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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttatgataattttcttttatttatatttacttgttgagatggttgaaattttgacttcttttccccactttttttctttgtatgcctacagGATGAGAAGATCGAGTGCTGCCGCTTTTCTAGGGATGGCATGAAACCGTTCCTGTTTTGCACTGTTGCAAAAG

Basic information

species Zea mays
transcript GRMZM2G158489_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G158489_T03 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os07g09000.1 (Oryza sativa), 3'ss of exon 5
gtatgttatgataattttcttttatttatatttacttgttgagatggttgaaattttgacttcttttccccactttttttctttgtatgcctacagGATGAGAAGATCGAGTGCTGCCGCTTTTCTAGGGATGGCATGAAACCGTTCCTGTTTTGCACTGTTGCAAAAG
||||| |  ||||| ||| |   | | || ||  |||||||||||  |  ||   || ||   ||         || |   ||| |||||    ||||||||||||| || || ||||||||||||||||||||||||||||| |||||||||||||| ||||||||||
gtatgatgcgataaatttgtgcaagtcatgttctcttgttgagatactgaaagccttaaccatttg-----gtgttctggttttctatgc----agGATGAGAAGATTGAATGTTGCCGCTTTTCTAGGGATGGCATGAAACCATTCCTGTTTTGCACCGTTGCAAAAG
















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|32912764|gb|CF017576.1|CF017576
EST:     TATGGAAGATAGATGAGGGCGCACCACTGGTCAATTTGACTCGATCCTCG                         GATGAGAAGATCGAGTGCTGCCGCTTTTCTAGGGATGGCATGAAACCGTTC
genomic: TATGGAAGATAGATGAGGGCGCACCACTGGTCAATTTGACTCGATCCTCGgtatgttatg ... atgcctacagGATGAGAAGATCGAGTGCTGCCGCTTTTCTAGGGATGGCATGAAACCGTTC
EST: gi|32834098|gb|CD973776.1|CD973776
EST:     TATGGAAGATAGATGAGGGCGCACCACTGGTCAATTTGACTCGATCCTCG                         GATGAGAAGATCGAGTGCTGCCGCTTTTCTAGGGATGGCATGAAACCGTTC
genomic: TATGGAAGATAGATGAGGGCGCACCACTGGTCAATTTGACTCGATCCTCGgtatgttatg ... atgcctacagGATGAGAAGATCGAGTGCTGCCGCTTTTCTAGGGATGGCATGAAACCGTTC
EST: gi|22490777|gb|BU050700.1|BU050700
EST:     TATGGAAGATAGATGAGGTCGCACCACTGGTCAATTTGACTCGATCCTCG                         GATGAGAAGATCGAGTGCTGCCGCTTTTCTAGGGATGGCATGAAACCGTTC
genomic: TATGGAAGATAGATGAGGGCGCACCACTGGTCAATTTGACTCGATCCTCGgtatgttatg ... atgcctacagGATGAGAAGATCGAGTGCTGCCGCTTTTCTAGGGATGGCATGAAACCGTTC

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), 49 (downstream exon)
Score: 168

CTTAGACTCAGAGTTCTTAGTTTCAACATCCATTGATGGATCTGCGAGAATATGGAAGATAGATGAGGGCGCACCACTGGTCAATTTGACTCGATCCTCGgtatgttatg ... atgcctacagGATGAGAAGATCGAGTGCTGCCGCTTTTCTAGGGATGGCATGAAACCGTTCCTGTTTTGCACTGTTGCAAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 151

CTTAGACTCAGAGTTCTTAGTTTCAACATCCATTGATGGATCTGCGAGAATATGGAAGATAGATGAGGGCGCACCACTGGTCAATTTGACTCGATCCTCGgtatgttatg ... atgcctacagGATGAGAAGATCGAGTGCTGCCGCTTTTCTAGGGATGGCATGAAACCGTTCCTGTTTTGCACTGTTGCAAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 112

CTTAGACTCAGAGTTCTTAGTTTCAACATCCATTGATGGATCTGCGAGAATATGGAAGATAGATGAGGGCGCACCACTGGTCAATTTGACTCGATCCTCGgtatgttatg ... atgcctacagGATGAGAAGATCGAGTGCTGCCGCTTTTCTAGGGATGGCATGAAACCGTTCCTGTTTTGCACTGTTGCAAAAG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 108

CTTAGACTCAGAGTTCTTAGTTTCAACATCCATTGATGGATCTGCGAGAATATGGAAGATAGATGAGGGCGCACCACTGGTCAATTTGACTCGATCCTCGgtatgttatg ... atgcctacagGATGAGAAGATCGAGTGCTGCCGCTTTTCTAGGGATGGCATGAAACCGTTCCTGTTTTGCACTGTTGCAAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agatggttgaaattttgacttcttttccccactttttttctttgtatgcctacagGATGAGAAGATCGAGTGCTGCCGCTTTTCTAGGGATGGCATGAAACCGTTCCTGTTTTGCACTGTTGCAAAAG
            ttttgac  putative branch site (score: 108)
            ttttgacttcttttcc  CT-rich tract
                                tttttttctttgtat  TA-rich tract