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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacagatactgcatgtcttgtatgatctgtgttattgttcaaggtttttggggagcaacaatcttttaacactgggtgcaaatttcagGCTTTACAAAGGTCTACTTCCTCTTTGGGGCCGCCAAGTTCCCT

Basic information

species Zea mays
transcript GRMZM2G118208_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G118208_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os03g15690.2 (Oryza sativa), 3'ss of exon 1
gtacagatactgcatgtcttgtatg-atctgtg-ttattgttcaaggtttttggggagcaacaatcttttaacactgggtgcaaatttcagGCTTTACAAAGGTCTACTTCCTCTTTGGGGCCGCCAAGTTCCCT
||| ||||||||||| ||||||||  |  ||||  |  ||||||| |||| |  || |  ||| || | ||| ||   |||| |||||||||||||| ||||| ||||||||||| ||||| ||||||||||| |
gtatagatactgcatttcttgtatacaattgtgacttctgttcaaagtttatttgggg--aca-tcctataatacaatgtgcgaatttcagGCTTTATAAAGGACTACTTCCTCTCTGGGGTCGCCAAGTTCCTT
















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|60347958|gb|DN214931.1|DN214931
EST:     TGCCTGGTCGATGGGCTTCCGAAGATTGTCCAATCTGAAGGTGCCTTTGG                         GCTTTACAAAGGTCTACTTCCTCTTTGGGGCCGCCAAGTTCCCT
genomic: TGCCTGGTCGATGGGCTTCCGAAGATTGTCCAATCTGAAGGTGCCTTTGGgtacagatac ... caaatttcagGCTTTACAAAGGTCTACTTCCTCTTTGGGGCCGCCAAGTTCCCT
EST: gi|76281616|gb|DV021184.1|DV021184
EST:     TGCCTGGTCGATGGGCTTCCGAAGATTGTCCAATCTGAAGGTGCCTTTGG                         GCTTTACAAAGGTCTACTTCCTCTTTGGGGCCGCCAAGTTCCCT
genomic: TGCCTGGTCGATGGGCTTCCGAAGATTGTCCAATCTGAAGGTGCCTTTGGgtacagatac ... caaatttcagGCTTTACAAAGGTCTACTTCCTCTTTGGGGCCGCCAAGTTCCCT
EST: gi|101382650|gb|EB813379.1|EB813379
EST:     TGCCTGGTCGATGGGCTTCCGAAGATTGTCCAATCTGAAGGTGCCTTTGG                         GCTTTACAAAGGTCTACTTCCTCTTTGGGGCCGCCAAGTTCCCT
genomic: TGCCTGGTCGATGGGCTTCCGAAGATTGTCCAATCTGAAGGTGCCTTTGGgtacagatac ... caaatttcagGCTTTACAAAGGTCTACTTCCTCTTTGGGGCCGCCAAGTTCCCT
EST: gi|74245908|gb|DT653822.1|DT653822
EST:     TGCCTGGTCGATGGGCTTCCGAAGATTGTCCAATCTGAAGGTGCCTTTGG                         GCTTTACAAAGGTCTACTTCCTCTTTGGGGCCGCCAAGTTCCCT
genomic: TGCCTGGTCGATGGGCTTCCGAAGATTGTCCAATCTGAAGGTGCCTTTGGgtacagatac ... caaatttcagGCTTTACAAAGGTCTACTTCCTCTTTGGGGCCGCCAAGTTCCCT
EST: gi|71417465|gb|DR804063.1|DR804063
EST:     GGCTTCCGAAGATTGTCCAATCTGAAGGTGCCTTTGG                         GCTTTACAAAGGTCTACTTCCTCTTTGGGGCCGCCAAGTTCCCT
genomic: GGCTTCCGAAGATTGTCCAATCTGAAGGTGCCTTTGGgtacagatac ... caaatttcagGCTTTACAAAGGTCTACTTCCTCTTTGGGGCCGCCAAGTTCCCT
EST: gi|60354997|gb|DN221970.1|DN221970
EST:     TGCCTGGTCGATGGGCTTCCGAAGATTGTCCAATCTGAAGGTGCCTTTGG                         GCTTTACAAAGGTCTACTTCCTCTTTGGGGCCGCCAAGTTCCCT
genomic: TGCCTGGTCGATGGGCTTCCGAAGATTGTCCAATCTGAAGGTGCCTTTGGgtacagatac ... caaatttcagGCTTTACAAAGGTCTACTTCCTCTTTGGGGCCGCCAAGTTCCCT
EST: gi|71767406|gb|DR965343.1|DR965343
EST:     TGCCTGGTCGATGGGCTTCCGAAGATTGTCCTATCTGAAGGTGCCTTTGG                         GCTTTACAAAGGTCTACTTCCTCTTTGGGGCCGCCAAGTTCCCT
genomic: TGCCTGGTCGATGGGCTTCCGAAGATTGTCCAATCTGAAGGTGCCTTTGGgtacagatac ... caaatttcagGCTTTACAAAGGTCTACTTCCTCTTTGGGGCCGCCAAGTTCCCT
EST: gi|91874483|gb|EB404440.1|EB404440
EST:     TGCCTGGTCGATGGGCTTCCGAAGATTGTCCCATCTGAAAGTGCCTTTGG                         GCTTTACAAAGGTCTACTTCCTCTTTGGGGCCGCCAAGTTCCCT
genomic: TGCCTGGTCGATGGGCTTCCGAAGATTGTCCAATCTGAAGGTGCCTTTGGgtacagatac ... caaatttcagGCTTTACAAAGGTCTACTTCCTCTTTGGGGCCGCCAAGTTCCCT
EST: gi|37398965|gb|CF636804.1|CF636804
EST:     TGCCTGGTCGATGGGCTTCCGAAGATTGTCCAATCTGAAGGTGCCTTTGG                         GCTTTACAAAGGTCTACTTCCTCTTTGGGGCCGCCAAGTTCCCT
genomic: TGCCTGGTCGATGGGCTTCCGAAGATTGTCCAATCTGAAGGTGCCTTTGGgtacagatac ... caaatttcagGCTTTACAAAGGTCTACTTCCTCTTTGGGGCCGCCAAGTTCCCT
EST: gi|78544938|gb|DV622436.1|DV622436
EST:     GTCGATGGGCTTCCGAAGATTGTCCAATCTGAAGGTGCCTTTGG                         GCTTTACAAAGGTCTACTTCCTCTTTGGGGCCGCCAAGTTCCCT
genomic: GTCGATGGGCTTCCGAAGATTGTCCAATCTGAAGGTGCCTTTGGgtacagatac ... caaatttcagGCTTTACAAAGGTCTACTTCCTCTTTGGGGCCGCCAAGTTCCCT
EST: gi|67010579|gb|CO439328.1|CO439328
EST:     TGCCTGGTCGATGGGCTTCCGAAGATTGTCCAATCTGAAGGTGCCTTTGG                         GCTTTACAAAGGTCTACTTCCTCTTTGGGGCCGCCAAGTTCCCT
genomic: TGCCTGGTCGATGGGCTTCCGAAGATTGTCCAATCTGAAGGTGCCTTTGGgtacagatac ... caaatttcagGCTTTACAAAGGTCTACTTCCTCTTTGGGGCCGCCAAGTTCCCT

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: 45 (upstream exon), 44 (downstream exon)
Score: 32

CCATGGAGGCTGTCAAAATTCGGGTCCAGACACAACCGGGATTTGCTCGCTGCCTGGTCGATGGGCTTCCGAAGATTGTCCAATCTGAAGGTGCCTTTGGgtacagatac ... caaatttcagGCTTTACAAAGGTCTACTTCCTCTTTGGGGCCGCCAAGTTCCCT


Block sizes: 47 (upstream exon), 44 (downstream exon)
Score: 39

CCATGGAGGCTGTCAAAATTCGGGTCCAGACACAACCGGGATTTGCTCGCTGCCTGGTCGATGGGCTTCCGAAGATTGTCCAATCTGAAGGTGCCTTTGGgtacagatac ... caaatttcagGCTTTACAAAGGTCTACTTCCTCTTTGGGGCCGCCAAGTTCCCT


Block sizes: 47 (upstream exon), 44 (downstream exon)
Score: 47

CCATGGAGGCTGTCAAAATTCGGGTCCAGACACAACCGGGATTTGCTCGCTGCCTGGTCGATGGGCTTCCGAAGATTGTCCAATCTGAAGGTGCCTTTGGgtacagatac ... caaatttcagGCTTTACAAAGGTCTACTTCCTCTTTGGGGCCGCCAAGTTCCCT


Block sizes: 47 (upstream exon), 43 (downstream exon)
Score: 12

CCATGGAGGCTGTCAAAATTCGGGTCCAGACACAACCGGGATTTGCTCGCTGCCTGGTCGATGGGCTTCCGAAGATTGTCCAATCTGAAGGTGCCTTTGGgtacagatac ... caaatttcagGCTTTACAAAGGTCTACTTCCTCTTTGGGGCCGCCAAGTTCCCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgttcaaggtttttggggagcaacaatcttttaacactgggtgcaaatttcagGCTTTACAAAGGTCTACTTCCTCTTTGGGGCCGCCAAGTTCCCT
                              ttttaac  putative branch site (score: 12)
                          aatcttttaa  TA-rich tract