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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgggaactgaaaaactgttaaatgttcttttgcaattattgttctgtactgtctgtgtacatgtgaatctgagttattaaaattgagctttgctgatgtctgttcattcttgcagGCCATTTTAATATTTTTGTTGGCGATCTTTGCCCGGAAGTAACAGATGCTGCTTTGTTTGCTTTTTTCGCTGGATTTACCAGTTGCTC

Basic information

species Oryza sativa
transcript LOC_Os11g40510.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g40510.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G008611_T01 (Zea mays), 3'ss of exon 6
-------------gttggga-actgaaaaactgttaaatgttct-tttgcaatta--ttgttctgtactgtctgtgtacatgtgaatctgagttattaaaattgagctttgctgatgtctgttcattcttgcagGCCATTTTAATATTTTTGTTGGCGATCTTTGCCCGGAAGTAACAGATGCTGCTTTGTTTGCTTTTTTCGCTGGATTTACCAGTTGCTC
             | ||     |||||| | |  |  || || | |||| | ||   ||| |    |   |    |||  ||    | ||  || | ||   | ||||||| || ||  | |||||   |||||| |||||||||||||||||||| ||||||||||||||||| || |||||| |||||||||| |||||| |||| |   | | ||||||
gtttggaactgaagctgaagtgctgaaataatcctgtattttatatttgtattttacttggttcaaatcatgcaggtatgtgaatgtatggtttctgaattctaagctttggtggtgaatcttcatctatgcagGTCATTTTAATATTTTTGTTGGGGATCTTTGCCCGGAAGTCACTGATGCTACTTTGTTTGCATTTTTCTCTGGTTACTCTACTTGCTC

upper sequence: LOC_Os11g40510.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM5G835213_T02 (Zea mays), 3'ss of exon 5
gttgggaactgaaa---aactgttaaat--gttct----tttgcaattat----tgttctgtactgtctgtgta--catgtgaatctgagttattaaaatt--gagctttgctgatgtctgttcattcttgcagGCCATTTTAATATTTTTGTTGGCGATCTTTGCCCGGAAGTAACAGATGCTGCTTTGTTTGCTTTTTTCGCTGGATTTACCAGTTGCTC
||| |||||||||    || || | ||    | ||    |||| | || |    |  |  || |      || |   |||||||| |  | | |   ||||   ||||||| || ||  | |||||   |||||| |||||||||||||||||||| ||||||||||||||||| || |||||| |||||||||| |||||| ||||||   | | ||||||
gtttggaactgaagctgaagtgctgaactaatcctgtattttgtatttgtattttacttggttcaagtcatgcaggtatgtgaatgtatggtttctgaattctaagctttggtggtgaatcttcatctatgcagGTCATTTTAATATTTTTGTTGGGGATCTTTGCCCGGAAGTCACTGATGCTACTTTGTTTGCATTTTTCTCTGGATACTCTACTTGCTC
















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|58688359|gb|CK077046.1|CK077046
EST:     AATAAAAGTCAATTGGGCATATGCAAGTACTCAAAGAGAGGATACATCAG                         GCCATTTTAATATTTTTGTTGGCGATCTTTGCCCGGAAGTAACAGATGCTG
genomic: AATAAAAGTCAATTGGGCATATGCAAGTACTCAAAGAGAGGATACATCAGgttgggaact ... attcttgcagGCCATTTTAATATTTTTGTTGGCGATCTTTGCCCGGAAGTAACAGATGCTG
EST: gi|86897973|gb|CI290697.1|CI290697
EST:     AATAAAAGTCAATTGGGCATATGCAAGTACTCAAAGAGAGGATACATCAG                         GCCATTTTAATATTTTTGTTGGCGATCTTTGCCCGGAAGTAACAGATGCTG
genomic: AATAAAAGTCAATTGGGCATATGCAAGTACTCAAAGAGAGGATACATCAGgttgggaact ... attcttgcagGCCATTTTAATATTTTTGTTGGCGATCTTTGCCCGGAAGTAACAGATGCTG
EST: gi|87012285|gb|CI293335.1|CI293335
EST:     AATAAAAGTCAATTGGGCATATGCAAGTACTCAAAGAGAGGATACATCAG                         GCCATTTTAATATTTTTGTTGGCGATCTTTGCCCGGAAGTAACAGATGCTG
genomic: AATAAAAGTCAATTGGGCATATGCAAGTACTCAAAGAGAGGATACATCAGgttgggaact ... attcttgcagGCCATTTTAATATTTTTGTTGGCGATCTTTGCCCGGAAGTAACAGATGCTG
EST: gi|87006051|gb|CI289468.1|CI289468
EST:     AATAAAAGTCAATTGGGCATATGCAAGTACTCAAAGAGAGGATACATCAG                         GCCATTTTAATATTTTTGTTGGCGATCTTTGCCCGGAAGTAACAGATGCTG
genomic: AATAAAAGTCAATTGGGCATATGCAAGTACTCAAAGAGAGGATACATCAGgttgggaact ... attcttgcagGCCATTTTAATATTTTTGTTGGCGATCTTTGCCCGGAAGTAACAGATGCTG
EST: gi|58602505|gb|CK013033.1|CK013033
EST:     AATAAAAGTCAATTGGGCATATGCAAGTACTCAAAGAGAGGATACATCAG                         GCCATTTTAATATTTTTGTTGGCGATCTTTGCCCGGAAGTAACAGATGCTG
genomic: AATAAAAGTCAATTGGGCATATGCAAGTACTCAAAGAGAGGATACATCAGgttgggaact ... attcttgcagGCCATTTTAATATTTTTGTTGGCGATCTTTGCCCGGAAGTAACAGATGCTG
EST: gi|58681227|gb|CK069914.1|CK069914
EST:     AATAAAAGTCAAGTGGGCATATGCAAGTACTCAAAGAGAGGATACATCAG                         GCCATTTTAATATTTTTGTTGGCGATCTTTGCCCGGAAGTAACAGATGCTG
genomic: AATAAAAGTCAATTGGGCATATGCAAGTACTCAAAGAGAGGATACATCAGgttgggaact ... attcttgcagGCCATTTTAATATTTTTGTTGGCGATCTTTGCCCGGAAGTAACAGATGCTG
EST: gi|86905007|gb|CI289154.1|CI289154
EST:     AATAAAAGTCAATTGGGCATATGCAAGTACTCAAAGAGAGGATACATCAG                         GCCATTTTAATATTTTTGTTGGCGATCTTTGCCCGGAAGTAACAGATGCTG
genomic: AATAAAAGTCAATTGGGCATATGCAAGTACTCAAAGAGAGGATACATCAGgttgggaact ... attcttgcagGCCATTTTAATATTTTTGTTGGCGATCTTTGCCCGGAAGTAACAGATGCTG
EST: gi|88321854|gb|CI672999.1|CI672999
EST:     AATAAAAGTCAATTGGGCATATGCAAGTACTCAAAGAGAGGATACATCAG                         GCCATTTTAATATTTTTGTTGGCGATCTTTGCCCGGAAGTAACAGATGCTG
genomic: AATAAAAGTCAATTGGGCATATGCAAGTACTCAAAGAGAGGATACATCAGgttgggaact ... attcttgcagGCCATTTTAATATTTTTGTTGGCGATCTTTGCCCGGAAGTAACAGATGCTG
EST: gi|58678674|gb|CK067361.1|CK067361
EST:     ATAAAAGTCAATTGGGCATATGCAAGTACTCAAAGAGAGGATACATCGAG                         GCCATTTTAATATTTTTGTTGGCGATCTTTGCCCGGAAGTAACAGATGCT
genomic: ATAAAAGTCAATTGGGCATATGCAAGTACTCAAAGAGAGGATACATC-AGgttgggaact ... attcttgcagGCCATTTTAATATTTTTGTTGGCGATCTTTGCCCGGAAGTAACAGATGCT
EST: gi|58690866|gb|CK079553.1|CK079553
EST:     AATAAAAGTCAATTGGGCATATGCAAGTACTCAAAGAGAGGATACATCAG                         GCCATTTTAATATTTTTGTTGGCGATCTTTGCCCGGAAGTAACAGATGCTG
genomic: AATAAAAGTCAATTGGGCATATGCAAGTACTCAAAGAGAGGATACATCAGgttgggaact ... attcttgcagGCCATTTTAATATTTTTGTTGGCGATCTTTGCCCGGAAGTAACAGATGCTG
EST: gi|87022688|gb|CI293578.1|CI293578
EST:     AATAAAAGTCAATTGGGCATATGCAAGTACTCAAAGAGAGGATACATCAG                         GCCATTTTAATATTTTTGTTGGCGATCTTTGCCCGGAAGTAACAGATGCTG
genomic: AATAAAAGTCAATTGGGCATATGCAAGTACTCAAAGAGAGGATACATCAGgttgggaact ... attcttgcagGCCATTTTAATATTTTTGTTGGCGATCTTTGCCCGGAAGTAACAGATGCTG
EST: gi|58694246|gb|CK082933.1|CK082933
EST:     AATAAAAGTCAATTGGGCATATGCAAGTACTCAAAGAGAGGATACATCAG                         GCCATTTTAATATTTTTGTTGGCGATCTTTGCCCGGAAGTAACAGATGCTG
genomic: AATAAAAGTCAATTGGGCATATGCAAGTACTCAAAGAGAGGATACATCAGgttgggaact ... attcttgcagGCCATTTTAATATTTTTGTTGGCGATCTTTGCCCGGAAGTAACAGATGCTG
EST: gi|25797088|gb|CA753049.1|CA753049
EST:     ATTTAAAGTCAATTGGGCATATGCAAGTACTCAAAGAGAGGATACATCAG                         GCCATTTTAATATTTTTGTTGGCGATCTTTGCCCGGAAGTAACAGATGCTG
genomic: AATAAAAGTCAATTGGGCATATGCAAGTACTCAAAGAGAGGATACATCAGgttgggaact ... attcttgcagGCCATTTTAATATTTTTGTTGGCGATCTTTGCCCGGAAGTAACAGATGCTG
EST: gi|58606512|gb|CK034545.1|CK034545
EST:     AATAAAAGTCAATTGGGCATATGCAAGTACTCAAAGAGAGGATACATCAG                         GCCATTTTAATATTTTTGTTGGCGATCTTTGCCCGGAAGTAACAGATGCTG
genomic: AATAAAAGTCAATTGGGCATATGCAAGTACTCAAAGAGAGGATACATCAGgttgggaact ... attcttgcagGCCATTTTAATATTTTTGTTGGCGATCTTTGCCCGGAAGTAACAGATGCTG
EST: gi|58601763|gb|CK012291.1|CK012291
EST:     ATAAAAGTCAA-TGGGCATATGCAAGTACTCAAAGAGAGGATACATCGAG                         GCCATTTTAATATTTTTG-TGGCGATC-TTGCCCGGAAGTAACAGATGCT
genomic: ATAAAAGTCAATTGGGCATATGCAAGTACTCAAAGAGAGGATACATC-AGgttgggaact ... attcttgcagGCCATTTTAATATTTTTGTTGGCGATCTTTGCCCGGAAGTAACAGATGCT
EST: gi|86596642|gb|CI286555.1|CI286555
EST:     AATAAAAGTCAATTGGGCATATGCAAGTACTCAAAGAGAGGATACATCAG                         GCCATTTTAATATTTTTGTTGGCGATCTTTGCCCGGAAGTAACAGATGCTG
genomic: AATAAAAGTCAATTGGGCATATGCAAGTACTCAAAGAGAGGATACATCAGgttgggaact ... attcttgcagGCCATTTTAATATTTTTGTTGGCGATCTTTGCCCGGAAGTAACAGATGCTG

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 1 RNA-Seqlibrary.


Block sizes: 31 (upstream exon), 72 (downstream exon)
Score: 206

GTTTGGCCAGCCAATAAAAGTCAATTGGGCATATGCAAGTACTCAAAGAGAGGATACATCAGgttgggaact ... attcttgcagGCCATTTTAATATTTTTGTTGGCGATCTTTGCCCGGAAGTAACAGATGCTGCTTTGTTTGCTTTTTTCGCTGGATTTACCAGTTGCTC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgtgaatctgagttattaaaattgagctttgctgatgtctgttcattcttgcagGCCATTTTAATATTTTTGTTGGCGATCTTTGCCCGGAAGTAACAGATGCTGCTTTGTTTGCTTTTTTCGCTGGATTTACCAGTTGCTC
                              tgctgat  putative branch site (score: 206)
                                          ttcattctt  putative PPT
         tgagttattaaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgggaactgaaaaactgttaaatgttcttttgcaattattgttctgtactgtctgtgtacatgtgaatctgagttattaaaattgagctttgctgatgtctgttcattcttgcagGCCATTTTAATATTTTTGTTGGCGATCTTTGCCCGGAAGTAACAGATGCTGCTTTGTTTGCTTTTTTCGCTGGATTTACCAGTTGCTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA