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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttctgttcacgaaatttattgctagtgcaggaagcgtttctgtatgcattattttccctattgtttctgtcatcctgagttaacaaggttctctgtgtagGCATATTTTCCCCCAATTTCTCAACCAGAAGGACGCCCCTTGACAATTCAAGATGCAAGAGGAAAAGAATGGCATTTTCAGTTTAGGTTTTGGCCAAATA

Basic information

species Zea mays
transcript GRMZM2G158162_T03
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G158162_T03 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os07g48200.1 (Oryza sativa), 3'ss of exon 5
---ttctgttcacgaaatttattgctagtgcaggaagcgtttctgtatgcattattttccctattgtttctgtcatcctgagttaacaaggttctctgtgtagGCATATTTTCCCCCAATTTCTCAACCAGAAGGACGCCCCTTGACAATTCAAGATGCAAGAGGAAAAGAATGGCATTTTCAGTTTAGGTTTTGGCCAAATA
   | |||     |      |||| |  | ||| |    | | |  |   |||  ||| | | ||  | |||||||||||||||  | || | |  | ||||||||||||| || ||||||||||| |||||||| || || |||||||||||||| |||| ||| |||||||||||||||||||| || || ||||||||||
aactactgggagtggggacaattgtttct-cagcataactattttaacatatttcttttcatgtt--tgctgtcatcctgagttgccgagatacattttgtagGCATATTTCCCTCCAATTTCTCAGCCAGAAGGTCGTCCTTTGACAATTCAAGACGCAAAAGGCAAAGAATGGCATTTTCAGTTCAGATTCTGGCCAAATA

upper sequence: GRMZM2G158162_T03 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA03G04330.1 (Glycine max), 3'ss of exon 7
----------------------------ttctgttcacgaaatttattgctagtgcaggaagcgtttctgtatgcattattttccctattgtttctgtcatcctg----agttaacaag---gttctctgtgtagGCATATTTTCCCCCAATTTCTCAACCAGAAGGACGCCCCTTGACAATTCAAGATGCAAGAGGAAAAGAATGGCATTTTCAGTTTAGGTTTTGGCCAAATA
                            |    || ||     | |||     |  |  ||   ||   |||    ||||||| | |   |  ||||  |   ||    |  | | |     |  |  |||| |||||||||| || ||||| ||||||||||| || |  || ||   ||| |||||||  | |||||||||||||   ||||||||||| |||||||||||||
gtaatttatcctaactcatctgttgaactggcctttactgttgtcattttatattaactaacaattctagtaaaagttatttttcttgacgagtctggtaatttgttaaaactgaaagacgagagcattgtgcagGCATATTTCCCTCCAATCTCTCAACCAGAGGGCCTTCCTTTACGAATCCAAGATGTGAAAGGAAAAGAATGGATGTTTCAGTTTAGATTTTGGCCAAATA
















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|5268958|gb|AI770922.1|AI770922
EST:     GAGATGCAGGCCGCATAGGGCGCCTTGTTCTTCCAAAAGCTTGTGCCGAG                         GCATATTTTCCCCCAATTTCTCAACCAGAAGGACGCCCCTTGACAATTCAA
genomic: GTGATGCAGGCCGCATAGGGCGCCTTGTTCTTCCAAAAGCTTGTGCCGAGgtaactttaa ... ctctgtgtagGCATATTTTCCCCCAATTTCTCAACCAGAAGGACGCCCCTTGACAATTCAA
EST: gi|67040653|gb|CO466908.1|CO466908
EST:     GTGATGCAGGCCGCATAGGGCGCCTTGTTCTTCCAAAAGCTTGTGCCGAG                         GCATATTTTCCCCCAATTTCTCAACCAGAAGGACGCCCCTTGACAATTCAA
genomic: GTGATGCAGGCCGCATAGGGCGCCTTGTTCTTCCAAAAGCTTGTGCCGAGgtaactttaa ... ctctgtgtagGCATATTTTCCCCCAATTTCTCAACCAGAAGGACGCCCCTTGACAATTCAA
EST: gi|13150757|gb|BG321079.1|BG321079
EST:     GTSATGCAGGCCGCATAGGGCGCCTTGTTCTTCCAAAAGCTTGTGCCGAG                         GCATATTTTCCCCCAATTTCTCAACCAGAAGGACGCCCCTTGACAATTCAA
genomic: GTGATGCAGGCCGCATAGGGCGCCTTGTTCTTCCAAAAGCTTGTGCCGAGgtaactttaa ... ctctgtgtagGCATATTTTCCCCCAATTTCTCAACCAGAAGGACGCCCCTTGACAATTCAA

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: 46 (upstream exon), 48 (downstream exon)
Score: 100

TTCAAATTCCACAATCGTTCCATTGTTCGAGAAGGTCCTGAGTGCGAGTGATGCAGGCCGCATAGGGCGCCTTGTTCTTCCAAAAGCTTGTGCCGAGgtaactttaa ... ctctgtgtagGCATATTTTCCCCCAATTTCTCAACCAGAAGGACGCCCCTTGACAATTCAAGATGCAAGAGGAAAAGAATGGCATTTTCAGTTTAGGTTTTGGCCAAATA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 89

TTCAAATTCCACAATCGTTCCATTGTTCGAGAAGGTCCTGAGTGCGAGTGATGCAGGCCGCATAGGGCGCCTTGTTCTTCCAAAAGCTTGTGCCGAGgtaactttaa ... ctctgtgtagGCATATTTTCCCCCAATTTCTCAACCAGAAGGACGCCCCTTGACAATTCAAGATGCAAGAGGAAAAGAATGGCATTTTCAGTTTAGGTTTTGGCCAAATA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 87

TTCAAATTCCACAATCGTTCCATTGTTCGAGAAGGTCCTGAGTGCGAGTGATGCAGGCCGCATAGGGCGCCTTGTTCTTCCAAAAGCTTGTGCCGAGgtaactttaa ... ctctgtgtagGCATATTTTCCCCCAATTTCTCAACCAGAAGGACGCCCCTTGACAATTCAAGATGCAAGAGGAAAAGAATGGCATTTTCAGTTTAGGTTTTGGCCAAATA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 179

TTCAAATTCCACAATCGTTCCATTGTTCGAGAAGGTCCTGAGTGCGAGTGATGCAGGCCGCATAGGGCGCCTTGTTCTTCCAAAAGCTTGTGCCGAGgtaactttaa ... ctctgtgtagGCATATTTTCCCCCAATTTCTCAACCAGAAGGACGCCCCTTGACAATTCAAGATGCAAGAGGAAAAGAATGGCATTTTCAGTTTAGGTTTTGGCCAAATA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcattattttccctattgtttctgtcatcctgagttaacaaggttctctgtgtagGCATATTTTCCCCCAATTTCTCAACCAGAAGGACGCCCCTTGACAATTCAAGATGCAAGAGGAAAAGAATGGCATTTTCAGTTTAGGTTTTGGCCAAATA
                                agttaac  putative branch site (score: 179)
                                           ttctctgt  putative PPT
             tattgttt  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
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttctgttcacgaaatttattgctagtgcaggaagcgtttctgtatgcattattttccctattgtttctgtcatcctgagttaacaaggttctctgtgtagGCATATTTTCCCCCAATTTCTCAACCAGAAGGACGCCCCTTGACAATTCAAGATGCAAGAGGAAAAGAATGGCATTTTCAGTTTAGGTTTTGGCCAAATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
ttctgtt
- - - - - - - - tattgct
- - - - - - - - - - - - gtgcagg
- - - - - - - - - - - - - - - - - - - - tgtatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catcctg