGGTTTAG                         CATCCAAGTGGAGAGAGAATAATGGTCATCATGTTGATTATGATCAACGGC
genomic: GCCTGGATCGCCTGAAGATAAGAAGCTTTACCTTACAGATCTTGGTTTAGgtatgcattt ... aattgtacaaCATCCAAGTGGAGAGAGAATAATGGTCATCATGTTGATTATGATCAACGGC
EST: gi|61118493|gb|DN559454.1|DN559454
EST:     GCCTGGATCGCCTGAAGATAAGAAGCTTTACCTTATAGATCTTGGTTTAG                         CATCCAAGTGGAGAGAGAATAATGGTCATCATGTTGATTATGATCAACGGC
genomic: GCCTGGATCGCCTGAAGATAAGAAGCTTTACCTTACAGATCTTGGTTTAGgtatgcattt ... aattgtacaaCATCCAAGTGGAGAGAGAATAATGGTCATCATGTTGATTATGATCAACGGC
EST: gi|32934388|gb|CF039200.1|CF039200
EST:     GCCTGGATCGCCTGAAGATAAGAAGCTTTACCTTATAGATCTTGGTTTAG                         CATCCAAGTGGAGAGAGAATAATGGTCATCATGTTGATTATGATCAACGGC
genomic: GCCTGGATCGCCTGAAGATAAGAAGCTTTACCTTACAGATCTTGGTTTAGgtatgcattt ... aattgtacaaCATCCAAGTGGAGAGAGAATAATGGTCATCATGTTGATTATGATCAACGGC
EST: gi|28390302|gb|CB250149.1|CB250149
EST:     TGAAGATAAGAAGCTTTACCTTATAGATCTTGGTTTAG                         CATCCAAGTGGAGAGAGAATAATGGTCATCATGTTGATTATGATCAACGGC
genomic: TGAAGATAAGAAGCTTTACCTTACAGATCTTGGTTTAGgtatgcattt ... aattgtacaaCATCCAAGTGGAGAGAGAATAATGGTCATCATGTTGATTATGATCAACGGC

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: 12 (upstream exon), 49 (downstream exon)
Score: 61

GTTTGTGCATGGTGATGTGAAACCAGAGAATTTTCTGCTTGGTCAGCCTGGATCGCCTGAAGATAAGAAGCTTTACCTTACAGATCTTGGTTTAGgtatgcattt ... aattgtacaaCATCCAAGTGGAGAGAGAATAATGGTCATCATGTTGATTATGATCAACGGCCTGATATCTTTAG


Block sizes: 14 (upstream exon), 49 (downstream exon)
Score: 35

GTTTGTGCATGGTGATGTGAAACCAGAGAATTTTCTGCTTGGTCAGCCTGGATCGCCTGAAGATAAGAAGCTTTACCTTACAGATCTTGGTTTAGgtatgcattt ... aattgtacaaCATCCAAGTGGAGAGAGAATAATGGTCATCATGTTGATTATGATCAACGGCCTGATATCTTTAG


Block sizes: 11 (upstream exon), 49 (downstream exon)
Score: 34

GTTTGTGCATGGTGATGTGAAACCAGAGAATTTTCTGCTTGGTCAGCCTGGATCGCCTGAAGATAAGAAGCTTTACCTTACAGATCTTGGTTTAGgtatgcattt ... aattgtacaaCATCCAAGTGGAGAGAGAATAATGGTCATCATGTTGATTATGATCAACGGCCTGATATCTTTAG


Block sizes: 10 (upstream exon), 49 (downstream exon)
Score: 36

GTTTGTGCATGGTGATGTGAAACCAGAGAATTTTCTGCTTGGTCAGCCTGGATCGCCTGAAGATAAGAAGCTTTACCTTACAGATCTTGGTTTAGgtatgcattt ... aattgtacaaCATCCAAGTGGAGAGAGAATAATGGTCATCATGTTGATTATGATCAACGGCCTGATATCTTTAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caattatctcccccttctttgttgttgttgatatgtggcacccaaaattgtacaaCATCCAAGTGGAGAGAGAATAATGGTCATCATGTTGATTATGATCAACGGCCTGATATCTTTAG
                         tgttgat  putative branch site (score: 36)
 aaaattgta  TA-rich tract