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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagctctcggctctttcccctctgttcctctccgccggcgaaattttttgaatcttctgtccctgacaaaaacaggtttattattatttttgtttggtgtcagGTCATCCTAAGATCATCCATCGTGACATTAAGGCGGCGAACATCCTTCTGGATTATAACTACGAGCCAAAG

Basic information

species Zea mays
transcript GRMZM2G358830_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G358830_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g54700.1 (Oryza sativa), 3'ss of exon 3
gtgagctctcggctctttcccctctgttcctctccgccggcgaaat-tttttgaatcttctgtccctgacaaaaacaggtttattattat-ttttgtttggtgtcagGTCATCCTAAGATCATCCATCGTGACATTAAGGCGGCGAACATCCTTCTGGATTATAACTACGAGCCAAAG
    | |    | |   |||  |||  ||||   | ||    |||| | |  | |   | ||   |||       | | |    |   ||  ||||  || ||||||||||||||||||| || ||| | ||||| ||||| || |||||||| ||||| || | || ||| ||||||
---ggattaaagtttagtcctttct--tcctaaacaccacataaatatatgcggaatctgtgaaactgt--ggttctgataagatggcatgctttgactgttgtcagGTCATCCTAAGATTATTCATAGAGACATCAAGGCAGCCAACATCCTGCTGGACTACACCTTCGAACCAAAG
















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|149104119|gb|EE289551.2|EE289551
EST:     GAAGATCGCGGTCGGCTCGGCCAAGGGCCTCGCCTATCTGCACGAAGACT                         GTCATCCTAAGATCATCCATCGTGACATTAAGGCGGCGAACATCCTTCTGG
genomic: GAAGATCGCGGTCGGCTCGGCCAAGGGCCTCGCCTATCTGCACGAAGACTgtgagctctc ... ttggtgtcagGTCATCCTAAGATCATCCATCGTGACATTAAGGCGGCGAACATCCTTCTGG
EST: gi|149084848|gb|EE174353.2|EE174353
EST:     GAAGATCGCGGTCGGCTCGGCCAAGGGCCTCGCCTATCTGCACGAAGACT                         GTCATCCTAAGATCATCCATCGTGACATTAAGGCGGCGAACATCCTTCTGG
genomic: GAAGATCGCGGTCGGCTCGGCCAAGGGCCTCGCCTATCTGCACGAAGACTgtgagctctc ... ttggtgtcagGTCATCCTAAGATCATCCATCGTGACATTAAGGCGGCGAACATCCTTCTGG
EST: gi|76926939|gb|DV171065.1|DV171065
EST:     GAAGATCGCGGTCGGCTCGGCCAAGGGCCTCGCCTATCTGCACGAAGACT                         GTCATCCTAAGATCATCCATCGTGACATTAAGGCGGCGAACATCCTTCTGG
genomic: GAAGATCGCGGTCGGCTCGGCCAAGGGCCTCGCCTATCTGCACGAAGACTgtgagctctc ... ttggtgtcagGTCATCCTAAGATCATCCATCGTGACATTAAGGCGGCGAACATCCTTCTGG
EST: gi|148952361|gb|EC898175.2|EC898175
EST:     GAAGATCGCGGTCGGCTCGGCCAAGGGCCTCGCCTATCTGCACGAAGACT                         GTCATCCTAAGATCATCCATCGTGACATTAAGGCGGCGAACATCCTTCTGG
genomic: GAAGATCGCGGTCGGCTCGGCCAAGGGCCTCGCCTATCTGCACGAAGACTgtgagctctc ... ttggtgtcagGTCATCCTAAGATCATCCATCGTGACATTAAGGCGGCGAACATCCTTCTGG
EST: gi|148929996|gb|EE285849.2|EE285849
EST:     GAAGATCGCGGTCGGCTCGGCCAAGGGCCTCGCCTATCTGCACGAAGACT                         GTCATCCTAAGATCATCCATCGTGACATTAAGGCGGCGAACATCCTTCTGG
genomic: GAAGATCGCGGTCGGCTCGGCCAAGGGCCTCGCCTATCTGCACGAAGACTgtgagctctc ... ttggtgtcagGTCATCCTAAGATCATCCATCGTGACATTAAGGCGGCGAACATCCTTCTGG
EST: gi|76017809|gb|DT944979.1|DT944979
EST:     GAAGATCGCGGTCGGCTCGGCCAAGGGCCTCGCCTATCTGCACGAAGACT                         GTCATCCTAAGATCATCCATCGTGACATTAAGGCGGCGAACATCCTTCTGG
genomic: GAAGATCGCGGTCGGCTCGGCCAAGGGCCTCGCCTATCTGCACGAAGACTgtgagctctc ... ttggtgtcagGTCATCCTAAGATCATCCATCGTGACATTAAGGCGGCGAACATCCTTCTGG
EST: gi|71769047|gb|DR966984.1|DR966984
EST:     GAAGATCGCGGTCGGCTCGGCCAAGGGCCTCGCCTATCTGCACGAAGACT                         GTCATCCTAAGATCATCCATCGTGACATTAAGGCGGCGAACATCCTTCTGG
genomic: GAAGATCGCGGTCGGCTCGGCCAAGGGCCTCGCCTATCTGCACGAAGACTgtgagctctc ... ttggtgtcagGTCATCCTAAGATCATCCATCGTGACATTAAGGCGGCGAACATCCTTCTGG

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), 45 (downstream exon)
Score: 12

GGAGTGGCAGGCCAACATTGGACTGGCCGAGGCGGTGGAAGATCGCGGTCGGCTCGGCCAAGGGCCTCGCCTATCTGCACGAAGACTgtgagctctc ... ttggtgtcagGTCATCCTAAGATCATCCATCGTGACATTAAGGCGGCGAACATCCTTCTGGATTATAACTACGAGCCAAAG


Block sizes: 46 (upstream exon), 45 (downstream exon)
Score: 67

GGAGTGGCAGGCCAACATTGGACTGGCCGAGGCGGTGGAAGATCGCGGTCGGCTCGGCCAAGGGCCTCGCCTATCTGCACGAAGACTgtgagctctc ... ttggtgtcagGTCATCCTAAGATCATCCATCGTGACATTAAGGCGGCGAACATCCTTCTGGATTATAACTACGAGCCAAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 172

GGAGTGGCAGGCCAACATTGGACTGGCCGAGGCGGTGGAAGATCGCGGTCGGCTCGGCCAAGGGCCTCGCCTATCTGCACGAAGACTgtgagctctc ... ttggtgtcagGTCATCCTAAGATCATCCATCGTGACATTAAGGCGGCGAACATCCTTCTGGATTATAACTACGAGCCAAAG


Block sizes: 49 (upstream exon), 40 (downstream exon)
Score: 24

GGAGTGGCAGGCCAACATTGGACTGGCCGAGGCGGTGGAAGATCGCGGTCGGCTCGGCCAAGGGCCTCGCCTATCTGCACGAAGACTgtgagctctc ... ttggtgtcagGTCATCCTAAGATCATCCATCGTGACATTAAGGCGGCGAACATCCTTCTGGATTATAACTACGAGCCAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaatcttctgtccctgacaaaaacaggtttattattatttttgtttggtgtcagGTCATCCTAAGATCATCCATCGTGACATTAAGGCGGCGAACATCCTTCTGGATTATAACTACGAGCCAAAG
            ccctgac  putative branch site (score: 24)
                                      tttttgttt  putative PPT
                   aaaaacaggtttatta  TA-rich tract