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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtacatcttatgtcagttcaaagtttgctaaaagaaaattgtgttgtattagtggcctatgtcatacttacctctccaactgctgttacagGGGGAGAAAGAAGAAGAGAAGGAAGAGGTTAAAACAATCAGCGGCATAATCAACTCAGCCCGCTCGCTAGGCGATGACGACGATGATATGCTTTCCGAGA

Basic information

species Zea mays
transcript GRMZM2G062738_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G062738_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os12g01449.1 (Oryza sativa), 3'ss of exon 2
----gtatgtac-atcttatgtcagttcaaagtttgctaaaagaaaattgtgttgtattagtggcctatg--tcatacttacctctccaactgctgt--tacagGGGGAGAAAGAAGAAGAGAAGGAAGAGGTTAAAACAATCAGCGGCATAATCAACTCAGCCCGCTCGCTAGGCGATGACGACGATGATATGCTTTCCGAGA---------
    ||   | | ||  | |   || | | |  ||| | |    || |     |||  |     | ||||  |   |||   || | ||| ||||||  | |||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||| |  ||          || || || || ||||| |||||||         
gtaagtgcatgccattctctactagcttagaacttg-tgagtttaactgtaactgttctgaacacgtatgcgtttaactgttcttttcaattgctgtggttcagGGGGAGAAAGAAGAAGAGAAGGAAGAGGTTAAAACAATCAGCGGCATAATCAATTCAGCTCTTTCA---------GATGATGACGACATGCTCTCCGAGATCGAGAGCC

upper sequence: GRMZM2G062738_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os11g01439.2 (Oryza sativa), 3'ss of exon 1
gtatgtacatcttatgtcagttcaaagtttgctaaaagaaaattgtgttgtattagt----ggcctatg--tcatacttacctctccaactgctgt--tacagGGGGAGAAAGAAGAAGAGAAGGAAGAGGTTAAAACAATCAGCGGCATAATCAACTCAGCCCGCTCGCTAGGCGATGACGACGATGATATGCTTTCCGAGA---------
      | |   | |  | ||||  |    | |||  |||  |  |  | || |||       | | ||  |   |||   || | ||| ||||||  | |||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||| |  ||          || || || || ||||| |||||||         
--ccaaaaaaactgtaactgttctgaacacg-taagtgaatgtcattctctactagctcaaaacttgtgagtttaactgttcttttcaattgctgtggttcagGGGGAGAAAGAAGAAGAGAAGGAAGAGGTTAAAACAATCAGCGGCATAATCAATTCAGCTCTTTCA---------GATGATGACGACATGCTCTCCGAGATCGAGAGCC
















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|32844451|gb|CD984132.1|CD984132
EST:     ACTATGTCCAAGCAAGGAAAAGGAAGGATAAGGCTAACAATTCTGAACAT                         GGGGAGAAAGAAGAAGAGAAGGAAGAGGTTAAAACAATCAGCGGCATAATC
genomic: ACTATGTCCAAGCAAGGAAAAGGAAGGATAAGGCTAACAATTCTGAACATgtatgtacat ... gctgttacagGGGGAGAAAGAAGAAGAGAAGGAAGAGGTTAAAACAATCAGCGGCATAATC
EST: gi|211089185|gb|FL460533.1|FL460533
EST:     ACTATGTCCAAGCAAGGAAAAGGAAGGATAAGGCTAACAATTCTGAACAT                         GGGGAGAAAGAAGAAGAGAAGGAAGAGGTTAAAACAATCAGCGGCATAATC
genomic: ACTATGTCCAAGCAAGGAAAAGGAAGGATAAGGCTAACAATTCTGAACATgtatgtacat ... gctgttacagGGGGAGAAAGAAGAAGAGAAGGAAGAGGTTAAAACAATCAGCGGCATAATC
EST: gi|211274725|gb|FL132302.1|FL132302
EST:     ACTATGTCCAAGCACGGAAAAGGAAGGATAAGGCTAACAATTCTGAACAT                         GGGGAGAAAGAAGAAGAGAAGGAAGAGGTTNAAAACAATCAGCGGCATAAT
genomic: ACTATGTCCAAGCAAGGAAAAGGAAGGATAAGGCTAACAATTCTGAACATgtatgtacat ... gctgttacagGGGGAGAAAGAAGAAGAGAAGGAAGAGGTT-AAAACAATCAGCGGCATAAT
EST: gi|32844934|gb|CD984615.1|CD984615
EST:     ACTATGTCCAAGCAAGGAAAAGGAAGGATAAGGCTACCAATTCTGAACAT                         GGGGAGAAAGAAGAAGAGAAGGAAGAGGTTAAAACAATCAGCGGCATAATC
genomic: ACTATGTCCAAGCAAGGAAAAGGAAGGATAAGGCTAACAATTCTGAACATgtatgtacat ... gctgttacagGGGGAGAAAGAAGAAGAGAAGGAAGAGGTTAAAACAATCAGCGGCATAATC

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 3 RNA-Seq libraries.


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 63

ACTATGTCCAAGCAAGGAAAAGGAAGGATAAGGCTAACAATTCTGAACATgtatgtacat ... gctgttacagGGGGAGAAAGAAGAAGAGAAGGAAGAGGTTAAAACAATCAGCGGCATAATCAACTCAGCCCGCTCGCTAGGCGATGACGACGATGATATGCTTTCCGAGA


Block sizes: 45 (upstream exon), 47 (downstream exon)
Score: 19

ACTATGTCCAAGCAAGGAAAAGGAAGGATAAGGCTAACAATTCTGAACATgtatgtacat ... gctgttacagGGGGAGAAAGAAGAAGAGAAGGAAGAGGTTAAAACAATCAGCGGCATAATCAACTCAGCCCGCTCGCTAGGCGATGACGACGATGATATGCTTTCCGAGA


Block sizes: 37 (upstream exon), 48 (downstream exon)
Score: 15

ACTATGTCCAAGCAAGGAAAAGGAAGGATAAGGCTAACAATTCTGAACATgtatgtacat ... gctgttacagGGGGAGAAAGAAGAAGAGAAGGAAGAGGTTAAAACAATCAGCGGCATAATCAACTCAGCCCGCTCGCTAGGCGATGACGACGATGATATGCTTTCCGAGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattgtgttgtattagtggcctatgtcatacttacctctccaactgctgttacagGGGGAGAAAGAAGAAGAGAAGGAAGAGGTTAAAACAATCAGCGGCATAATCAACTCAGCCCGCTCGCTAGGCGATGACGACGATGATATGCTTTCCGAGA
                            tacttac  putative branch site (score: 15)
       ttgtatta  TA-rich tract