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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAAAAAATTAGATCATTTCCTGTGCGCAGATTGTGTCAAAGAAAATGGCACGAAGAGACCTTCAAATTCATATCCAGCATCATCAAATTCTGATTCTAAGgttggttacttaacctctatctcttgactgactgtctaccgatgttctgtttgaagataacttatctttaattctttaaaactttaagcgcagtagaaat...

Basic information

species Oryza sativa
transcript LOC_Os09g21770.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g21770.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G091265_T05 (Zea mays), 5'ss of exon 4
CAAAAAATTAGATCATTTCCTGTGCGCAGATTGTGTCAAAGAAAATGGCACGAAGAGACCTTCAAATTCATATCCAGCATCATCAAATTCTGATTCTAAGgttggttacttaacctctatctcttgactg-----actgtctaccgatgttctgtttgaagataa---cttatctttaattctttaaaactttaagcgcagtagaaat
 |||||  ||||||||| | ||||| | |||||||  |||||||||||  | |||||||| |||||||||||  |||  ||| |||| || |||||||||||  ||   ||   || |||| | ||||||     | ||| ||   || || |||||  | |||    ||||| | |  |||  ||  | ||| || |||  |     
AAAAAAGATAGATCATTACATGTGCTCGGATTGTGCTAAAGAAAATGGTGCAAAGAGACCCTCAAATTCATACTCAGTTTCACCAAACTCAGATTCTAAGgtgtgtgcttttctctttatcacatgactgcataaattgttta--aatcttatgttttcatatagtttcttatttctgcttcgatatgatttttag-gcaaaa-----
















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|88304356|gb|CI515629.1|CI515629
EST:     GCATCATCAAATTGTGATTCTAAG                         GTTGAGCCAAAAAAGCGGAAGAGGTAATTGCTGTGACACGAGCCATCCGTG
genomic: GCATCATCAAATTCTGATTCTAAGgttggttact ... ccaactgcagGTTGAGCCAAAAAAGCGGAAGAGGTAATTGCTGTGACACGAGCCATCCGTG
EST: gi|58598945|gb|CK009473.1|CK009473
EST:     CGAAGAGACCTTCAAATTCATATCCAGCATCATCAAATTCTGATTCTAAG                         GTTGAGCCAAAAAAGCGGAAGAGGTAATTGCTGTGACACGAGCCATCCGTG
genomic: CGAAGAGACCTTCAAATTCATATCCAGCATCATCAAATTCTGATTCTAAGgttggttact ... ccaactgcagGTTGAGCCAAAAAAGCGGAAGAGGTAATTGCTGTGACACGAGCCATCCGTG
EST: gi|88319397|gb|CI515858.1|CI515858
EST:     CATATCCAGCATCATCAAATTCTGATTCTAAG                         GTTGAGCCAAAAAAGCGGAAGAGGTAATTGCTGTGACACGAGCCATCCGTG
genomic: CATATCCAGCATCATCAAATTCTGATTCTAAGgttggttact ... ccaactgcagGTTGAGCCAAAAAAGCGGAAGAGGTAATTGCTGTGACACGAGCCATCCGTG
EST: gi|88380180|gb|CI516167.1|CI516167
EST:     CAGCATCATCAAATTCTGATTCTAAG                         GTTGAGCCAAAAAAGCGGAAGAGGGTAATTGCTGTGACACGAGCCATCCGT
genomic: CAGCATCATCAAATTCTGATTCTAAGgttggttact ... ccaactgcagGTTGAGCCAAAAAAGCGGAAGA-GGTAATTGCTGTGACACGAGCCATCCGT
EST: gi|86256715|gb|CI061478.1|CI061478
EST:     CGAAGAGACCTTCAAATTCATATCCAGCATCATCAAATTCTGATTCTAAG                         GTTGAGCCAAAAAAGCGGAAGAGGTAATTGCTGTGACACGAGCCATCCGTG
genomic: CGAAGAGACCTTCAAATTCATATCCAGCATCATCAAATTCTGATTCTAAGgttggttact ... ccaactgcagGTTGAGCCAAAAAAGCGGAAGAGGTAATTGCTGTGACACGAGCCATCCGTG
EST: gi|88380089|gb|CI513679.1|CI513679
EST:     CGAAGAGACCTTCNAATTCATATCCAGCATCATCAAATTCTGATTCTAAG                         GTTGAGCCAAAAAAGCGGAAGAGGTAATTGCTGTGACACGAGCCATCCGTG
genomic: CGAAGAGACCTTCAAATTCATATCCAGCATCATCAAATTCTGATTCTAAGgttggttact ... ccaactgcagGTTGAGCCAAAAAAGCGGAAGAGGTAATTGCTGTGACACGAGCCATCCGTG
EST: gi|88216494|gb|CI216343.1|CI216343
EST:     CGAAGAGACCTTCAAATTCATATCCAGCATCATCAAATTCTGATTCTAAG                         GTTGAGCCAAAAAAGCGGAAGAGGTAATTGCTGTGACACGAGCCATCCGTG
genomic: CGAAGAGACCTTCAAATTCATATCCAGCATCATCAAATTCTGATTCTAAGgttggttact ... ccaactgcagGTTGAGCCAAAAAAGCGGAAGAGGTAATTGCTGTGACACGAGCCATCCGTG
EST: gi|29638119|gb|CB643128.1|CB643128
EST:     CGAAGAGACCTTCAAATTCATATCCAGCATCATCAAATTCTGATTCTAAG                         GTTGAGCCAAAAAAGCGGAAGAGGTAATTGCTGTGACACGAGCCATCCGTG
genomic: CGAAGAGACCTTCAAATTCATATCCAGCATCATCAAATTCTGATTCTAAGgttggttact ... ccaactgcagGTTGAGCCAAAAAAGCGGAAGAGGTAATTGCTGTGACACGAGCCATCCGTG
EST: gi|88468415|gb|CI514897.1|CI514897
EST:     AATTCATATCCAGCATCATCAAATTCTGATTCTAAG                         GTTGAGCCAAAAAAGCGGAAGAGGTAATTGCTGTGACACGAGCCATCCGTG
genomic: AATTCATATCCAGCATCATCAAATTCTGATTCTAAGgttggttact ... ccaactgcagGTTGAGCCAAAAAAGCGGAAGAGGTAATTGCTGTGACACGAGCCATCCGTG
EST: gi|88459347|gb|CI517025.1|CI517025
EST:     ATCAAATTCTGATTCTAAG                         GTTGAGCCAAAAAAGCGGAAGAGGTAATTGCTGTGACACGAGCCATCCGTG
genomic: ATCAAATTCTGATTCTAAGgttggttact ... ccaactgcagGTTGAGCCAAAAAAGCGGAAGAGGTAATTGCTGTGACACGAGCCATCCGTG
EST: gi|88419946|gb|CI516395.1|CI516395
EST:     ATCATCAAATTCTGATTCTAAG                         GTTGAGCCAAAAAAGCGGAAGAGGTAATTGCTGTGACACGAGCCATCCGTG
genomic: ATCATCAAATTCTGATTCTAAGgttggttact ... ccaactgcagGTTGAGCCAAAAAAGCGGAAGAGGTAATTGCTGTGACACGAGCCATCCGTG
EST: gi|15857112|gb|BI809924.1|BI809924
EST:     CGAAGAGACCTTCAAATTCATATCCAGCATCATC-AATTCTGATTCTAAG                         GTTGAGCCCAAAAAGCGGAAGAGGTAATTGCTGTGACACGAGCCATCC-TG
genomic: CGAAGAGACCTTCAAATTCATATCCAGCATCATCAAATTCTGATTCTAAGgttggttact ... ccaactgcagGTTGAGCCAAAAAAGCGGAAGAGGTAATTGCTGTGACACGAGCCATCCGTG
EST: gi|29638253|gb|CB643262.1|CB643262
EST:     CGAAGAGACCTTCAAATTCATATCCAGCATCATCAAATTCTGATTCTAAG                         GTTGAGCCAAAAAAGCGGAAGAGGTAATTGCTGTGACACGAGCCATCCGTG
genomic: CGAAGAGACCTTCAAATTCATATCCAGCATCATCAAATTCTGATTCTAAGgttggttact ... ccaactgcagGTTGAGCCAAAAAAGCGGAAGAGGTAATTGCTGTGACACGAGCCATCCGTG
EST: gi|86492656|gb|CI135289.1|CI135289
EST:     CGAAGAGACCTTCAAATTCATATCCAGCATCATCAAATTCTGATTCTAAG                         GTTGAGCCCAAAAAGCGGAAGAGGTAATTGCTGTGACACGAGCCATCCGTG
genomic: CGAAGAGACCTTCAAATTCATATCCAGCATCATCAAATTCTGATTCTAAGgttggttact ... ccaactgcagGTTGAGCCAAAAAAGCGGAAGAGGTAATTGCTGTGACACGAGCCATCCGTG
EST: gi|33658502|gb|CF281115.1|CF281115
EST:     CGAAGAGACCTTCAAATTCATATCCAGCATCATCAAATTCTGATTCTAAG                         GTTGAGCCAAAAAAGCGGAAGAGGTAATTGCTGTGACACGAGCCATCCGTG
genomic: CGAAGAGACCTTCAAATTCATATCCAGCATCATCAAATTCTGATTCTAAGgttggttact ... ccaactgcagGTTGAGCCAAAAAAGCGGAAGAGGTAATTGCTGTGACACGAGCCATCCGTG
EST: gi|88449121|gb|CI560582.1|CI560582
EST:     TTCATATCCAGCATCATCAAATTCTGATTCTAAG                         GTTGAGCCAAAAAAGCGGAAGAGGTAATTGCTGTGACACGAGCCATCCGTG
genomic: TTCATATCCAGCATCATCAAATTCTGATTCTAAGgttggttact ... ccaactgcagGTTGAGCCAAAAAAGCGGAAGAGGTAATTGCTGTGACACGAGCCATCCGTG
EST: gi|88508994|gb|CI436500.1|CI436500
EST:     ATTCATATCCAGCATCATCAAATTCTGATTCTAAG                         GTTGAGCCAAAAAAGCGGAAGAGGTAATTGCTGTGACACGAGCCATCCGTG
genomic: ATTCATATCCAGCATCATCAAATTCTGATTCTAAGgttggttact ... ccaactgcagGTTGAGCCAAAAAAGCGGAAGAGGTAATTGCTGTGACACGAGCCATCCGTG
EST: gi|29638118|gb|CB643127.1|CB643127
EST:     CGAAGAGACCTTCAAATTCATATCCAGCATCATCAAATTCTGATTCTAAG                         GTTGAGCCAAAAAAGCGGAAGAGGTAATTGCTGTGACACGAGCCATCCGTG
genomic: CGAAGAGACCTTCAAATTCATATCCAGCATCATCAAATTCTGATTCTAAGgttggttact ... ccaactgcagGTTGAGCCAAAAAAGCGGAAGAGGTAATTGCTGTGACACGAGCCATCCGTG
EST: gi|88259025|gb|CI363318.1|CI363318
EST:     CGAAGAGACCTTCAAATTCATATCCAGCATCATCAAATTCTGATTCTAAG                         GTTGAGCCAAAAAAGCGGAAGAGGTAATTGCTGTGACACGAGCCATCCGTG
genomic: CGAAGAGACCTTCAAATTCATATCCAGCATCATCAAATTCTGATTCTAAGgttggttact ... ccaactgcagGTTGAGCCAAAAAAGCGGAAGAGGTAATTGCTGTGACACGAGCCATCCGTG
EST: gi|88286019|gb|CI515143.1|CI515143
EST:     ATTCTGATTCTAAG                         GTTGAGCCAAAAAAGCGGAAGAGGTAATTGCTGTGACACGAGCCATCCGTG
genomic: ATTCTGATTCTAAGgttggttact ... ccaactgcagGTTGAGCCAAAAAAGCGGAAGAGGTAATTGCTGTGACACGAGCCATCCGTG

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: 75 (upstream exon), 72 (downstream exon)
Score: 78

CAAAAAATTAGATCATTTCCTGTGCGCAGATTGTGTCAAAGAAAATGGCACGAAGAGACCTTCAAATTCATATCCAGCATCATCAAATTCTGATTCTAAGgttggttact ... ccaactgcagGTTGAGCCAAAAAAGCGGAAGAGGTAATTGCTGTGACACGAGCCATCCGTGGTGAGGAGATGCACTGTTTATGGCGTCAGCTCTTCATTGCTGGTGCAAA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAAAAAATTAGATCATTTCCTGTGCGCAGATTGTGTCAAAGAAAATGGCACGAAGAGACCTTCAAATTCATATCCAGCATCATCAAATTCTGATTCTAAGgttggttacttaacctctatctcttgactgactgtctaccgatgttctgtttgaagataacttatctttaattctttaaaactttaagcgcagtagaaat

- - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA