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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtgcatatgcatgctagctttcaatagaattgataacaacctacaagtttcaattgtcattgtgatatagtactaacctattccaagttcatatgcgcagGTGGTTACAGAGTATTCTGATGATGAGCTTGAATTAGTATTAGAAGCCTGTGAAAGGATGAACGCTATCTGACGGCTGCAGTTGTTTCAAACGACCCTTT

Basic information

species Oryza sativa
transcript LOC_Os05g45960.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g45960.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G090087_T03 (Zea mays), 3'ss of exon 12
---gtgcatatgcatgctagctttcaatagaattgataacaacctacaagtttcaattgtcattgtgatatagtactaacctattccaagttcatatgcgcagGTGGTTACAGAGTATTCTGATGATGAGCTTGAATTAGTATTAGAAGCCTGTGAAAGGATGAACGC-TATCTGACGGCTGCAGTTGTTTCAAACGACCCTTT
          |  ||   |  |||| ||    ||||   |  |    |  | |   |  || |  ||||  |  |||  |||||||  | | || |  | ||||| || ||||| || ||||| ||| ||||||| || || ||||||||||| ||||||||||| ||  ||||||| ||||||||||| |||||||||||   
ttgtcaggagttaatcacatgtttctatgttgttgacctcttctattagatctgcttaatcttaatgattaa--actgtcctattctgattccaca-acccagGTAGTCACAGAATACTCTGAGGATCAGCTTGAGTTGGTCTTAGAAGCCTGCGAAAGGATGAATGCGCATCTGACAGCTGCAGTTGTCTCAAACGACCCGC-
















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|86436669|gb|CI118391.1|CI118391
EST:     GAGCTTGTGACAAGGGAGATCTTTGGTCCTTTCCAG                         GTGGTTACAGAGTATTCTGATGATGAGCTTGAATTAGTATTAGAAGCCTGT
genomic: GAGCTTGTGACAAGGGAGATCTTTGGTCCTTTCCAGgtaagagatt ... atatgcgcagGTGGTTACAGAGTATTCTGATGATGAGCTTGAATTAGTATTAGAAGCCTGT
EST: gi|44673853|gb|CR287287.1|CR287287
EST:     AAAGTGGCAATTTTGAGCTTGTGACAAGGGAGATCTTTGGTCCTTTCCAG                         GTGGTTACAGAGTATTCTGATGATGAGCTTGAATTAGTATTAGAAGCCTGT
genomic: AAAGTGGCAATTTTGAGCTTGTGACAAGGGAGATCTTTGGTCCTTTCCAGgtaagagatt ... atatgcgcagGTGGTTACAGAGTATTCTGATGATGAGCTTGAATTAGTATTAGAAGCCTGT
EST: gi|88848173|gb|CI086695.1|CI086695
EST:     AGTGGCAATTTTGAGCTTGTGACAAGGGAGATCTTTGGTCCTTTCCAG                         GTGGTTACAGAGTATTCTGATGATGAGCTTGAATTAGTATTAGAAGCCTGT
genomic: AGTGGCAATTTTGAGCTTGTGACAAGGGAGATCTTTGGTCCTTTCCAGgtaagagatt ... atatgcgcagGTGGTTACAGAGTATTCTGATGATGAGCTTGAATTAGTATTAGAAGCCTGT
EST: gi|9865361|gb|AU101111.1|AU101111
EST:     AAAGTGGCAATTTTGAGCTTGTGACAAGGGAGATCTTTGGTCCTTTCCAG                         GTGGTTACAGAGTATTCTGATGATGAGCTTGAATTAGTATTAGAAGCCTGT
genomic: AAAGTGGCAATTTTGAGCTTGTGACAAGGGAGATCTTTGGTCCTTTCCAGgtaagagatt ... atatgcgcagGTGGTTACAGAGTATTCTGATGATGAGCTTGAATTAGTATTAGAAGCCTGT
EST: gi|88962017|gb|CI097170.1|CI097170
EST:     AAAGTGGCAATTTTGAGCTTGTGACAAGGGAGATCTTTGGTCCTTTCCAG                         GTGGTTACAGAGTATTCTGATGATGAGCTTGAATTAGTATTAGAAGCCTGT
genomic: AAAGTGGCAATTTTGAGCTTGTGACAAGGGAGATCTTTGGTCCTTTCCAGgtaagagatt ... atatgcgcagGTGGTTACAGAGTATTCTGATGATGAGCTTGAATTAGTATTAGAAGCCTGT
EST: gi|89180443|gb|CI044722.1|CI044722
EST:     AAAGTGGCAATTTTGAGCTTGTGACAAGGGAGATCTTTGGTCCTTTCCAG                         GTGGTTACAGAGTATTCTGATGATGAGCTTGAATTAGTATTAGAAGCCTGT
genomic: AAAGTGGCAATTTTGAGCTTGTGACAAGGGAGATCTTTGGTCCTTTCCAGgtaagagatt ... atatgcgcagGTGGTTACAGAGTATTCTGATGATGAGCTTGAATTAGTATTAGAAGCCTGT
EST: gi|88907945|gb|CI090541.1|CI090541
EST:     AAAGTGGCAATTTTGAGCTTGTGACAAGGGAGATCTTTGGTCCTTTCCAG                         GTGGTTACAGAGTATTCTGATGATGAGCTTGAATTAGTATTAGAAGCCTGT
genomic: AAAGTGGCAATTTTGAGCTTGTGACAAGGGAGATCTTTGGTCCTTTCCAGgtaagagatt ... atatgcgcagGTGGTTACAGAGTATTCTGATGATGAGCTTGAATTAGTATTAGAAGCCTGT
EST: gi|29632954|gb|CB637963.1|CB637963
EST:     AAAGTGGCAATTTTGAGCTTGTGACAAGGGAGATCTTTGGTCCTTTCCAG                         GTGGTTACAGAGTATTTTGATGATGAGCTTGAATTAGTATTAGAAGCCTGT
genomic: AAAGTGGCAATTTTGAGCTTGTGACAAGGGAGATCTTTGGTCCTTTCCAGgtaagagatt ... atatgcgcagGTGGTTACAGAGTATTCTGATGATGAGCTTGAATTAGTATTAGAAGCCTGT
EST: gi|86851512|gb|CI314095.1|CI314095
EST:     AAAGTGCCAATTTTGAGCTT-TGACAAGGGAGATCTTTGGTCCTTTCCAG                         GTGGTTACAGAGTATTCTGATTATGAGCTTGAATTAGTATTAGAAGCCTAT
genomic: AAAGTGGCAATTTTGAGCTTGTGACAAGGGAGATCTTTGGTCCTTTCCAGgtaagagatt ... atatgcgcagGTGGTTACAGAGTATTCTGATGATGAGCTTGAATTAGTATTAGAAGCCTGT
EST: gi|58656949|gb|CK045629.1|CK045629
EST:     TTGAGCTTGTGACAAGGGAGATCTTTGGTCCTTTCCAG                         GTGGTTACAGAGTATTCTGATGATGAGCTTGAATTAGTATTAGAAGCCTGT
genomic: TTGAGCTTGTGACAAGGGAGATCTTTGGTCCTTTCCAGgtaagagatt ... atatgcgcagGTGGTTACAGAGTATTCTGATGATGAGCTTGAATTAGTATTAGAAGCCTGT
EST: gi|29617924|gb|CB622936.1|CB622936
EST:     AAAGTGGCAATTTTGAGCTTGTGACAAGGGAGATCTTTGGTCCTTTCCAG                         GTGGTTACAGAGTATTCTGATGATGAGCTTGAATTAGTATTAGAAGCCTGT
genomic: AAAGTGGCAATTTTGAGCTTGTGACAAGGGAGATCTTTGGTCCTTTCCAGgtaagagatt ... atatgcgcagGTGGTTACAGAGTATTCTGATGATGAGCTTGAATTAGTATTAGAAGCCTGT
EST: gi|88968032|gb|CI098274.1|CI098274
EST:     AAAGTGGCAATTTTGAGCTTGTGACAAGGGAGATCTTTGGTCCTTTCCAG                         GTGGTTACAGAGTATTCTGATGATGAGCTTGAATTAGTATTAGAAGCCTGT
genomic: AAAGTGGCAATTTTGAGCTTGTGACAAGGGAGATCTTTGGTCCTTTCCAGgtaagagatt ... atatgcgcagGTGGTTACAGAGTATTCTGATGATGAGCTTGAATTAGTATTAGAAGCCTGT
EST: gi|218484591|gb|FG954366.1|FG954366
EST:     AAAGTGGCAATTTTGAGCTTGTGACAAGGGAGATCTTTGGTCCTTTCCAG                         GTGGTTACAGAGTATTCTGATGATGAGCTTGAATTAGTATTAGAAGCCTGT
genomic: AAAGTGGCAATTTTGAGCTTGTGACAAGGGAGATCTTTGGTCCTTTCCAGgtaagagatt ... atatgcgcagGTGGTTACAGAGTATTCTGATGATGAGCTTGAATTAGTATTAGAAGCCTGT
EST: gi|88908314|gb|CI090907.1|CI090907
EST:     AAAGTGGCAATTTTGAGCTTGTGACAAGGGAGATCTTTGGTCCTTTCCAG                         GTGGTTACAGAGTATTCTGATGATGAGCTTGAATTAGTATTAGAAGCCTGT
genomic: AAAGTGGCAATTTTGAGCTTGTGACAAGGGAGATCTTTGGTCCTTTCCAGgtaagagatt ... atatgcgcagGTGGTTACAGAGTATTCTGATGATGAGCTTGAATTAGTATTAGAAGCCTGT
EST: gi|88976781|gb|CI257525.1|CI257525
EST:     AAAGTGGCAATTTTGAGCTTGTGACAAGGGAGATCTTTGGTCCTTTCCAG                         GTGGTTACAGAGTATTCTGATGATGAGCTTGAATTAGTATTAGAAGCCTGT
genomic: AAAGTGGCAATTTTGAGCTTGTGACAAGGGAGATCTTTGGTCCTTTCCAGgtaagagatt ... atatgcgcagGTGGTTACAGAGTATTCTGATGATGAGCTTGAATTAGTATTAGAAGCCTGT
EST: gi|86493002|gb|CI135635.1|CI135635
EST:     AAAGTGGCAATTTTGAGCTTGTGACAAGGGAGATCTTTGGTCCTTTCCAG                         GTGGTTACAGAGTATTCTGATGATGAGCTTGAATTAGTATTAGAAGCCTGT
genomic: AAAGTGGCAATTTTGAGCTTGTGACAAGGGAGATCTTTGGTCCTTTCCAGgtaagagatt ... atatgcgcagGTGGTTACAGAGTATTCTGATGATGAGCTTGAATTAGTATTAGAAGCCTGT

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: 65 (upstream exon), 62 (downstream exon)
Score: 23

TGGTGCCTTCAAACCAACTGCTGTATTTGTTCCTCTATCGGAAATCCTTAAAAGTGGCAATTTTGAGCTTGTGACAAGGGAGATCTTTGGTCCTTTCCAGgtaagagatt ... atatgcgcagGTGGTTACAGAGTATTCTGATGATGAGCTTGAATTAGTATTAGAAGCCTGTGAAAGGATGAACGCTATCTGACGGCTGCAGTTGTTTCAAACGACCCTTT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtttcaattgtcattgtgatatagtactaacctattccaagttcatatgcgcagGTGGTTACAGAGTATTCTGATGATGAGCTTGAATTAGTATTAGAAGCCTGTGAAAGGATGAACGCTATCTGACGGCTGCAGTTGTTTCAAACGACCCTTT
                         tactaac  putative branch site (score: 23)
                   atatagta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcatatgcatgctagctttcaatagaattgataacaacctacaagtttcaattgtcattgtgatatagtactaacctattccaagttcatatgcgcagGTGGTTACAGAGTATTCTGATGATGAGCTTGAATTAGTATTAGAAGCCTGTGAAAGGATGAACGCTATCTGACGGCTGCAGTTGTTTCAAACGACCCTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
gtgcata
- - - -tgcatgc
- - - - - - - - gctttca
- - - - - - - - - - - - - - - - - aacaacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgtgat