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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgaaactacgaataatctgtgaagtttcatttataaaatatttgtatttagattgaaacatatatctttccagTGTATCAGATCTTCTTGACTTCATAAGCCCAGACCAGGAAAGAAAAGAAAGGGATATGCAAAGGAAATGCAGGCGTGCAAAG

Basic information

species Zea mays
transcript GRMZM2G086030_T01
intron # 21
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G086030_T01 (Zea mays), 3'ss of exon 21
lower sequence: LOC_Os04g55230.1 (Oryza sativa), 3'ss of exon 21
gtatgaaactacgaataatctgtgaagtttcatttataaaatatttgtatttagattgaaacatatatctttccagTGTATCAGATCTTCTTGACTTCATAAGCCCAGACCAGGAAAGAAAAGAAAGGGATATGCAAAGGAAATGCAGGCGTGCAAAG
         || |||||  ||||| | | ||| |   ||| | |    || | ||||||||||| ||||||||||||||||||||||| ||||||| ||||||||| || |||||||||||||| |||||||  ||||| ||  ||||||||||||||
--------gtatgaatacactgtgcattatcagtcgcaaactgtgatgatctggattgaaacatttatctttccagTGTATCAGATCTACTTGACTACATAAGCCCGGATCAGGAAAGAAAAGAGAGGGATACACAAAGAAAGGGCAGGCGTGCAAAG
















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|31353676|gb|CD438033.1|CD438033
EST:     GAGGCATGCCAAAACCTGATTCATCTATTGCAAGTAAAGGACATCCTTAG                         TGTATCAGATCTTCTTGACTTCATAAGCCCAGACCAGGAAAGAAAAG
genomic: GAGGCATGCCAAAACCTGATTCATCTATTGCAAGTAAAGGACATC-TTAGgtatgaaact ... atctttccagTGTATCAGATCTTCTTGACTTCATAAGCCCAGACCAGGAAAGAAAAG
EST: gi|211017605|gb|FL188943.1|FL188943
EST:     AGAGGCATGCCAAAACCTGATTCATCTATTGCAAGTAAAGGACATCTTAG                         TGTATCAGATCTTCTTGACTTCATAAGCCCAGACCAGGAAAGAAAAGAAAG
genomic: AGAGGCATGCCAAAACCTGATTCATCTATTGCAAGTAAAGGACATCTTAGgtatgaaact ... atctttccagTGTATCAGATCTTCTTGACTTCATAAGCCCAGACCAGGAAAGAAAAGAAAG
EST: gi|67035470|gb|CO464003.1|CO464003
EST:     AGGGGCATGCCAAAACCTGATTCATCTATTGCAAGTAAAGGACATCTTAG                         TGTATCAGATCTTCTTGACTTCATAAGCCCGGACCAGGAAAGAAAAGAAAG
genomic: AGAGGCATGCCAAAACCTGATTCATCTATTGCAAGTAAAGGACATCTTAGgtatgaaact ... atctttccagTGTATCAGATCTTCTTGACTTCATAAGCCCAGACCAGGAAAGAAAAGAAAG
EST: gi|31354896|gb|CD439253.1|CD439253
EST:     AGAGGCATGCCAAAACCTGATTCATCTATTGCAAGTAAAGGACATCTTAG                         TGTATCAGATCTTCTTGACTTCATAAGCCCAGACCAGGAAAGAAAAGAAAG
genomic: AGAGGCATGCCAAAACCTGATTCATCTATTGCAAGTAAAGGACATCTTAGgtatgaaact ... atctttccagTGTATCAGATCTTCTTGACTTCATAAGCCCAGACCAGGAAAGAAAAGAAAG

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: 136

GGCTAGAATATTTTGAGTCAAAAGCATTAGAACAACAAGAGGCGGCTCGAAGAGGCATGCCAAAACCTGATTCATCTATTGCAAGTAAAGGACATCTTAGgtatgaaact ... atctttccagTGTATCAGATCTTCTTGACTTCATAAGCCCAGACCAGGAAAGAAAAGAAAGGGATATGCAAAGGAAATGCAGGCGTGCAAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 278

GGCTAGAATATTTTGAGTCAAAAGCATTAGAACAACAAGAGGCGGCTCGAAGAGGCATGCCAAAACCTGATTCATCTATTGCAAGTAAAGGACATCTTAGgtatgaaact ... atctttccagTGTATCAGATCTTCTTGACTTCATAAGCCCAGACCAGGAAAGAAAAGAAAGGGATATGCAAAGGAAATGCAGGCGTGCAAAG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 64

GGCTAGAATATTTTGAGTCAAAAGCATTAGAACAACAAGAGGCGGCTCGAAGAGGCATGCCAAAACCTGATTCATCTATTGCAAGTAAAGGACATCTTAGgtatgaaact ... atctttccagTGTATCAGATCTTCTTGACTTCATAAGCCCAGACCAGGAAAGAAAAGAAAGGGATATGCAAAGGAAATGCAGGCGTGCAAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 434

GGCTAGAATATTTTGAGTCAAAAGCATTAGAACAACAAGAGGCGGCTCGAAGAGGCATGCCAAAACCTGATTCATCTATTGCAAGTAAAGGACATCTTAGgtatgaaact ... atctttccagTGTATCAGATCTTCTTGACTTCATAAGCCCAGACCAGGAAAGAAAAGAAAGGGATATGCAAAGGAAATGCAGGCGTGCAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgaagtttcatttataaaatatttgtatttagattgaaacatatatctttccagTGTATCAGATCTTCTTGACTTCATAAGCCCAGACCAGGAAAGAAAAGAAAGGGATATGCAAAGGAAATGCAGGCGTGCAAAG
                                            tatctttcc  CT-rich tract
      tttcatttataaaata  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgaaactacgaataatctgtgaagtttcatttataaaatatttgtatttagattgaaacatatatctttccagTGTATCAGATCTTCTTGACTTCATAAGCCCAGACCAGGAAAGAAAAGAAAGGGATATGCAAAGGAAATGCAGGCGTGCAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG