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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtcggctcgatcaatcactatctgtctgccatgcatgatagagtaactcgtcatgttgatgatgctaactcatctggcgatattcccgcagGCTGGTGACGACTTCTGCTGGTCTGTCAAGGATATTGTCAAGAAGCTAAATCAAGCGTTCAAATCATCCTTCTGATGGGTTTAGCTTCTGACCAAACTTA

Basic information

species Zea mays
transcript GRMZM2G019806_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G019806_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g51580.1 (Oryza sativa), 3'ss of exon 4
gtgagtcggctcgatcaatcactatctgtctgccatgcatgatagagtaactcgtcatgttg-atga--tgctaactcatc-tggcgatattcccgcagGCTGGTGACGACTTCTGCTGGTCTGTCAAGGATATTGTCAAGAAGCTAAATCAAGCGTTCAAATCATCCTTCTGATGGGTTTAGCTTC-TGACCAAACTTA
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gtaagct--cccaatctccctcgaatttattttaacccccaaattaatcaccttttacgctacatggattaaaaaggaatggtgatgatgttcttgcagGCTGGAGAGAACTTCTCATTATCAGTCAAAGATATCGTCAAGAAGCTAAATCAAGCATTCAAGTTATCCCTGTGAAGGACTTGCTTTCCTGATCAAGTCT-
















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|32789182|gb|CD941418.1|CD941418
EST:     ATGTGCTCCCCTTCACAGCCTCCTCCCTCGACATCACCATCATGGCCATG                         GCTGGTGACGACTTCTGCTTGTCTGTCAAGGATATTGTCAAGAAGCTAAAT
genomic: ATGTGCTCCCCTTCACAGCCTCCTCCCTCGACATCACCATCATGGCCATGgtgagtcggc ... attcccgcagGCTGGTGACGACTTCTGCTGGTCTGTCAAGGATATTGTCAAGAAGCTAAAT
EST: gi|76013247|gb|DT940417.1|DT940417
EST:     ATGTGCTCCCCTTCACAGCCTCCTCCCTCGACATCACCATCATGGCCATG                         GCTGGTGACGACTTCTGCTGGTCTGTCAAGGATATTGTCAAGAAGCTAAAT
genomic: ATGTGCTCCCCTTCACAGCCTCCTCCCTCGACATCACCATCATGGCCATGgtgagtcggc ... attcccgcagGCTGGTGACGACTTCTGCTGGTCTGTCAAGGATATTGTCAAGAAGCTAAAT
EST: gi|32790818|gb|CD943054.1|CD943054
EST:     ATGTGCTCCCCTTCACAGCCTCCTCCCTCGACATCACCATCATGGCCATG                         GCTGGTGACGACTTCTGCTTGTCTGTCAAGGATATTGTCAAGAAGCTAAAT
genomic: ATGTGCTCCCCTTCACAGCCTCCTCCCTCGACATCACCATCATGGCCATGgtgagtcggc ... attcccgcagGCTGGTGACGACTTCTGCTGGTCTGTCAAGGATATTGTCAAGAAGCTAAAT
EST: gi|32804355|gb|CD956591.1|CD956591
EST:     ATGTGCTCCCCTTCACAGCCTCCTCCCTCGACATCACCATCATGGCCATG                         GCTGGTGACGACTTCTGCTTGTCTGTCAAGGATATTGTCAAGAAGCTAAAT
genomic: ATGTGCTCCCCTTCACAGCCTCCTCCCTCGACATCACCATCATGGCCATGgtgagtcggc ... attcccgcagGCTGGTGACGACTTCTGCTGGTCTGTCAAGGATATTGTCAAGAAGCTAAAT

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: 19 (upstream exon), 38 (downstream exon)
Score: 3

CGCCGCCCTCTCTGAGGTCGAGCGCCTTGGCCTCTCCATCATGAACACCAATGTGCTCCCCTTCACAGCCTCCTCCCTCGACATCACCATCATGGCCATGgtgagtcggc ... attcccgcagGCTGGTGACGACTTCTGCTGGTCTGTCAAGGATATTGTCAAGAAGCTAAATCAAGCGTTCAAATCATCCTTCTGATGGGTTTAGCTTCTGACCAAACTTA


Block sizes: 12 (upstream exon), 48 (downstream exon)
Score: 6

CGCCGCCCTCTCTGAGGTCGAGCGCCTTGGCCTCTCCATCATGAACACCAATGTGCTCCCCTTCACAGCCTCCTCCCTCGACATCACCATCATGGCCATGgtgagtcggc ... attcccgcagGCTGGTGACGACTTCTGCTGGTCTGTCAAGGATATTGTCAAGAAGCTAAATCAAGCGTTCAAATCATCCTTCTGATGGGTTTAGCTTCTGACCAAACTTA


Block sizes: 40 (upstream exon), 49 (downstream exon)
Score: 7

CGCCGCCCTCTCTGAGGTCGAGCGCCTTGGCCTCTCCATCATGAACACCAATGTGCTCCCCTTCACAGCCTCCTCCCTCGACATCACCATCATGGCCATGgtgagtcggc ... attcccgcagGCTGGTGACGACTTCTGCTGGTCTGTCAAGGATATTGTCAAGAAGCTAAATCAAGCGTTCAAATCATCCTTCTGATGGGTTTAGCTTCTGACCAAACTTA


Block sizes: 24 (upstream exon), 47 (downstream exon)
Score: 7

CGCCGCCCTCTCTGAGGTCGAGCGCCTTGGCCTCTCCATCATGAACACCAATGTGCTCCCCTTCACAGCCTCCTCCCTCGACATCACCATCATGGCCATGgtgagtcggc ... attcccgcagGCTGGTGACGACTTCTGCTGGTCTGTCAAGGATATTGTCAAGAAGCTAAATCAAGCGTTCAAATCATCCTTCTGATGGGTTTAGCTTCTGACCAAACTTA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatagagtaactcgtcatgttgatgatgctaactcatctggcgatattcccgcagGCTGGTGACGACTTCTGCTGGTCTGTCAAGGATATTGTCAAGAAGCTAAATCAAGCGTTCAAATCATCCTTCTGATGGGTTTAGCTTCTGACCAAACTTA
                          tgctaac  putative branch site (score: 7)
 tattccc  putative PPT
 atatt  TA-rich tract