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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttagtacacggttgatttaaattattgtggtaatgcacttttacaacactctagaaaaggattcttgttgatattttttttaattatatattgcgctcagATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATTATCAATGAGGAGTTTGGTGATGGAAT

Basic information

species Oryza sativa
transcript LOC_Os10g33270.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g33270.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G134747_T02 (Zea mays), 3'ss of exon 1
---ttagtacacggttgatttaaattattgtggta-atgcacttttacaacactctagaaaaggattcttgttgatattttttttaattatatattgcgctcagATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATTATCAATGAGGAGTTTGGTGATGGAAT----------------------------
   ||  | ||  | |   |||  |||||   ||  ||   |  | |||| |   ||||| |   || ||||  | ||| ||    | ||||| |||| | |||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||                            
gcttttatccagagctttgttagtttatttcagtttatcagcactaacaagatattagaataacctttttgtcaacattgtt----actatatgttgctcacagATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATCATCAATGAGGAGTTTGGTGATGGAATGTAAGAGATACCAGTGCTTCATTTATGC

upper sequence: LOC_Os10g33270.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G134747_T01 (Zea mays), 3'ss of exon 1
---ttagtacacggttgatttaaattattgtggta-atgcacttttacaacactctagaaaaggattcttgttgatattttttttaattatatattgcgctcagATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATTATCAATGAGGAGTTTGGTGATGGAAT
   ||  | ||  | |   |||  |||||   ||  ||   |  | |||| |   ||||| |   || ||||  | ||| ||    | ||||| |||| | |||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||
gcttttatccagagctttgttagtttatttcagtttatcagcactaacaagatattagaataacctttttgtcaacattgtt----actatatgttgctcacagATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATCATCAATGAGGAGTTTGGTGATGGAAT

upper sequence: LOC_Os10g33270.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA10G00790.1 (Glycine max), 3'ss of exon 1
-ttagtacacggttgatttaaat-tattgtg-gtaatgcacttttacaacactctagaaaaggatt-cttgttgatattttttttaattatatattgcgctcagATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATTATCAATGAGGAGTTTGGTGATGGAAT
 | || |  |   || |  |||| | |   | ||||||||  |  ||  |  | || | |    |   ||||||    || |  | ||  | |||| |    || |||||||||||||||||||||||||| ||||||||||| ||||| ||||||||||||||||||||||| ||
ttgaggattctaatgttggaaatatgtcaagtgtaatgcatatcaacttccttttatatatatttaatttgttggg--ttatgctgatcttctatttcat--agGTTGAATGAAGCTGTTATGCATTTTGGGGAGAGCATCAAAGAAATAATCAATGAGGAGTTTGGTGATGGGAT

upper sequence: LOC_Os10g33270.1 (Oryza sativa), 3'ss of exon 1
lower sequence: AT3G23490.1 (Arabidopsis thaliana), 3'ss of exon 1
ttagtacacggttgatttaaattattgtggtaatgcacttttacaacactctagaaaaggattcttgttgatattttttttaattatatattgcgctcagATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATTATCAATGAGGAGTTTGGTGATGGAAT
                     ||  | ||| ||      ||||||    | |      || ||  | ||||| | |       ||  || |||   | || ||||||||||| || ||||||||||| ||||| || ||||| ||||||||||| || ||||| ||||| ||
-------------------gtttgctctggaaag-----tttaca----tttttgggtggcttagttttgatgtct----gggtttgattttg-atttagGTTGAATGAAGCAGTGATGCATTTTGGTGAGAGTATAAAGGAGATTATCAATGAAGATTTTGGAGATGGCAT

upper sequence: LOC_Os10g33270.1 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv05s0049g01520.t01 (Vitis vinifera), 3'ss of exon 1
ttagtacacggttgatttaaattattgtggtaatgcacttttacaacactctagaaaaggattcttgttgatatttttt--ttaattatatattgcgctc---agATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATTATCAATGAGGAGTTTGGTGATGGAAT
  || |     |||  | |  | | |  |||  ||||     | |  | |||   ||    ||||   ||   | |||   ||   |   | |    ||    |||||||||||||| || ||||||||||| ||||||||||||||||||||||||||||||||||| ||||| ||
-cagaagcaatttg--tcatctaagtaaggttttgcataagcatacaaatctctgaatt--ttctgactggcgtgtttccatttgctgactttccaactttgaagATTGAATGAAGCCGTGATGCATTTTGGTGAGAGCATCAAGGAAATTATCAATGAGGAGTTTGGCGATGGCAT

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|87010351|gb|CI281241.1|CI281241
EST:     CCGTTCCGCTCCTACCACCCGGACATCGTCCACGAGCCCGCNATCTACAG                         ATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATTATCAA
genomic: CCGTTCCGCTCCTACCACCCGGACATCGTCCACGAGCCCGCCATCTACAGgtgcctcctc ... ttgcgctcagATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATTATCAA
EST: gi|86535937|gb|CI176143.1|CI176143
EST:     CCGTTCCGCTCCTACCACCCGGACATCGTCCACGAGCCCGCCATCTACAG                         ATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATTATCAA
genomic: CCGTTCCGCTCCTACCACCCGGACATCGTCCACGAGCCCGCCATCTACAGgtgcctcctc ... ttgcgctcagATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATTATCAA
EST: gi|86254024|gb|CI058751.1|CI058751
EST:     CCGTTCCGCTCCTACCACCCGGACATCGTCCACGAGCCCGCCATCTACAG                         ATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATTATCAA
genomic: CCGTTCCGCTCCTACCACCCGGACATCGTCCACGAGCCCGCCATCTACAGgtgcctcctc ... ttgcgctcagATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATTATCAA
EST: gi|25798783|gb|CA754744.1|CA754744
EST:     CCGTTCCGCTCCTACCACCCGGACATCGTCCACGAGCCCGCCATCTACAG                         ATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATTATCAA
genomic: CCGTTCCGCTCCTACCACCCGGACATCGTCCACGAGCCCGCCATCTACAGgtgcctcctc ... ttgcgctcagATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATTATCAA
EST: gi|58693386|gb|CK082073.1|CK082073
EST:     CCGTTCCGCTCCTACCACCCGGACATCGTCCACGAGCCCGCAATCTACAG                         ATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATTATCAA
genomic: CCGTTCCGCTCCTACCACCCGGACATCGTCCACGAGCCCGCCATCTACAGgtgcctcctc ... ttgcgctcagATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATTATCAA
EST: gi|88463661|gb|CI696136.1|CI696136
EST:     CCGTTCCGCTCCTACCACCCGGACATCGTCCACGAGCCCGCCATCTACAG                         ATTGAATGAAGCTGTTATGCATTTGGGAGAGAGCATCAAGGAAATTATCAA
genomic: CCGTTCCGCTCCTACCACCCGGACATCGTCCACGAGCCCGCCATCTACAGgtgcctcctc ... ttgcgctcagATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATTATCAA
EST: gi|88578606|gb|CI687547.1|CI687547
EST:     CCGTTCCGCTCCTACCACCCGGACATCGTCCACGAGCCCGCCATCTACAG                         ATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATTATCAA
genomic: CCGTTCCGCTCCTACCACCCGGACATCGTCCACGAGCCCGCCATCTACAGgtgcctcctc ... ttgcgctcagATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATTATCAA
EST: gi|88514316|gb|CI441822.1|CI441822
EST:     CTCCTACCACCCGGACATCGTCCACGAGCCCGCCATCTACAG                         ATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATTATCAA
genomic: CTCCTACCACCCGGACATCGTCCACGAGCCCGCCATCTACAGgtgcctcctc ... ttgcgctcagATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATTATCAA
EST: gi|88979062|gb|CI025570.1|CI025570
EST:     CCGTTCCGCTCCTACCACCCGGACATCGTCCACGAGCCCGCCATCTACAG                         ATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATTATCAA
genomic: CCGTTCCGCTCCTACCACCCGGACATCGTCCACGAGCCCGCCATCTACAGgtgcctcctc ... ttgcgctcagATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATTATCAA
EST: gi|86418185|gb|CI032394.1|CI032394
EST:     CCGTTCCGCTCCTACCACCCGGACATCGTCCACGAGCCCGCCATCTACAG                         ATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATTATCAA
genomic: CCGTTCCGCTCCTACCACCCGGACATCGTCCACGAGCCCGCCATCTACAGgtgcctcctc ... ttgcgctcagATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATTATCAA
EST: gi|88998125|gb|CI038010.1|CI038010
EST:     CCGGACATCGTCCACGAGCCCGCCATCTACAG                         ATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATTATCAA
genomic: CCGGACATCGTCCACGAGCCCGCCATCTACAGgtgcctcctc ... ttgcgctcagATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATTATCAA
EST: gi|86855243|gb|CI265169.1|CI265169
EST:     CCGTTCCGCTCCTACCACCCGGACATCGTCCACGAGCCCGCCATCTACAG                         ATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATTATCAA
genomic: CCGTTCCGCTCCTACCACCCGGACATCGTCCACGAGCCCGCCATCTACAGgtgcctcctc ... ttgcgctcagATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATTATCAA
EST: gi|86533060|gb|CI173266.1|CI173266
EST:     CCGCCATCTACAG                         ATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATTATCAA
genomic: CCGCCATCTACAGgtgcctcctc ... ttgcgctcagATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATTATCAA

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: 53 (upstream exon), 72 (downstream exon)
Score: 53

CGGCCGTGCCGGGGCTCACCGACGACCTCGTCGCGCTCATGATGGAGCCGCCGTTCCGCTCCTACCACCCGGACATCGTCCACGAGCCCGCCATCTACAGgtgcctcctc ... ttgcgctcagATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATTATCAATGAGGAGTTTGGTGATGGAAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acactctagaaaaggattcttgttgatattttttttaattatatattgcgctcagATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATTATCAATGAGGAGTTTGGTGATGGAAT
                                ttttaat  putative branch site (score: 53)
         aaaaggattcttgttg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttagtacacggttgatttaaattattgtggtaatgcacttttacaacactctagaaaaggattcttgttgatattttttttaattatatattgcgctcagATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATTATCAATGAGGAGTTTGGTGATGGAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - gttgatt
- - - - - - - - - - - - - - - -aatgcac
- - - - - - - - - - - - - - - - - - - - -tacaaca
- - - - - - - - - - - - - - - - - - - - - - - - - ctagaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttgttg