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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtctctgctgtaatctgtcacttgtactatctctctttgttatagtatttcttttaactatttgttgatgcgattgactcttaacctgtttgcattgcagGCCACTTATCCTGCGTATGGAACTTACGACTACAGCCATCAAATGCCTCAATCTGCTCCTCAAGCAGCTGCTTACGGCGCCTATCCTCCAACATACCCCG

Basic information

species Oryza sativa
transcript LOC_Os03g11200.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g11200.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G178294_T04 (Zea mays), 3'ss of exon 12
gtctctgctgtaatctgtcacttgtact--atctc--tctttgttatagtatttcttttaactatttgttgatgcgattg-actcttaacctgtttgcattgcagGCCACTTATCCTGCGTATGGAACTTACGACTACAGCCATCAAATGCCTCAATCTGCTCCTCAAGCAGCTGCTTACGGCGCCTATCCTCCAACATACCCCG
 ||| |||| |    | | ||    | |  ||||   | ||||||    |||   ||    |||  |  || |  ||||| |   || | || |||   ||  ||||  | |||||||| |||||||||||||||||||||||||||||||| ||  ||||||||||||||||||| || || || ||||||||||||||| | |
atctttgcttttgatttttacaaacagtcaatcttattatttgtttggctataaattcgtgcta--tagtggtttgattgtatgtttgaactcttt---ttttagGCTGCATATCCTGCATATGGAACTTACGACTACAGCCATCAAATGCCCCAGCCTGCTCCTCAAGCAGCTGCCTATGGTGCTTATCCTCCAACATACTCTG

upper sequence: LOC_Os03g11200.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM5G808775_T01 (Zea mays), 3'ss of exon 6
----gtctctgctgtaatctgtcacttgtactatctctctttgttatagtatttcttttaactatttgttgatgcgattgactcttaacctgtttgcattgcagGCCACTTATCCTGCGTATGGAACTTACGACTACAGCCATCAAATGCCTCAATCTGCTCCTCAAGCAGCTGCTTACGGCGCCTATCCTCCAACATACCCCG
     |     || | ||   |   ||   ||||   | | ||||||||| |||    |   || || |  |||  ||  |||   |   | ||||||||| ||||  | |||||||| ||||||||||| |||||||||||||||||||| ||  ||||||||||| ||||||| || ||||| ||||||||||||||| | |
aaaaatagtcactcttattatttgttta-gctataaatttgtgttatagtgttttgactgtatagtttt--atgt-atcaacttcaactttttttgcattgtagGCTGCATATCCTGCATATGGAACTTATGACTACAGCCATCAAATGCCACAGCCTGCTCCTCAAACAGCTGCCTATGGCGCTTATCCTCCAACATACTCTG
















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|29629938|gb|CB634947.1|CB634947
EST:     CGACATCTGAAGCATCGGGCCAACAATGGGGAGCTGCTTATGCACCACAG                         GCCACTTATCCTGCGTATGGAACTTACGACTACAGCCATCAAATGCCTCAA
genomic: CGACATCTGAAGCATCGGGGCAACAATGGGGAGCTGCTTATGCACCACAGgtttttatat ... tgcattgcagGCCACTTATCCTGCGTATGGAACTTACGACTACAGCCATCAAATGCCTCAA
EST: gi|29628808|gb|CB633819.1|CB633819
EST:     CGACATCTGAAGCATCGGGCCAACAATGGGGAGCTGCTTATGCACCACAG                         GCCACTTATCCTGCGTATGGAACTTACGACTACAGCCATCAAATGCCTCAA
genomic: CGACATCTGAAGCATCGGGGCAACAATGGGGAGCTGCTTATGCACCACAGgtttttatat ... tgcattgcagGCCACTTATCCTGCGTATGGAACTTACGACTACAGCCATCAAATGCCTCAA
EST: gi|89174096|gb|CI041989.1|CI041989
EST:     CGACATCTGAAGCATCGGGGCAACAATGGGGAGCTGCTTATGCACCACAG                         GCCACTTATCCTGCGTATGGAACTTACGACTACAGCCATCAAATGCCTCAA
genomic: CGACATCTGAAGCATCGGGGCAACAATGGGGAGCTGCTTATGCACCACAGgtttttatat ... tgcattgcagGCCACTTATCCTGCGTATGGAACTTACGACTACAGCCATCAAATGCCTCAA
EST: gi|58592425|gb|CF990733.1|CF990733
EST:     CGACATCTGAAGCATCGGGCCAACAATGGGGAGCTGCTTATGCACCACAG                         GCCACTTATCCTGCGTATGGAACTTACGACTACAGCCATCAAATGCCTCAA
genomic: CGACATCTGAAGCATCGGGGCAACAATGGGGAGCTGCTTATGCACCACAGgtttttatat ... tgcattgcagGCCACTTATCCTGCGTATGGAACTTACGACTACAGCCATCAAATGCCTCAA
EST: gi|89184800|gb|CI048356.1|CI048356
EST:     CGACATCTGAAGCATCGGGGCAACAATGGGGAGCTGCTTATGCACCACAG                         GCCACTTATCCTGCGTATGGAACTTACGACTACAGCCATCAAATGCCTCAA
genomic: CGACATCTGAAGCATCGGGGCAACAATGGGGAGCTGCTTATGCACCACAGgtttttatat ... tgcattgcagGCCACTTATCCTGCGTATGGAACTTACGACTACAGCCATCAAATGCCTCAA
EST: gi|89176256|gb|CI043277.1|CI043277
EST:     CGACATCTGAAGCATCGGGGCAACAATGGGGAGCTGCTTATGCACCACAG                         GCCACTTATCCTGCGTATGGAACTTACGACTACAGCCATCAAATGCCTCAA
genomic: CGACATCTGAAGCATCGGGGCAACAATGGGGAGCTGCTTATGCACCACAGgtttttatat ... tgcattgcagGCCACTTATCCTGCGTATGGAACTTACGACTACAGCCATCAAATGCCTCAA
EST: gi|86497082|gb|CI139715.1|CI139715
EST:     CGACATCTGAAGCATCGGGGCAACAATGGGGAGCTGCTTATGCACCACAG                         GCCACTTATCCTGCGTATGGAACTTACGACTACAGCCATCAAATGCCTCAA
genomic: CGACATCTGAAGCATCGGGGCAACAATGGGGAGCTGCTTATGCACCACAGgtttttatat ... tgcattgcagGCCACTTATCCTGCGTATGGAACTTACGACTACAGCCATCAAATGCCTCAA
EST: gi|58671000|gb|CK059686.1|CK059686
EST:     ATGGGGAGCTGCTTATGCACCACAG                         GCCACTTATCCTGCGTATGGAACTTACGACTACAGCCATCAAATGCCTCAA
genomic: ATGGGGAGCTGCTTATGCACCACAGgtttttatat ... tgcattgcagGCCACTTATCCTGCGTATGGAACTTACGACTACAGCCATCAAATGCCTCAA
EST: gi|87041196|gb|CI195818.1|CI195818
EST:     CGACATCTGAAGCATCGGGGCAACAATGGGGAGCTGCTTATGCACCACAG                         GCCACTTATCCTGCGTATGGAACTTACGACTACAGCCATCAAATGCCTCAA
genomic: CGACATCTGAAGCATCGGGGCAACAATGGGGAGCTGCTTATGCACCACAGgtttttatat ... tgcattgcagGCCACTTATCCTGCGTATGGAACTTACGACTACAGCCATCAAATGCCTCAA
EST: gi|24468907|gb|CA305856.1|CA305856
EST:     CGACATCTGAAGCATCGGGCCAACAATGGGGAGCTGCTTATGCACCACAG                         GCCACTTATCCTGCGTATGGAACTTACGACTACAGCCATCAAATGCCTCAA
genomic: CGACATCTGAAGCATCGGGGCAACAATGGGGAGCTGCTTATGCACCACAGgtttttatat ... tgcattgcagGCCACTTATCCTGCGTATGGAACTTACGACTACAGCCATCAAATGCCTCAA
EST: gi|86493516|gb|CI136149.1|CI136149
EST:     CGACATCTGAAGCATCGGGGCAACAATGGGGAGCTGCTTATGCACCACAG                         GCCACTTATCCTGCGTATGGAACTTACGACTACAGCCATCAAATGCCTCAA
genomic: CGACATCTGAAGCATCGGGGCAACAATGGGGAGCTGCTTATGCACCACAGgtttttatat ... tgcattgcagGCCACTTATCCTGCGTATGGAACTTACGACTACAGCCATCAAATGCCTCAA
EST: gi|88200911|gb|CI198763.1|CI198763
EST:     CGACATCTGAAGCATCGGGGCAACAATGGGGAGCTGCTTATGCACCACAG                         GCCACTTATCCTGCGTATGGAACTTACGACTACAGCCATCAAATGCCTCAA
genomic: CGACATCTGAAGCATCGGGGCAACAATGGGGAGCTGCTTATGCACCACAGgtttttatat ... tgcattgcagGCCACTTATCCTGCGTATGGAACTTACGACTACAGCCATCAAATGCCTCAA
EST: gi|86479247|gb|CI121880.1|CI121880
EST:     CGACATCTGAAGCATCGGGGCAACAATGGGGAGCTGCTTATGCACCACAG                         GCCACTTATCCTGCGTATGGAACTTACGACTACAGCCATCAAATGCCTCAA
genomic: CGACATCTGAAGCATCGGGGCAACAATGGGGAGCTGCTTATGCACCACAGgtttttatat ... tgcattgcagGCCACTTATCCTGCGTATGGAACTTACGACTACAGCCATCAAATGCCTCAA
EST: gi|86827107|gb|CI270823.1|CI270823
EST:     CGACATCTGAAGCATCGGGGCAACAATGGGGAGCTGCTTATGCACCACAG                         GCCACTTATCCTGCGTATGGAACTTACGACTACAGCCATCAAATGCCTCAA
genomic: CGACATCTGAAGCATCGGGGCAACAATGGGGAGCTGCTTATGCACCACAGgtttttatat ... tgcattgcagGCCACTTATCCTGCGTATGGAACTTACGACTACAGCCATCAAATGCCTCAA
EST: gi|29625008|gb|CB630019.1|CB630019
EST:     CGACATCTGAAGCATCGGGCCAACAATGGGGAGCTGCTTATGCACCACAG                         GCCACTTATCCTGCGTATGGAACTTACGACTACAGCCATCAAATGCCTCAA
genomic: CGACATCTGAAGCATCGGGGCAACAATGGGGAGCTGCTTATGCACCACAGgtttttatat ... tgcattgcagGCCACTTATCCTGCGTATGGAACTTACGACTACAGCCATCAAATGCCTCAA
EST: gi|88236165|gb|CI235367.1|CI235367
EST:     CGACATCTGAAGCATCGGGGCAACAATGGGGAGCTGCTTATGCACCACAG                         GCCGCTTATCCTGCGTATGGAACTTACGACTACAGCCATCAAATGCCTCAA
genomic: CGACATCTGAAGCATCGGGGCAACAATGGGGAGCTGCTTATGCACCACAGgtttttatat ... tgcattgcagGCCACTTATCCTGCGTATGGAACTTACGACTACAGCCATCAAATGCCTCAA
EST: gi|89175874|gb|CI042895.1|CI042895
EST:     CGACATCTGAAGCATCGGGGCAACAATGGGGAGCTGCTTATGCACCACAG                         GCCACTTATCCTGCGTATGGAACTTACGACTACAGCCATCAAATGCCTCAA
genomic: CGACATCTGAAGCATCGGGGCAACAATGGGGAGCTGCTTATGCACCACAGgtttttatat ... tgcattgcagGCCACTTATCCTGCGTATGGAACTTACGACTACAGCCATCAAATGCCTCAA
EST: gi|88222149|gb|CI222105.1|CI222105
EST:     CAACAATGGGGAGCTGCTTATGCACCACAG                         GCCACTTATCCTGCGTATGGAACTTACGACTACAGCCATCAAATGCCTCAA
genomic: CAACAATGGGGAGCTGCTTATGCACCACAGgtttttatat ... tgcattgcagGCCACTTATCCTGCGTATGGAACTTACGACTACAGCCATCAAATGCCTCAA
EST: gi|88849567|gb|CI089475.1|CI089475
EST:     TATGCACCACAG                         GCCACTTATCCTGCGTATGGAACTTACGACTACAGCCATCAAATGCCTCAA
genomic: TATGCACCACAGgtttttatat ... tgcattgcagGCCACTTATCCTGCGTATGGAACTTACGACTACAGCCATCAAATGCCTCAA
EST: gi|86480699|gb|CI123332.1|CI123332
EST:     CGACATCTGAAGCATCGGGGCAACAATGGGGAGCTGCTTATGCACCACAG                         GCCACTTATCCTGCGTATGGAACTTACGACTACAGCCATCAAATGCCTCAA
genomic: CGACATCTGAAGCATCGGGGCAACAATGGGGAGCTGCTTATGCACCACAGgtttttatat ... tgcattgcagGCCACTTATCCTGCGTATGGAACTTACGACTACAGCCATCAAATGCCTCAA
EST: gi|88222399|gb|CI222355.1|CI222355
EST:     GGCAACAATGGGGAGCTGCTTATGCACCACAG                         GCCACTTATCCTGCGTATGGAACTTACGACTACAGCCATCAAATGCCTCAA
genomic: GGCAACAATGGGGAGCTGCTTATGCACCACAGgtttttatat ... tgcattgcagGCCACTTATCCTGCGTATGGAACTTACGACTACAGCCATCAAATGCCTCAA
EST: gi|86482600|gb|CI125233.1|CI125233
EST:     AGCATCGGGGCAACAATGGGGATCTGCTTATGCACCACAG                         GCCACTTATCCTGCGTATGGAACTTACGACTACAGCCATCAAATGCCTCAA
genomic: AGCATCGGGGCAACAATGGGGAGCTGCTTATGCACCACAGgtttttatat ... tgcattgcagGCCACTTATCCTGCGTATGGAACTTACGACTACAGCCATCAAATGCCTCAA

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: 73 (upstream exon), 51 (downstream exon)
Score: 25

GCCAGTTGTGGGAACTGATCCAAATGCTCATAATCCTCCAGTTTGGCCAGCGACATCTGAAGCATCGGGGCAACAATGGGGAGCTGCTTATGCACCACAGgtttttatat ... tgcattgcagGCCACTTATCCTGCGTATGGAACTTACGACTACAGCCATCAAATGCCTCAATCTGCTCCTCAAGCAGCTGCTTACGGCGCCTATCCTCCAACATACCCCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatttcttttaactatttgttgatgcgattgactcttaacctgtttgcattgcagGCCACTTATCCTGCGTATGGAACTTACGACTACAGCCATCAAATGCCTCAATCTGCTCCTCAAGCAGCTGCTTACGGCGCCTATCCTCCAACATACCCCG
                                 tcttaac  putative branch site (score: 25)
                                       cctgttt  CT-rich tract
      ttttaactatttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctctgctgtaatctgtcacttgtactatctctctttgttatagtatttcttttaactatttgttgatgcgattgactcttaacctgtttgcattgcagGCCACTTATCCTGCGTATGGAACTTACGACTACAGCCATCAAATGCCTCAATCTGCTCCTCAAGCAGCTGCTTACGGCGCCTATCCTCCAACATACCCCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- -tctgctg
- - - - - - - ctgtcac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gttgatg