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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttccttttgttggaaggaactgtacatcttactagtaccaaatatgaaactgacgaacattcccccttctctgcatgtcgtttgagcagACGGCTGGACAGGAATTCCCTTTCTGGCCAAGTACCTTTAAATCTGAATAACCTCACCAAAGTCATTGAACT

Basic information

species Zea mays
transcript GRMZM2G023715_T02
intron # 9
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|148933999|gb|EC878000.2|EC878000
EST:     ACCGGGAATATCCCGGACTCTCTTGGGTTTGTTAGTACACTCGAAGTTGT                         ACGGCTGGACAGGAATTCCCTTTCTGGCCAAGTACCTTTAAATCTGAATAA
genomic: ACCGGGAATATCCCGGACTCTCTTGGGTTTGTTAGTACACTCGAAGTTGTgtaagtttcc ... gtttgagcagACGGCTGGACAGGAATTCCCTTTCTGGCCAAGTACCTTTAAATCTGAATAA
EST: gi|76291830|gb|DV031398.1|DV031398
EST:     ACCGGGAATATCCCGGACTCTCTTGGGTTTGTTAGTACACTCGAAGTTGT                         ACGGCTGGACAGGAATTCCCTTTCTGGCCAAGTACCTTTAAATCTGAATAA
genomic: ACCGGGAATATCCCGGACTCTCTTGGGTTTGTTAGTACACTCGAAGTTGTgtaagtttcc ... gtttgagcagACGGCTGGACAGGAATTCCCTTTCTGGCCAAGTACCTTTAAATCTGAATAA
EST: gi|148981984|gb|EE028044.2|EE028044
EST:     CCGGGAATATCCCGGACTCTCTTTGGGTT-GTTAGTACACTCGAAGTTGT                         ACGGCTGGACAGGAATTCCCTTTCTGGCCAAGTACCTTTAAATCT
genomic: CCGGGAATATCCCGGACTCTCTT-GGGTTTGTTAGTACACTCGAAGTTGTgtaagtttcc ... gtttgagcagACGGCTGGACAGGAATTCCCTTTCTGGCCAAGTACCTTTAAATCT
EST: gi|71768120|gb|DR966057.1|DR966057
EST:     ACCGGGAATATCCCGGACTCTCTTGGGTTTGTTAGTACACTCGAAGTTGT                         ACGGCTGGACAGGAATTCCCTTTCTGGCCAAGTACCTTTAAATCTGAATAA
genomic: ACCGGGAATATCCCGGACTCTCTTGGGTTTGTTAGTACACTCGAAGTTGTgtaagtttcc ... gtttgagcagACGGCTGGACAGGAATTCCCTTTCTGGCCAAGTACCTTTAAATCTGAATAA
EST: gi|148981983|gb|EE028043.2|EE028043
EST:     ACCGGGAATATCCCGGACTCTCTTGGGTTTGTTAGTACACTCGAAGTTGT                         ACGGCTGGACAGGAATTCCCTTTCTGGCCAAGTACCTTTAAATCTGAATAA
genomic: ACCGGGAATATCCCGGACTCTCTTGGGTTTGTTAGTACACTCGAAGTTGTgtaagtttcc ... gtttgagcagACGGCTGGACAGGAATTCCCTTTCTGGCCAAGTACCTTTAAATCTGAATAA

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: 49 (upstream exon), 49 (downstream exon)
Score: 29

GCTCTTCGATGGAAACAGATTCACCGGGAATATCCCGGACTCTCTTGGGTTTGTTAGTACACTCGAAGTTGTgtaagtttcc ... gtttgagcagACGGCTGGACAGGAATTCCCTTTCTGGCCAAGTACCTTTAAATCTGAATAACCTCACCAAAGTCATTGAACT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 74

GCTCTTCGATGGAAACAGATTCACCGGGAATATCCCGGACTCTCTTGGGTTTGTTAGTACACTCGAAGTTGTgtaagtttcc ... gtttgagcagACGGCTGGACAGGAATTCCCTTTCTGGCCAAGTACCTTTAAATCTGAATAACCTCACCAAAGTCATTGAACT


Block sizes: 42 (upstream exon), 46 (downstream exon)
Score: 13

GCTCTTCGATGGAAACAGATTCACCGGGAATATCCCGGACTCTCTTGGGTTTGTTAGTACACTCGAAGTTGTgtaagtttcc ... gtttgagcagACGGCTGGACAGGAATTCCCTTTCTGGCCAAGTACCTTTAAATCTGAATAACCTCACCAAAGTCATTGAACT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaccaaatatgaaactgacgaacattcccccttctctgcatgtcgtttgagcagACGGCTGGACAGGAATTCCCTTTCTGGCCAAGTACCTTTAAATCTGAATAACCTCACCAAAGTCATTGAACT
             aactgac  putative branch site (score: 13)
     aaatatgaaa  TA-rich tract