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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actttcagtaaaaatgagtgacaattcagaaacatctaataatccaaatactgcttctgctataacatcgtatttttctaacaagtgaactttctcacagATTTTACCCCTACAGTGCGTAATTCTGCACAGAAGAAGAACAGTAGTAAAACAGGTGTAATTGTTGGGGTTGTGATTGGTGCAGCAGTTTTAGGAGTACT

Basic information

species Zea mays
transcript GRMZM2G155837_T01
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G155837_T01 (Zea mays), 3'ss of exon 14
lower sequence: LOC_Os04g52600.1 (Oryza sativa), 3'ss of exon 18
------actttcagtaaaaatga--gtgacaattcagaaacatctaataatccaaatactgct-------tctgctataacatcgtattttt---ctaacaagtgaactttctcacagATTTTACCCCTACAGTGCGTAATTCTGC---ACAGAAGAAGAACAGTAGTAAAACAGGTGTAATTGTTGGGGTTGTGATTGGTGCAGCAGTTTTAGGAGTACT
      || || | || | || |  ||  ||||    |||      ||  || |    | | |       |||||  ||| |||  ||||||   |||||||||||||||  |  ||||||| ||||| || ||| |||     ||   ||| || ||||  | ||||||||||||||| |||||||| |||||| ||||||  |||||||||||  |   
gtactcaccttaactatagataatggttccaatatgaaaatgatgtattttctagggtcagttgtaccattctgcc-taagatcacattttttttctaacaagtgaacttcttgtcagATTTCACCCCCACGGTGGGTATCGTGGCAGAACAAAACAAGAGTACTAGTAAAACAGGTGTTATTGTTGGCGTTGTGGTTGGTGTGGCAGTTTTAGGTTT---

upper sequence: GRMZM2G155837_T01 (Zea mays), 3'ss of exon 14
lower sequence: LOC_Os04g52630.1 (Oryza sativa), 3'ss of exon 16
--actttcagtaaaaatgagtgacaattcagaaacatcta------ataatc------caaatactgcttctg-ctataacatcgtatttttctaacaagtgaactttctcacagATTTTACCCCTACAGTGCGTAATTCTGCA---CAGAAGAAGAACAGTAGTAAAACAGGTGTAATTGTTGGGGTTGTGATTGGTGCAGCAGTTTTAGGAGTACT
  |||  |  |||  | || | |   ||   | |    ||      ||| ||      ||| || ||| | |   | ||| |||  ||| || |  |  ||   ||| ||   |||||| | |||||| ||||| | | |||||   || | |||||  |||||||||||||||||||||||||| |||||  ||||||  |||||||| ||  |   
gtactccccttaactacgaatcatggtttcaatatgattatgatttatattctggggtcaactattgcatttaattgtaagatcacattcttttctcttgt---cttcctgttagATTTCATCCCTACGGTGCGCAGTGCTGCAGCACAAAGGAAGAGTAGTAGTAAAACAGGTGTAATTGTTGGAGTTGTAGTTGGTGTGGCAGTTTTTGGTTT---
















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|18383718|gb|BM416918.1|BM416918
EST:     TGCTCAAGGCTACTACGGGCCTGCAATCTCAGCTTTGAGTGCAACTCCAA                         ATTTTACCCCTACAGTGCGTAATTCTGCACAGAAGAAGA
genomic: TGCTCAAGGCTACTACGGGCCTGCAATCTCAGCTTTGAGTGCAACTCCAAgtactcccct ... tttctcacagATTTTACCCCTACAGTGCGTAATTCTGCACAGAAGAAGA




















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: 48 (upstream exon), 46 (downstream exon)
Score: 51

TTTCTTGAGATTCATCTTTTCTGGGCTGGCAAGGGCACTTGTTGCATTCCTGCTCAAGGCTACTACGGGCCTGCAATCTCAGCTTTGAGTGCAACTCCAAgtactcccct ... tttctcacagATTTTACCCCTACAGTGCGTAATTCTGCACAGAAGAAGAACAGTAGTAAAACAGGTGTAATTGTTGGGGTTGTGATTGGTGCAGCAGTTTTAGGAGTACT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 145

TTTCTTGAGATTCATCTTTTCTGGGCTGGCAAGGGCACTTGTTGCATTCCTGCTCAAGGCTACTACGGGCCTGCAATCTCAGCTTTGAGTGCAACTCCAAgtactcccct ... tttctcacagATTTTACCCCTACAGTGCGTAATTCTGCACAGAAGAAGAACAGTAGTAAAACAGGTGTAATTGTTGGGGTTGTGATTGGTGCAGCAGTTTTAGGAGTACT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 132

TTTCTTGAGATTCATCTTTTCTGGGCTGGCAAGGGCACTTGTTGCATTCCTGCTCAAGGCTACTACGGGCCTGCAATCTCAGCTTTGAGTGCAACTCCAAgtactcccct ... tttctcacagATTTTACCCCTACAGTGCGTAATTCTGCACAGAAGAAGAACAGTAGTAAAACAGGTGTAATTGTTGGGGTTGTGATTGGTGCAGCAGTTTTAGGAGTACT


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

TTTCTTGAGATTCATCTTTTCTGGGCTGGCAAGGGCACTTGTTGCATTCCTGCTCAAGGCTACTACGGGCCTGCAATCTCAGCTTTGAGTGCAACTCCAAgtactcccct ... tttctcacagATTTTACCCCTACAGTGCGTAATTCTGCACAGAAGAAGAACAGTAGTAAAACAGGTGTAATTGTTGGGGTTGTGATTGGTGCAGCAGTTTTAGGAGTACT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaatactgcttctgctataacatcgtatttttctaacaagtgaactttctcacagATTTTACCCCTACAGTGCGTAATTCTGCACAGAAGAAGAACAGTAGTAAAACAGGTGTAATTGTTGGGGTTGTGATTGGTGCAGCAGTTTTAGGAGTACT
                              ttctaac  putative branch site (score: 97)
                                            ctttctcac  putative PPT
                         tatttttctaacaa  TA-rich tract