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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAGAAAAAAGGGAGAAAAAACGGGAGTTACCCCATATTTTTTGCTGAACCTATGCGAGCATCCAATTCATTTGTTGGCACGGAGGAGTACATTGCGCCTgtacgtgcatatggtcttctaacttacctgttctatactgtttggcaagcttttattcattcccaatatttcatctttggtactgagtctgtgcatccttgtctgtttgcag

Basic information

species Oryza sativa
transcript LOC_Os12g01140.1
intron # 19
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g01140.1 (Oryza sativa), 5'ss of exon 19
lower sequence: GRMZM2G001457_T02 (Zea mays), 5'ss of exon 18
TGAGAAAAAAGGGAGAAAAAACGGGAGTTACCCCATATTTTTTGCTGAACCTATGCGAGCATCCAATTCATTTGTTGGCACGGAGGAGTACATTGCGCCTgtacgtgcatatg--------gtcttctaactt-acctgttctatactgtttggc---aagcttttattcattcccaatattt--catctttggtactga--gtctgtgc-----atccttgt-ctgtttgcag-------
  |||||||  |||| || | | ||||| | |||||||||||||||||||| ||||||||||| ||||| |||||||| || |||||||||||||| || |||  |  ||||          | || |  ||  || |  |||||    |||  |   |   ||| |||  ||  |  |||||  ||| | || || | |   |||||       ||||||||  ||| ||||        
GAAGAAAAAGAGGAGGAAGAGCAGGAGTAATCCCATATTTTTTGCTGAACCAATGCGAGCATCAAATTCTTTTGTTGGTACAGAGGAGTACATTGCACCGgtatttatatatatatgtaatatgttgttgctccactttatctatgtgattttccctaacattttcatttcttgtctctatttgacatgtgtgatagtcatcatctgttttatcaatccttgtattgtatgcatgctgtag

upper sequence: LOC_Os11g01140.1 (Oryza sativa), 5'ss of exon 19
lower sequence: GLYMA15G04850.1 (Glycine max), 5'ss of exon 19
-TGAGAAAAAAGGGAGAAAAAACGGGAGTTACCCCATATTTTTTGCTGAACCTATGCGAGCATCCAATTCATTTGTTGGCACGGAGGAGTACATTGCGCCTgtacgtgcatatggtcttctaacttacctgttctatactgtttggcaagcttttattcattcccaatatttcatctttggtactgagtctgtgcatccttgt-ctgtttgcag
   | | || |   ||||||  |  ||| |  || || ||| | || |||||  || ||||||| ||||| |||||||||||||| ||||||||||| || ||  ||     |  ||     || ||| | | |  || | ||  |||       |   |    || |     ||   |||| |  | |  ||   |  ||||  ||  || | 
GAAAAAGAAGAAACAGAAAAGTCAAGAGGT-TCCAATGTTTATGGCAGAACCAGTGAGAGCATCAAATTCTTTTGTTGGCACGGAAGAGTACATTGCTCCGgtttgt-----tattccctggacatac-tatacattattattgagcag-----caaaaaactacagttcaatatgcatggttc-aaatacgtattttattgtgttgaatgta-

upper sequence: LOC_Os11g01140.1 (Oryza sativa), 5'ss of exon 19
lower sequence: GLYMA13G40550.1 (Glycine max), 5'ss of exon 18
-TGAGAAAAAAGGGAGAAAAAACGGGAGTTACCCCATATTTTTTGCTGAACCTATGCGAGCATCCAATTCATTTGTTGGCACGGAGGAGTACATTGCGCCTgtacgtgcatatggtcttctaacttacctgttctatactgtttggcaagcttttattcattcccaatatttcatctttggtactgagtctgtgcatccttgtctgtttgcag
   | | || |   ||||||  |  ||| |  || || ||| | || ||||| ||| ||||||| ||||| |||||||||||||| ||||||||||| || ||  ||   |||    | ||        | | |  || | ||  |||        | |  | | ||||  |  | | | ||| ||| | |    ||  || |          
GAAAAAGAAGAAACAGAAAAGTCAAGAGGT-TCCAATGTTTATGGCAGAACCAATGAGAGCATCAAATTCTTTTGTTGGCACGGAAGAGTACATTGCTCCGgtttgt---tat----tcctggacatattatacattattattgagcagcaaaaactacggttcaaatacgtattttattgtattgaatgtaccaattattatacaca-----

upper sequence: LOC_Os11g01140.1 (Oryza sativa), 5'ss of exon 19
lower sequence: AT3G45780.1 (Arabidopsis thaliana), 5'ss of exon 18
TGAGAAAAAAGGGAGAAAAAACGGGAGTTACCCCA-TATTTTTTGCTGAACCTATGCGAGCATCCAATTCATTTGTTGGCACGGAGGAGTACATTGCGCCTgtacgtgcatatggtcttctaacttacctgttctatactgtttggcaagcttttattcattcccaatatttcatctttggtactgagtctgtgcatccttgtctgtttgcag
 ||  ||||||  | |||| |    |   || ||| | ||  | |||||||| ||||| ||||| || |||||||||||||| || ||||||||||| || ||  ||  ||    | | | || |||  |    |        |    | | ||   | |   ||| || || || | |  ||  ||                          
-GAAGAAAAAGCAACAAAAGAGTCAACAAACTCCAATCTTCATGGCTGAACCAATGCGTGCATCAAACTCATTTGTTGGCACTGAAGAGTACATTGCTCCGgttagtatattatatataccaatttaagtacagtgattaaggtatttaccattgtcttaa--ccagtagttgatgtctcatatggatag-----------------------

upper sequence: LOC_Os11g01140.1 (Oryza sativa), 5'ss of exon 19
lower sequence: Vv06s0004g03700.t01 (Vitis vinifera), 5'ss of exon 19
TGAGAAAAAAGGGAGAAAAAACGGGAGTT--ACCCCATATTTTTTGCTGAACCTATGCGAGCATCCAATTCATTTGTTGGCACGGAGGAGTACATTGCGCCTgtacgtgcatatggtcttctaacttacctgttctatactgtttggcaagcttttattcattcccaatatttcatctttggtactgagtctgtgcatccttgtctgtttgcag
  | | |||||| |  | ||| |  |     |||| |||||  | |||||||||||||||||||| |||||||| ||||| || || |||||||| || || ||  |||||       ||  ||| | |  | | |||  | |||   | |     | |  |||    | | |  |  | | | |||  |||||  |  ||||  |     || 
--AAAGAAAAGGCAACATAAAGGTCAACAGAACCCAATATTCATGGCTGAACCTATGCGAGCATCAAATTCATTCGTTGGTACTGAAGAGTACATAGCTCCGgtttgtgcac-----ttttaaacctgc--gctttattttattttttatgaaaagaat--ttctgggtctatagttgtggatgctgcctctgttta--cttgagtacagaca-

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|29644412|gb|CB649419.1|CB649419
EST:     CTATGCGAGCATCCAATTCATTTGTTGGCACGGAGGAGTACATTGCGCCT                         GAGATTATTACAGGAGCTGGCCATACAAGCGCTGTTGATTGGTGGGCTCTA
genomic: CTATGCGAGCATCCAATTCATTTGTTGGCACGGAGGAGTACATTGCGCCTgtacgtgcat ... ctgtttgcagGAGATTATTACAGGAGCTGGCCATACAAGCGCTGTTGATTGGTGGGCTCTA
EST: gi|25806002|gb|CA761963.1|CA761963
EST:     CTATGCGAGCATCCAATTCATTTGTGGGCACGGAGGAGTACATTGCGCCT                         GAGATTATTACAGGAGCTGGCCATACAAGCGCTGTTGATTGGTGGGCTCTA
genomic: CTATGCGAGCATCCAATTCATTTGTTGGCACGGAGGAGTACATTGCGCCTgtacgtgcat ... ctgtttgcagGAGATTATTACAGGAGCTGGCCATACAAGCGCTGTTGATTGGTGGGCTCTA
EST: gi|66913937|gb|CX100785.1|CX100785
EST:     CTATGCGAGCATCCAATTCATTTGTTGGCACGGAGGAGTACATTGCGCCT                         GAGATTATTACAGGAGCTGGCAATACAAGCGCTGTTGACTGGTGGGCTCTA
genomic: CTATGCGAGCATCCAATTCATTTGTTGGCACGGAGGAGTACATTGCGCCTgtacgtgcat ... ctgtttgcagGAGATTATTACAGGAGCTGGCCATACAAGCGCTGTTGATTGGTGGGCTCTA
EST: gi|29621738|gb|CB626749.1|CB626749
EST:     GCATCCAATTCATTTGTTGGCACGGAGGAGTACATTGCGCCT                         GAGATTATTACAGGAGCTGGCCATACAAGCGCTGTTGATTGGTGGGCTCTA
genomic: GCATCCAATTCATTTGTTGGCACGGAGGAGTACATTGCGCCTgtacgtgcat ... ctgtttgcagGAGATTATTACAGGAGCTGGCCATACAAGCGCTGTTGATTGGTGGGCTCTA
EST: gi|29623925|gb|CB628936.1|CB628936
EST:     CTATGCGAGCATCCAATTCATTTGTTGGCACGGAGGAGTACATTGCGCCT                         GAGATTATTACAGGAGCTGGCCATACAAGCGCTGTTGATTGGTGGGCTCTA
genomic: CTATGCGAGCATCCAATTCATTTGTTGGCACGGAGGAGTACATTGCGCCTgtacgtgcat ... ctgtttgcagGAGATTATTACAGGAGCTGGCCATACAAGCGCTGTTGATTGGTGGGCTCTA
EST: gi|29630467|gb|CB635476.1|CB635476
EST:     CTATGCGAGCATCCAATTCATTTGTTGGCACGGAGGAGTACATTGCGCCT                         GAGATTATTACAGGAGCTGGCCATACAAGCGCTGTTGATTGGTGGGCTCTA
genomic: CTATGCGAGCATCCAATTCATTTGTTGGCACGGAGGAGTACATTGCGCCTgtacgtgcat ... ctgtttgcagGAGATTATTACAGGAGCTGGCCATACAAGCGCTGTTGATTGGTGGGCTCTA
EST: gi|29641401|gb|CB646408.1|CB646408
EST:     CATCCAATTCATTTGTTGGCACGGAGGAGTACATTGCGCCT                         GAGATTATTACAGGAGCTGGCCATACAAGCGCTGTTGATTGGTGGGCTCTA
genomic: CATCCAATTCATTTGTTGGCACGGAGGAGTACATTGCGCCTgtacgtgcat ... ctgtttgcagGAGATTATTACAGGAGCTGGCCATACAAGCGCTGTTGATTGGTGGGCTCTA
EST: gi|29663823|gb|CB660098.1|CB660098
EST:     CATCCAATTCATTTGTTGGCACGGAGGAGTACATTGCGCCT                         GAGATTATTACAGGAGCTGGCCATACAAGCGCTGTTGATTGGTGGGCTCTA
genomic: CATCCAATTCATTTGTTGGCACGGAGGAGTACATTGCGCCTgtacgtgcat ... ctgtttgcagGAGATTATTACAGGAGCTGGCCATACAAGCGCTGTTGATTGGTGGGCTCTA
EST: gi|29678745|gb|CB675020.1|CB675020
EST:     CTATGCGAGCATCCAATTCATTTGTTGGCACGGAGGAGTACATTGCGCCT                         GAGATTATTACAGGAGCTGGCCATACAAGCGCTGTTGATTGGTGGGCTCTA
genomic: CTATGCGAGCATCCAATTCATTTGTTGGCACGGAGGAGTACATTGCGCCTgtacgtgcat ... ctgtttgcagGAGATTATTACAGGAGCTGGCCATACAAGCGCTGTTGATTGGTGGGCTCTA
EST: gi|29622723|gb|CB627734.1|CB627734
EST:     CTATGCGAGCATCCAATTCATTTGTTGGCACGGAGGAGTACATTGCGCCT                         GAGATTATTACAGGAGCTGGCCATAC
genomic: CTATGCGAGCATCCAATTCATTTGTTGGCACGGAGGAGTACATTGCGCCTgtacgtgcat ... ctgtttgcagGAGATTATTACAGGAGCTGGCCATAC
EST: gi|88299110|gb|CI570080.1|CI570080
EST:     CTATGCGAGCATCCAATTCATTTGTTGGCACGGAGGAGTACATTGCGCCT                         GAGATTATTACAGGAGCTGGCCATACAAGCGCTGTTGATTGGTGGGCTCTA
genomic: CTATGCGAGCATCCAATTCATTTGTTGGCACGGAGGAGTACATTGCGCCTgtacgtgcat ... ctgtttgcagGAGATTATTACAGGAGCTGGCCATACAAGCGCTGTTGATTGGTGGGCTCTA
EST: gi|29630120|gb|CB635129.1|CB635129
EST:     CTATGCGAGCATCCAATTCATTTGTTGGCACGGAGGAGTACATTGCGCCT                         GAGATTATTACAGGAGCTGGCCATACAAGCGCTGTTGATTGGTGGGCTCTA
genomic: CTATGCGAGCATCCAATTCATTTGTTGGCACGGAGGAGTACATTGCGCCTgtacgtgcat ... ctgtttgcagGAGATTATTACAGGAGCTGGCCATACAAGCGCTGTTGATTGGTGGGCTCTA
EST: gi|29634078|gb|CB639087.1|CB639087
EST:     AGCATCCAATTCATTTGTTGGCACGGAGGAGTACATTGCGCTT                         GAGATTATTACAGGAGCTGGCCATACAAGCGCTGTTGATTGGTGGGCTCTA
genomic: AGCATCCAATTCATTTGTTGGCACGGAGGAGTACATTGCGCCTgtacgtgcat ... ctgtttgcagGAGATTATTACAGGAGCTGGCCATACAAGCGCTGTTGATTGGTGGGCTCTA
EST: gi|29672021|gb|CB668296.1|CB668296
EST:     GCATCCAATTCATTTGTTGGCACGGAGGAGTACATTGCGCCT                         GAGATTATTACAGGAGCTGGCCATACAAGCGCTGTTGATTGGTGGGCTCTA
genomic: GCATCCAATTCATTTGTTGGCACGGAGGAGTACATTGCGCCTgtacgtgcat ... ctgtttgcagGAGATTATTACAGGAGCTGGCCATACAAGCGCTGTTGATTGGTGGGCTCTA
EST: gi|58695041|gb|CK083728.1|CK083728
EST:     CTATGCGAGCATCCAATTCATTTGTTGGCACGGAGGAGTACATTGCGCCT                         GAGATTATTACAGGAGCTGGCCATACAAGCGCTGTTGATTGGTGGGCTCTA
genomic: CTATGCGAGCATCCAATTCATTTGTTGGCACGGAGGAGTACATTGCGCCTgtacgtgcat ... ctgtttgcagGAGATTATTACAGGAGCTGGCCATACAAGCGCTGTTGATTGGTGGGCTCTA
EST: gi|29623926|gb|CB628937.1|CB628937
EST:     CTATGCGAGCATCCAATTCATTTGTTGGCACGGAGGAGTACATTGCGCCT                         GAGATTATTACAGGAGCTGGCCATACAAGCGCTGTTGATTGGTGGGCTCTA
genomic: CTATGCGAGCATCCAATTCATTTGTTGGCACGGAGGAGTACATTGCGCCTgtacgtgcat ... ctgtttgcagGAGATTATTACAGGAGCTGGCCATACAAGCGCTGTTGATTGGTGGGCTCTA
EST: gi|29624138|gb|CB629149.1|CB629149
EST:     CTATGCGAGCATCCAATTCATTTGTTGGCACGGAGGAGTACATTGCGCCT                         GAGATTATTACAGGAGCTGGCCATACAAGCGCTGTTGATTGGTGGGCTCTA
genomic: CTATGCGAGCATCCAATTCATTTGTTGGCACGGAGGAGTACATTGCGCCTgtacgtgcat ... ctgtttgcagGAGATTATTACAGGAGCTGGCCATACAAGCGCTGTTGATTGGTGGGCTCTA
EST: gi|29646711|gb|CB651718.1|CB651718
EST:     CTATGCGAGCATCCAATTCATTTGTTGGCACGGAGGAGTACATTGCGCCT                         GAGATTATTACAGGAGCTGGCCATACAAGCGCTGTTGATTGGTGGGCTCTA
genomic: CTATGCGAGCATCCAATTCATTTGTTGGCACGGAGGAGTACATTGCGCCTgtacgtgcat ... ctgtttgcagGAGATTATTACAGGAGCTGGCCATACAAGCGCTGTTGATTGGTGGGCTCTA
EST: gi|33680724|gb|CF308963.1|CF308963
EST:     CTATGCGAGCATCCAATTCATTTGTTGGCACGGAGGAGTACATTGCGCCT                         GAGATTATTACAGGAGCTGGCCATACAAGCGCTGTTGATTGGTGGGCTCTA
genomic: CTATGCGAGCATCCAATTCATTTGTTGGCACGGAGGAGTACATTGCGCCTgtacgtgcat ... ctgtttgcagGAGATTATTACAGGAGCTGGCCATACAAGCGCTGTTGATTGGTGGGCTCTA
EST: gi|29622724|gb|CB627735.1|CB627735
EST:     CTATGCGAGCATCCAATTCATTTGTTGGCACGGAGGAGTACATTGCGCCT                         GAGATTATTACAGGAGCTGGCCATACAAGCGCTGTTGATTGGTGGGCTCTA
genomic: CTATGCGAGCATCCAATTCATTTGTTGGCACGGAGGAGTACATTGCGCCTgtacgtgcat ... ctgtttgcagGAGATTATTACAGGAGCTGGCCATACAAGCGCTGTTGATTGGTGGGCTCTA
EST: gi|29674379|gb|CB670654.1|CB670654
EST:     NTATGCGAGCATCCAATTCATTTGTTGGCACGGAGGAGTACATTGCGCCT                         GAGATTATTACAGGAGCTGGCCATACAAGCGCTGTTGATTGGTGGGCTCTA
genomic: CTATGCGAGCATCCAATTCATTTGTTGGCACGGAGGAGTACATTGCGCCTgtacgtgcat ... ctgtttgcagGAGATTATTACAGGAGCTGGCCATACAAGCGCTGTTGATTGGTGGGCTCTA
EST: gi|29677072|gb|CB673347.1|CB673347
EST:     CTATGCGAGCATCCAATTCATTTGTTGGCACGGAGGAGTACATTGCGCCT                         GAGATTATTACAGGAGCTGGCCATACAAGCGCTGTTGATTGGTGGGCTCTA
genomic: CTATGCGAGCATCCAATTCATTTGTTGGCACGGAGGAGTACATTGCGCCTgtacgtgcat ... ctgtttgcagGAGATTATTACAGGAGCTGGCCATACAAGCGCTGTTGATTGGTGGGCTCTA

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), 52 (downstream exon)
Score: 28

TGAGAAAAAAGGGAGAAAAAACGGGAGTTACCCCATATTTTTTGCTGAACCTATGCGAGCATCCAATTCATTTGTTGGCACGGAGGAGTACATTGCGCCTgtacgtgcat ... ctgtttgcagGAGATTATTACAGGAGCTGGCCATACAAGCGCTGTTGATTGGTGGGCTCTAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGAGAAAAAAGGGAGAAAAAACGGGAGTTACCCCATATTTTTTGCTGAACCTATGCGAGCATCCAATTCATTTGTTGGCACGGAGGAGTACATTGCGCCTgtacgtgcatatggtcttctaacttacctgttctatactgtttggcaagcttttattcattcccaatatttcatctttggtactgagtctgtgcatccttgtctgtttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG