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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggtaactccagtagcctgattgtatttcaccctgcacatttttgtaatgtttcttgtgcactgtacagATCAAAGAGTTGAATTCCTATGTCACCTTGAGGAAAAC

Basic information

species Zea mays
transcript GRMZM2G330650_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G330650_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g25390.1 (Oryza sativa), 3'ss of exon 3
gttggtaactcc----agtagcctg---attgtatttcaccc-tgcacatttttgtaat-gtttcttgtgcactgtacagATCAAAGAGTTGAATTCCTATGTCACCTTGAGGAAAAC
||||||| ||||      ||  ||     |||||   || |  |||| | |  |||||  ||||||| || |||||||||||||||||||||||||||||||||||||||||||| ||
gttggtacctccctttgatatgctatttgttgtagcccatctgtgcatactcatgtaaaagtttcttatgaactgtacagATCAAAGAGTTGAATTCCTATGTCACCTTGAGGAAGAC
















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|211019324|gb|FL371811.1|FL371811
EST:     ATAATCCACCTGAGATCAACAAGCAGCTAAATGACAGAAAACAGTTCATG                         ATCAAAGAGTTGAATTCCTATGTCACCTTGAGGAAAAC
genomic: ATAATCCACCTGAGATCAACAAGCAGCTAAATGACAGAAAACAGTTCATGgttggtaact ... cactgtacagATCAAAGAGTTGAATTCCTATGTCACCTTGAGGAAAAC
EST: gi|78122353|gb|DV540737.1|DV540737
EST:     ATAATCCACCTGAGATCAACAAGCAGCTAAATGACAGAAAACAGTTCATG                         ATCAAAGAGTTGAATTCCTATGTCACCTTGAGGAAAAC
genomic: ATAATCCACCTGAGATCAACAAGCAGCTAAATGACAGAAAACAGTTCATGgttggtaact ... cactgtacagATCAAAGAGTTGAATTCCTATGTCACCTTGAGGAAAAC
EST: gi|211320442|gb|FL345947.1|FL345947
EST:     ATAATCCACCTGAGATCAACAAGCAGCTAAATGACAGAAAACAGTTCATG                         ATCAAAGAGTTGAATTCCTATGTCACCTTGAGGAAAAC
genomic: ATAATCCACCTGAGATCAACAAGCAGCTAAATGACAGAAAACAGTTCATGgttggtaact ... cactgtacagATCAAAGAGTTGAATTCCTATGTCACCTTGAGGAAAAC

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: 47 (upstream exon), 48 (downstream exon)
Score: 103

CTTGATCAAAGAGTTTGATCGCATTCTCAAAGATGAGGAGTCAAATAATCCACCTGAGATCAACAAGCAGCTAAATGACAGAAAACAGTTCATGgttggtaact ... cactgtacagATCAAAGAGTTGAATTCCTATGTCACCTTGAGGAAAAC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 115

CTTGATCAAAGAGTTTGATCGCATTCTCAAAGATGAGGAGTCAAATAATCCACCTGAGATCAACAAGCAGCTAAATGACAGAAAACAGTTCATGgttggtaact ... cactgtacagATCAAAGAGTTGAATTCCTATGTCACCTTGAGGAAAAC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 202

CTTGATCAAAGAGTTTGATCGCATTCTCAAAGATGAGGAGTCAAATAATCCACCTGAGATCAACAAGCAGCTAAATGACAGAAAACAGTTCATGgttggtaact ... cactgtacagATCAAAGAGTTGAATTCCTATGTCACCTTGAGGAAAAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 179

CTTGATCAAAGAGTTTGATCGCATTCTCAAAGATGAGGAGTCAAATAATCCACCTGAGATCAACAAGCAGCTAAATGACAGAAAACAGTTCATGgttggtaact ... cactgtacagATCAAAGAGTTGAATTCCTATGTCACCTTGAGGAAAAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcctgattgtatttcaccctgcacatttttgtaatgtttcttgtgcactgtacagATCAAAGAGTTGAATTCCTATGTCACCTTGAGGAAAAC
 gcctgat  putative branch site (score: 179)
                        atttttgtaatgttt  TA-rich tract