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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtcatcgacgacagctctgacgaaaccaaaggctatacgtaccataattaaaactgcagtgtgtgtgtgtgtgtgtgtgtgtgtgtgtcatatgaacacacagGGCCTGAGATCTGGAAGGACACCGCCGGTAAGGTGGACATATTCGTGGCCGGTTCAGGCTCGGGAGGCACGGTGTCTGGCGTCGGCAAGTACCTCAAGAC

Basic information

species Zea mays
transcript GRMZM2G443985_T04
intron # 18
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|78180091|gb|DV550464.1|DV550464
EST:     CGACCAGTTCTCCAACAGAGCGAATCCTGAAGCGCATGTTAGATGGACTG                         GGCCTGAGATCTGGAAGGACACTGCCGGCAAGGTGGACGTATTCGTGGCCG
genomic: CGACCAGTTCTCCAACAGAGCGAATCCTGAAGCGCATGTTAGATGGACTGgtacgtcatc ... gaacacacagGGCCTGAGATCTGGAAGGACACCGCCGGTAAGGTGGACATATTCGTGGCCG
EST: gi|74231924|gb|DT639838.1|DT639838
EST:     CGACCAGTTCTCCAACAGAGCGAATCCTGAAGCGCATGTTAGATGGACTG                         GGCCTGAAATCTGGAAGGACACCGC
genomic: CGACCAGTTCTCCAACAGAGCGAATCCTGAAGCGCATGTTAGATGGACTGgtacgtcatc ... gaacacacagGGCCTGAGATCTGGAAGGACACCGC
EST: gi|71439507|gb|DR820557.1|DR820557
EST:     CGACCAGTTCTCCAACAGAGCGAATCCTGAAGCGCATGTTAGATGGACTG                         GGCCTGAGATCTGGAAGGACACCGCCGGTAANGTGGACATATTCGTGGCCG
genomic: CGACCAGTTCTCCAACAGAGCGAATCCTGAAGCGCATGTTAGATGGACTGgtacgtcatc ... gaacacacagGGCCTGAGATCTGGAAGGACACCGCCGGTAAGGTGGACATATTCGTGGCCG
EST: gi|78083294|gb|DV511687.1|DV511687
EST:     CGACCAGTTCTCCAACAGAGCGAATCCTGAAGCGCATGTTAGATGGACTG                         GGCCTGAGATCTGGAAGGACACCGCCGGTAAGGTGGACATATTCGTGGCCG
genomic: CGACCAGTTCTCCAACAGAGCGAATCCTGAAGCGCATGTTAGATGGACTGgtacgtcatc ... gaacacacagGGCCTGAGATCTGGAAGGACACCGCCGGTAAGGTGGACATATTCGTGGCCG
EST: gi|71418512|gb|DR804465.1|DR804465
EST:     CGACCAGTTCTCCAACAGAGCGAATCCTGAAGCGCATGTTAGATGGACTG                         GGCCTGAGATCTGGAAGGACACCGCCGGTAAGGTGGACATATTCGTGGCCT
genomic: CGACCAGTTCTCCAACAGAGCGAATCCTGAAGCGCATGTTAGATGGACTGgtacgtcatc ... gaacacacagGGCCTGAGATCTGGAAGGACACCGCCGGTAAGGTGGACATATTCGTGGCCG
EST: gi|89252818|gb|DY624604.1|DY624604
EST:     CGACCAGTTCTCCAACAGAGCGAATCCTGAAGCGCATGTTAGATGGACTG                         GGCCTGAGATCTGGAAGGACACCGCCGGTAAGGTGGACATATTCGTGGCCG
genomic: CGACCAGTTCTCCAACAGAGCGAATCCTGAAGCGCATGTTAGATGGACTGgtacgtcatc ... gaacacacagGGCCTGAGATCTGGAAGGACACCGCCGGTAAGGTGGACATATTCGTGGCCG
EST: gi|93016171|gb|EB641691.1|EB641691
EST:     CGACCAGTTCTCCAACAGAGCGAATCCTGAAGCGCATGTTAGATGGACTG                         GGCCTGAGATCTGGAAGGACACCGCCGGTAAGGTGGACATATTCGTGGCCG
genomic: CGACCAGTTCTCCAACAGAGCGAATCCTGAAGCGCATGTTAGATGGACTGgtacgtcatc ... gaacacacagGGCCTGAGATCTGGAAGGACACCGCCGGTAAGGTGGACATATTCGTGGCCG
EST: gi|78076561|gb|DV504995.1|DV504995
EST:     CGACCAGTTCTCCAACAGAGCGAATCCTGAAGCGCATGTTAGATGGACTG                         GGGCTGAGATCTGGAAGGACACCGC
genomic: CGACCAGTTCTCCAACAGAGCGAATCCTGAAGCGCATGTTAGATGGACTGgtacgtcatc ... gaacacacagGGCCTGAGATCTGGAAGGACACCGC
EST: gi|6973455|gb|AW438149.1|AW438149
EST:     CGACCAGTTCTCCAACAGAGCGAATCCTGAAGCGCATGTTAGATGGACTG                         GGCCTGAGATCTGGAAGGACACTGCCGGCAAGGTGGACGTATTCGTGGCCG
genomic: CGACCAGTTCTCCAACAGAGCGAATCCTGAAGCGCATGTTAGATGGACTGgtacgtcatc ... gaacacacagGGCCTGAGATCTGGAAGGACACCGCCGGTAAGGTGGACATATTCGTGGCCG
EST: gi|148990681|gb|EE032078.2|EE032078
EST:     CGACCAGTTCTCCAACAGAGCGAATCCTGAAGCGCATGTTAGATGGACTG                         GGCCTGAGATCTGGAAGGACACCGCCGGTAAGGTGGACATATTCGTGGCCG
genomic: CGACCAGTTCTCCAACAGAGCGAATCCTGAAGCGCATGTTAGATGGACTGgtacgtcatc ... gaacacacagGGCCTGAGATCTGGAAGGACACCGCCGGTAAGGTGGACATATTCGTGGCCG
EST: gi|78084510|gb|DV512903.1|DV512903
EST:     CGACCAGTTCTCCCACAGAGCGAATCCTGAAGCGCATGTTAGATGGACTG                         GGCCTGAGATCTGGAAGGA
genomic: CGACCAGTTCTCCAACAGAGCGAATCCTGAAGCGCATGTTAGATGGACTGgtacgtcatc ... gaacacacagGGCCTGAGATCTGGAAGGA
EST: gi|91871743|gb|EB401700.1|EB401700
EST:     GACCAGTTCTCCAACAGAGCGAATCCCTGA-GCGCATGTTAGATGGACTG                         GGCCTGAGATCTGGAAGGA
genomic: GACCAGTTCTCCAACAGAGCGAATCC-TGAAGCGCATGTTAGATGGACTGgtacgtcatc ... gaacacacagGGCCTGAGATCTGGAAGGA
EST: gi|78109441|gb|DV527857.1|DV527857
EST:     CGACCAGTTCTCCAACAGAGCGAATCCTGAAGCGCATGTTAGATGGACTG                         GGCCTGAGATCTGGAAGGACACCCGCCG-TAAGGTGGACATATTCGTGGCC
genomic: CGACCAGTTCTCCAACAGAGCGAATCCTGAAGCGCATGTTAGATGGACTGgtacgtcatc ... gaacacacagGGCCTGAGATCTGGAAGGACACC-GCCGGTAAGGTGGACATATTCGTGGCC
EST: gi|93012122|gb|EB637642.1|EB637642
EST:     GACCAGTTCTCCAACAGAGCGAATCCTTGA-GCGCATGTTAGATGGACTG                         GGCCTGAGATCTGGA
genomic: GACCAGTTCTCCAACAGAGCGAATCCT-GAAGCGCATGTTAGATGGACTGgtacgtcatc ... gaacacacagGGCCTGAGATCTGGA

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: 41 (upstream exon), 45 (downstream exon)
Score: 5

ACCGCCAAGGTCGAGGAGCTCAAGAAGGAGCTGCCCAACGTGCACGTCCTCGACCAGTTCTCCAACAGAGCGAATCCTGAAGCGCATGTTAGATGGACTGgtacgtcatc ... gaacacacagGGCCTGAGATCTGGAAGGACACCGCCGGTAAGGTGGACATATTCGTGGCCGGTTCAGGCTCGGGAGGCACGGTGTCTGGCGTCGGCAAGTACCTCAAGAC


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 40

ACCGCCAAGGTCGAGGAGCTCAAGAAGGAGCTGCCCAACGTGCACGTCCTCGACCAGTTCTCCAACAGAGCGAATCCTGAAGCGCATGTTAGATGGACTGgtacgtcatc ... gaacacacagGGCCTGAGATCTGGAAGGACACCGCCGGTAAGGTGGACATATTCGTGGCCGGTTCAGGCTCGGGAGGCACGGTGTCTGGCGTCGGCAAGTACCTCAAGAC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 41

ACCGCCAAGGTCGAGGAGCTCAAGAAGGAGCTGCCCAACGTGCACGTCCTCGACCAGTTCTCCAACAGAGCGAATCCTGAAGCGCATGTTAGATGGACTGgtacgtcatc ... gaacacacagGGCCTGAGATCTGGAAGGACACCGCCGGTAAGGTGGACATATTCGTGGCCGGTTCAGGCTCGGGAGGCACGGTGTCTGGCGTCGGCAAGTACCTCAAGAC


Block sizes: 46 (upstream exon), 47 (downstream exon)
Score: 9

ACCGCCAAGGTCGAGGAGCTCAAGAAGGAGCTGCCCAACGTGCACGTCCTCGACCAGTTCTCCAACAGAGCGAATCCTGAAGCGCATGTTAGATGGACTGgtacgtcatc ... gaacacacagGGCCTGAGATCTGGAAGGACACCGCCGGTAAGGTGGACATATTCGTGGCCGGTTCAGGCTCGGGAGGCACGGTGTCTGGCGTCGGCAAGTACCTCAAGAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaaactgcagtgtgtgtgtgtgtgtgtgtgtgtgtgtgtcatatgaacacacagGGCCTGAGATCTGGAAGGACACCGCCGGTAAGGTGGACATATTCGTGGCCGGTTCAGGCTCGGGAGGCACGGTGTCTGGCGTCGGCAAGTACCTCAAGAC
                                         atatgaa  TA-rich tract