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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttattctctctctttatcttgggaccttttcttttgtgatggtagctttgttcttgaggctgttttgttatattgtttttccatactcatgattatgtttgcagGTTGTAACTGAGACACTGAATCCAATATGGAATCAGACGTTTGATTTTGTTGTTGAAGATGCCTTGCATGATTTACTCATGGTGGAAGTATGGGATCATG

Basic information

species Oryza sativa
transcript LOC_Os08g20544.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g20544.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G049347_T01 (Zea mays), 3'ss of exon 11
gttattctctctctttatcttgggaccttttcttttgtgatggtagctttgttcttgaggctgttttgttatattgtttttc-catactcatgattatgtttgcagGTTGTAACTGAGACACTGAATCCAATATGGAATCAGACGTTTGATTTTGTTGTTGAAGATGCCTTGCATGATTTACTCATGGTGGAAGTATGGGATCATG
                       |   || |||||    ||   ||  |  |   |  |||  | |  || | |      || |||| |  | | |||  ||||||||||| || || || || |||||||||||||| ||||| ||||||||  | || ||||||||  |||||||||| |||||||||||||||||||| ||||
-----------------------gtttttatctttcccaatctcagagt--tctgtagggccatatacttttttcaaggctctcatagt--tcagtattgttgcagGTTGTGACAGACACGCTAAATCCAATATGGAACCAGACATTTGATTTCATGGTAGAAGATGCACTGCATGATTTGCTCATGGTGGAAGTATGGGACCATG
















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|87025940|gb|CI257098.1|CI257098
EST:     CATTTGTAGTCCTGTACCTGAAGAAGGGAGAAACCAAAAAGAAGACAAGG                         GTTGTAACTGAGACACTGAATCCAATATGGAATCAGACGTTTGATTTTGTT
genomic: CATTTGTAGTCCTGTACCTGAAGAAGGGAGAAACCAAAAAGAAGACAAGGgttattctct ... atgtttgcagGTTGTAACTGAGACACTGAATCCAATATGGAATCAGACGTTTGATTTTGTT
EST: gi|88903570|gb|CI089108.1|CI089108
EST:     CATTTGTAGTCCTGTACCTGAAGAAGGGAGAAACCAAAAAGAAGACAAGG                         GTTGTAACTGAGACACTGAATCCAATATGGAATCAGACGTTTGATTTTGTT
genomic: CATTTGTAGTCCTGTACCTGAAGAAGGGAGAAACCAAAAAGAAGACAAGGgttattctct ... atgtttgcagGTTGTAACTGAGACACTGAATCCAATATGGAATCAGACGTTTGATTTTGTT
EST: gi|89173078|gb|CI040971.1|CI040971
EST:     CATTTGTAGTCCTGTACCTGAAGAAGGGAGAAACCAAAAAGAAGACAAGG                         GTTGTAACTGAGACACTGAATCCAATATGGAATCAGACGTTTGATTTTGTT
genomic: CATTTGTAGTCCTGTACCTGAAGAAGGGAGAAACCAAAAAGAAGACAAGGgttattctct ... atgtttgcagGTTGTAACTGAGACACTGAATCCAATATGGAATCAGACGTTTGATTTTGTT
EST: gi|88519736|gb|CI447390.1|CI447390
EST:     TGAAGAAGGGAGAAACCAAAAAGAAGACAAGG                         GTTGTAACTGAGACACTGAATCCAATATGGAATCAGACGTTTGATTTTGTT
genomic: TGAAGAAGGGAGAAACCAAAAAGAAGACAAGGgttattctct ... atgtttgcagGTTGTAACTGAGACACTGAATCCAATATGGAATCAGACGTTTGATTTTGTT
EST: gi|88229969|gb|CI229845.1|CI229845
EST:     CATTTGTAGTCCTGTACCTGAAGAAGGGAGAAACCTAAAAGAAGACAAGG                         GTTGTAACTGAGACACTGAATCCAATATGGAATCAGACGTTTGATTTTGTT
genomic: CATTTGTAGTCCTGTACCTGAAGAAGGGAGAAACCAAAAAGAAGACAAGGgttattctct ... atgtttgcagGTTGTAACTGAGACACTGAATCCAATATGGAATCAGACGTTTGATTTTGTT
EST: gi|86435352|gb|CI106585.1|CI106585
EST:     CATTTGTAGTCCTGTACCTGAAGAAGGGAGAAACCTAAAAGAAGACAAGG                         GTTGTAACTGAGACACTGAATCCAATATGGAATCAGACGTTTGATTTTGTT
genomic: CATTTGTAGTCCTGTACCTGAAGAAGGGAGAAACCAAAAAGAAGACAAGGgttattctct ... atgtttgcagGTTGTAACTGAGACACTGAATCCAATATGGAATCAGACGTTTGATTTTGTT
EST: gi|88487066|gb|CI424337.1|CI424337
EST:     AAAAGAAGACAAGG                         GTTGTAACTGAGACACTGAATCCCATATGGAATCAGACGTTTGATTTTGTT
genomic: AAAAGAAGACAAGGgttattctct ... atgtttgcagGTTGTAACTGAGACACTGAATCCAATATGGAATCAGACGTTTGATTTTGTT
EST: gi|58683940|gb|CK072627.1|CK072627
EST:     CATTTGTAGTCCTGTACCTGAAGAAGGGAGAAACCATAAAGAAGACAAGG                         GTTGTAACTGAGACACTGAATCCAATATGGAATCAGACGTTTGATTTTGTT
genomic: CATTTGTAGTCCTGTACCTGAAGAAGGGAGAAACCAAAAAGAAGACAAGGgttattctct ... atgtttgcagGTTGTAACTGAGACACTGAATCCAATATGGAATCAGACGTTTGATTTTGTT
EST: gi|88994440|gb|CI117592.1|CI117592
EST:     CATTTGTAGTCCTGTACCTGAAGAAGGGAGAAACCCAAAAGAAGACAAGG                         GTTGTAACTGAGACACTGAATCCNATATGGAATCAGACGTTTGATTTTGTT
genomic: CATTTGTAGTCCTGTACCTGAAGAAGGGAGAAACCAAAAAGAAGACAAGGgttattctct ... atgtttgcagGTTGTAACTGAGACACTGAATCCAATATGGAATCAGACGTTTGATTTTGTT
EST: gi|86880248|gb|CI320914.1|CI320914
EST:     CA-TTGTAGTCC-GTACCTGAAGAAGGGAGAAACCAAAAAGAAGACAAGG                         GTTGTAACTGAGACACTGAATCCAATATGGAATCAGACGTTTGATTTTGTT
genomic: CATTTGTAGTCCTGTACCTGAAGAAGGGAGAAACCAAAAAGAAGACAAGGgttattctct ... atgtttgcagGTTGTAACTGAGACACTGAATCCAATATGGAATCAGACGTTTGATTTTGTT
EST: gi|58667270|gb|CK055956.1|CK055956
EST:     ATTTGTAGTCCTGTACCTGAAGAAGGGGAGAAACCTAAAAGAAGACAAGG                         GTTGTAACTGAGACACTGAATCCAATATGGAATCAGACGTTTGATTTTGTT
genomic: ATTTGTAGTCCTGTACCTGAAGAA-GGGAGAAACCAAAAAGAAGACAAGGgttattctct ... atgtttgcagGTTGTAACTGAGACACTGAATCCAATATGGAATCAGACGTTTGATTTTGTT
EST: gi|86522202|gb|CI162408.1|CI162408
EST:     CATTTGTAGTCCTGTACCTGAAGAAGGGAGAAACCAAAAAGAAGACAAGG                         GTTGTAACTGAGACACTGAATCCAATATGGAATCAGACGTTTGATTTTGTT
genomic: CATTTGTAGTCCTGTACCTGAAGAAGGGAGAAACCAAAAAGAAGACAAGGgttattctct ... atgtttgcagGTTGTAACTGAGACACTGAATCCAATATGGAATCAGACGTTTGATTTTGTT
EST: gi|86483091|gb|CI125724.1|CI125724
EST:     GAAACCCAAAAGAAGACAAGG                         GTTGTAACTGAGACACTGAATCCAATATGGAATCAGACGTTTGATTTTGTT
genomic: GAAACCAAAAAGAAGACAAGGgttattctct ... atgtttgcagGTTGTAACTGAGACACTGAATCCAATATGGAATCAGACGTTTGATTTTGTT
EST: gi|58689663|gb|CK078350.1|CK078350
EST:     TACCTGAAGAAGGGAGAAACCTTAAAGAAGACAAGG                         GTTGTAACTGAGACACTGAATCCAATATGGAATCAGACGTTTGATTTTGTT
genomic: TACCTGAAGAAGGGAGAAACCAAAAAGAAGACAAGGgttattctct ... atgtttgcagGTTGTAACTGAGACACTGAATCCAATATGGAATCAGACGTTTGATTTTGTT
EST: gi|88905946|gb|CI089532.1|CI089532
EST:     CATTTGTAGTCCTGTACCTGAAGAAGGGAGAAACCAAAAAGAAGACAAGG                         GTTGTAACTGAGACACTGAATCCAATATGGAATCAGACGTTTGATTTTGTT
genomic: CATTTGTAGTCCTGTACCTGAAGAAGGGAGAAACCAAAAAGAAGACAAGGgttattctct ... atgtttgcagGTTGTAACTGAGACACTGAATCCAATATGGAATCAGACGTTTGATTTTGTT
EST: gi|89163077|gb|CI099967.1|CI099967
EST:     CATTTGTAGTCCTGTACCTGAAGAAGGGAGAAACCCAAAAGAAGACAAGG                         GTTGTAACTGAGACACTGAATCCAATATGGAATCAGACGTTTGATTTTGTT
genomic: CATTTGTAGTCCTGTACCTGAAGAAGGGAGAAACCAAAAAGAAGACAAGGgttattctct ... atgtttgcagGTTGTAACTGAGACACTGAATCCAATATGGAATCAGACGTTTGATTTTGTT
EST: gi|88956625|gb|CI092821.1|CI092821
EST:     CATTCGTAGTCCTGTACCTGAAGAAGGGAGAAACCAAAAAGAAGACAAGG                         GTTGTAACTGAGACACTGAATCCAATATGGAATCAGACGTTTGATTTTGTT
genomic: CATTTGTAGTCCTGTACCTGAAGAAGGGAGAAACCAAAAAGAAGACAAGGgttattctct ... atgtttgcagGTTGTAACTGAGACACTGAATCCAATATGGAATCAGACGTTTGATTTTGTT
EST: gi|58679477|gb|CK068164.1|CK068164
EST:     CATTTGTAGTCCTGTACCTGAAGAAGGGAGAAACCAAAAAGAAGACAAGG                         GTTGTAACTGAGACACTGAATCCAATATGGAATCAGACGTTTGATTTTGTT
genomic: CATTTGTAGTCCTGTACCTGAAGAAGGGAGAAACCAAAAAGAAGACAAGGgttattctct ... atgtttgcagGTTGTAACTGAGACACTGAATCCAATATGGAATCAGACGTTTGATTTTGTT

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: 66 (upstream exon), 49 (downstream exon)
Score: 22

TATCTCAGCAGAGGACTTGCCACCAATGGATGTGATGGGCAAGGCTGACCCATTTGTAGTCCTGTACCTGAAGAAGGGAGAAACCAAAAAGAAGACAAGGgttattctct ... atgtttgcagGTTGTAACTGAGACACTGAATCCAATATGGAATCAGACGTTTGATTTTGTTGTTGAAGATGCCTTGCATGATTTACTCATGGTGGAAGTATGGGATCATG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttcttgaggctgttttgttatattgtttttccatactcatgattatgtttgcagGTTGTAACTGAGACACTGAATCCAATATGGAATCAGACGTTTGATTTTGTTGTTGAAGATGCCTTGCATGATTTACTCATGGTGGAAGTATGGGATCATG
             ttttgttatattgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttattctctctctttatcttgggaccttttcttttgtgatggtagctttgttcttgaggctgttttgttatattgtttttccatactcatgattatgtttgcagGTTGTAACTGAGACACTGAATCCAATATGGAATCAGACGTTTGATTTTGTTGTTGAAGATGCCTTGCATGATTTACTCATGGTGGAAGTATGGGATCATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG