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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgccgtttctctctcataaataatcatgtatagactttgtttaaggatgcaagtgatgacaccaatgggtcggttgtgtggtccatttttatcatactccccttgctttgaataagatgagttttgggtcaacccagttgccctacctatgtactaaacggactattcttggtgtctttatctagGTGAGGCAGAATCAGGATTGGAGCGGCTACATCAATGTGCAGAGAAAGAACTTCAAATATACCTTGATGCAGAATCTCCCTCGAAAGACTTCAATGATTT

Basic information

species Zea mays
transcript GRMZM2G006428_T01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G006428_T01 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os04g41470.1 (Oryza sativa), 3'ss of exon 13
gtttgccgtttctctctcataaataatcatgtatagactttgtttaaggatgcaagtgatgacaccaatgggtcggttgtgtggtccatttttatcatactccccttgctttga-ataagatgagttttgggtcaacccagttgccctacctatgtactaaacggactattcttggtgtct--ttatctagGTGAGGCAGAATCAGGATTGGAGCGGCTACATCAATGTGCAGAGAAAGAACTTCAAATATACCTTGATGCAGAATCTCCCTCGAAAGACTTCAATGATTT
                                                                                                       | | | ||||   ||| |  |  |    |   || ||  |  |  |  ||  ||      ||  |||||||| ||  |  ||||||||||||||| |||||||| ||||||||||| ||||||||||||||||||||||||||| |||||||||| |||||||||||||| ||||| |||||||| ||
----------------------------------------------------------------------------------------------------gttcgtagttttgctgtaatactaaat---agcatacgcaagtatc--agttacttatc---tggtttattcttgttgcttatttatctagGTGAGGCGGAATCAGGTTTGGAGCGGCTGCATCAATGTGCAGAGAAAGAACTTCAAGTATACCTTGAAGCAGAATCTCCCTCAAAAGATTTCAATGACTT
















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|211198902|gb|FL376281.1|FL376281
EST:     CCTGCCAGAGCATGAGCATGCCAAAAGACAGTTCTTTGAATATCTGCAAG                         GTGAGGCAGAATCAGGTTTGGAGCGGCTACATCAATGTGCAGAGAAAGAAC
genomic: CCTGCCAGAGCATGAGCATGCCAAAAGACAGTTCTTTGAATATCTGCAAGgtttgccgtt ... ctttatctagGTGAGGCAGAATCAGGATTGGAGCGGCTACATCAATGTGCAGAGAAAGAAC
EST: gi|22521335|gb|BU080146.1|BU080146
EST:     CCTGCCAGAGCATGAGCATGCCAAAAGACAGTTCTTTGAATATCTGCAAG                         GTGAGGCAGAATCTGGTTTGGAGCGGCTACATCAATGTGCAGAGAAAGAAC
genomic: CCTGCCAGAGCATGAGCATGCCAAAAGACAGTTCTTTGAATATCTGCAAGgtttgccgtt ... ctttatctagGTGAGGCAGAATCAGGATTGGAGCGGCTACATCAATGTGCAGAGAAAGAAC
EST: gi|60396362|gb|DN229231.1|DN229231
EST:     CCTGCCAGAGCATGAGCATGCCAAAAGACAGTTCTTTGAATATCTGCAAG                         GTGAGGCAGAATCAGGATTGGAGCGGCTACATCAATGTGCAGAGAAAGAAC
genomic: CCTGCCAGAGCATGAGCATGCCAAAAGACAGTTCTTTGAATATCTGCAAGgtttgccgtt ... ctttatctagGTGAGGCAGAATCAGGATTGGAGCGGCTACATCAATGTGCAGAGAAAGAAC

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), 49 (downstream exon)
Score: 144

ATTGTCGAATGCAGAAGGGTATTGAAGTGGACTTATGCCTATGGATTTTACCTGCCAGAGCATGAGCATGCCAAAAGACAGTTCTTTGAATATCTGCAAGgtttgccgtt ... ctttatctagGTGAGGCAGAATCAGGATTGGAGCGGCTACATCAATGTGCAGAGAAAGAACTTCAAATATACCTTGATGCAGAATCTCCCTCGAAAGACTTCAATGATTT


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 153

ATTGTCGAATGCAGAAGGGTATTGAAGTGGACTTATGCCTATGGATTTTACCTGCCAGAGCATGAGCATGCCAAAAGACAGTTCTTTGAATATCTGCAAGgtttgccgtt ... ctttatctagGTGAGGCAGAATCAGGATTGGAGCGGCTACATCAATGTGCAGAGAAAGAACTTCAAATATACCTTGATGCAGAATCTCCCTCGAAAGACTTCAATGATTT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 150

ATTGTCGAATGCAGAAGGGTATTGAAGTGGACTTATGCCTATGGATTTTACCTGCCAGAGCATGAGCATGCCAAAAGACAGTTCTTTGAATATCTGCAAGgtttgccgtt ... ctttatctagGTGAGGCAGAATCAGGATTGGAGCGGCTACATCAATGTGCAGAGAAAGAACTTCAAATATACCTTGATGCAGAATCTCCCTCGAAAGACTTCAATGATTT


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 88

ATTGTCGAATGCAGAAGGGTATTGAAGTGGACTTATGCCTATGGATTTTACCTGCCAGAGCATGAGCATGCCAAAAGACAGTTCTTTGAATATCTGCAAGgtttgccgtt ... ctttatctagGTGAGGCAGAATCAGGATTGGAGCGGCTACATCAATGTGCAGAGAAAGAACTTCAAATATACCTTGATGCAGAATCTCCCTCGAAAGACTTCAATGATTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacccagttgccctacctatgtactaaacggactattcttggtgtctttatctagGTGAGGCAGAATCAGGATTGGAGCGGCTACATCAATGTGCAGAGAAAGAACTTCAAATATACCTTGATGCAGAATCTCCCTCGAAAGACTTCAATGATTT
                     tactaaa  putative branch site (score: 88)
                                            tctttatct  putative PPT
                                              tttatcta  TA-rich tract