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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggtggggccatcgtttgattaatcgcccctccctcataataatgtgtacgtgtccaatgtgattgccttttattttggccgggaaacaccatgtgatggaatgcgtgtatggtgtgtgccttcaatttgcagGCATTCAGGGGATGGCGCCGAGTAACAACAAGGCTTTGGAGCTGGTTGCTTGACTTGACCCTGTATCATGTAATTTGTATGCCAATCATTTGCAGTGATA

Basic information

species Zea mays
transcript GRMZM2G170243_T01
intron # 2
splice site 3'
intron type U2

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|166658029|gb|EG246642.1|EG246642
EST:     GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCAACATCTTGGAG                         GCATTCAGGGGATGGCGCCGAG
genomic: GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCAACATCTTGGAGgtaggtgggg ... caatttgcagGCATTCAGGGGATGGCGCCGAG
EST: gi|32939953|gb|CF044772.1|CF044772
EST:     GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCAACATCTTGGAG                         GCATTCAGGGGATGGCGCCGAGTAACAACAAGGCTTTGGAGCTGGTTGCTT
genomic: GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCAACATCTTGGAGgtaggtgggg ... caatttgcagGCATTCAGGGGATGGCGCCGAGTAACAACAAGGCTTTGGAGCTGGTTGCTT
EST: gi|33097458|gb|CF057418.1|CF057418
EST:     GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCAACATCTTGGAG                         GCATTCAGGGGATGGCGCCGAGTAACAACAAGGCTTTGGAGCTGGTTGCTT
genomic: GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCAACATCTTGGAGgtaggtgggg ... caatttgcagGCATTCAGGGGATGGCGCCGAGTAACAACAAGGCTTTGGAGCTGGTTGCTT
EST: gi|5714211|gb|AI944196.1|AI944196
EST:     GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCAACATCTTGGAG                         GCATTCAGGGGATGGCGCCGAGTAACAACAAGGCTTTGGAGCTGGTTGCTT
genomic: GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCAACATCTTGGAGgtaggtgggg ... caatttgcagGCATTCAGGGGATGGCGCCGAGTAACAACAAGGCTTTGGAGCTGGTTGCTT
EST: gi|5804650|gb|AI979620.1|AI979620
EST:     GTTCAGCTAGACCGCAAATCTCGGAATCTGCCAACATNCTTGGAG                         GCATTCAGGGGATGGCGCCGAGTAACAACAAGGCTTTGGAGCTGGTTGCT
genomic: GTTCAGCTAGACCGCAAATCTCGGAATCTGCCAACAT-CTTGGAGgtaggtgggg ... caatttgcagGCATTCAGGGGATGGCGCCGAGTAACAACAAGGCTTTGGAGCTGGTTGCT
EST: gi|32943289|gb|CF048108.1|CF048108
EST:     GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCAACATCTTGGAG                         GCATTCAGGGGATGGCGCCGAGTAACAACAAGGCTTTGGAGCTGGTTGCTT
genomic: GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCAACATCTTGGAGgtaggtgggg ... caatttgcagGCATTCAGGGGATGGCGCCGAGTAACAACAAGGCTTTGGAGCTGGTTGCTT
EST: gi|78109084|gb|DV527501.1|DV527501
EST:     GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCAACATCTTGGAG                         GCATTCAGGGGATGGCGCCGAGTAACAACAAGGCTTTGGAGCTGGTTGCTT
genomic: GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCAACATCTTGGAGgtaggtgggg ... caatttgcagGCATTCAGGGGATGGCGCCGAGTAACAACAAGGCTTTGGAGCTGGTTGCTT
EST: gi|61118249|gb|DN559210.1|DN559210
EST:     GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCAACATCTTGGAG                         GCATTCAGGGGATGGCGCCGAGTAACAACAAGGCTTTGGAGCTGGTTGCTT
genomic: GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCAACATCTTGGAGgtaggtgggg ... caatttgcagGCATTCAGGGGATGGCGCCGAGTAACAACAAGGCTTTGGAGCTGGTTGCTT
EST: gi|211100809|gb|FL317184.1|FL317184
EST:     ACCGCAAATCTCGGAATCTGCCAACATCTTGGAG                         GCATTCAGGGGATGGCGCCGAGTAACAACAAGGCTTTGGAGCTGGTTGCTT
genomic: ACCGCAAATCTCGGAATCTGCCAACATCTTGGAGgtaggtgggg ... caatttgcagGCATTCAGGGGATGGCGCCGAGTAACAACAAGGCTTTGGAGCTGGTTGCTT
EST: gi|89250984|gb|DY622770.1|DY622770
EST:     GAAAGTGTTCAGTTAGACCGCAAATCTCGGATTCTGCCAACATCTTGGAG                         GCATTCAGGGGAGGGCGCCGAGTAACAACAAGGCTTTGGAGCTGGTTGCTT
genomic: GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCAACATCTTGGAGgtaggtgggg ... caatttgcagGCATTCAGGGGATGGCGCCGAGTAACAACAAGGCTTTGGAGCTGGTTGCTT
EST: gi|32944695|gb|CF049514.1|CF049514
EST:     GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCAACATCTTGGAG                         GCATTCAGGGGATGGCGCCGAGTAACAACAAGGCTTTGGAGCTGGTTGCTT
genomic: GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCAACATCTTGGAGgtaggtgggg ... caatttgcagGCATTCAGGGGATGGCGCCGAGTAACAACAAGGCTTTGGAGCTGGTTGCTT

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), 48 (downstream exon)
Score: 174

ATACCACCGATGATATATCTGAAGAGGTGCTACGGGCATCGACTGCTCTAGAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCAACATCTTGGAGgtaggtgggg ... caatttgcagGCATTCAGGGGATGGCGCCGAGTAACAACAAGGCTTTGGAGCTGGTTGCTTGACTTGACCCTGTATCATGTAATTTGTATGCCAATCATTTGCAGTGATA


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 67

ATACCACCGATGATATATCTGAAGAGGTGCTACGGGCATCGACTGCTCTAGAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCAACATCTTGGAGgtaggtgggg ... caatttgcagGCATTCAGGGGATGGCGCCGAGTAACAACAAGGCTTTGGAGCTGGTTGCTTGACTTGACCCTGTATCATGTAATTTGTATGCCAATCATTTGCAGTGATA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 97

ATACCACCGATGATATATCTGAAGAGGTGCTACGGGCATCGACTGCTCTAGAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCAACATCTTGGAGgtaggtgggg ... caatttgcagGCATTCAGGGGATGGCGCCGAGTAACAACAAGGCTTTGGAGCTGGTTGCTTGACTTGACCCTGTATCATGTAATTTGTATGCCAATCATTTGCAGTGATA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 75

ATACCACCGATGATATATCTGAAGAGGTGCTACGGGCATCGACTGCTCTAGAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCAACATCTTGGAGgtaggtgggg ... caatttgcagGCATTCAGGGGATGGCGCCGAGTAACAACAAGGCTTTGGAGCTGGTTGCTTGACTTGACCCTGTATCATGTAATTTGTATGCCAATCATTTGCAGTGATA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gccgggaaacaccatgtgatggaatgcgtgtatggtgtgtgccttcaatttgcagGCATTCAGGGGATGGCGCCGAGTAACAACAAGGCTTTGGAGCTGGTTGCTTGACTTGACCCTGTATCATGTAATTTGTATGCCAATCATTTGCAGTGATA
                                       tgccttc  CT-rich tract
                                           ttcaattt  TA-rich tract