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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TATAAGCACTCTAAAGTTTGCTGAAAGGGTTTCTGGAGTTGAGTTAGGTGCTGCAAGAAGTAATAAAGAGGGAAAGGATATAAAAGAGCTGCTGGAACAGgttcttgctttttatgttctgtctgactcatcattaactgaaatttctttgcttttgttttacataattgctgaactatttagttctaggaagaagggga...

Basic information

species Oryza sativa
transcript LOC_Os05g44560.1
intron # 18
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g44560.1 (Oryza sativa), 5'ss of exon 18
lower sequence: GRMZM2G173700_T03 (Zea mays), 5'ss of exon 15
TATAAGCACTCTAAAGTTTGCTGAAAGGGTTTCTGGAGTTGAGTTAGGTGCTGCAAGAAGTAATAAAGAGGGAAAGGATATAAAAGAGCTGCTGGAACAGgttcttgctttttatgttctgtctgactcatcattaactgaaatttctttgcttttg-ttttaca-taatt---gctgaactatttagttctaggaagaagggga----
|||||| ||| ||||||||||||||||||| |||||||| |||||||||||||| |||||||| || |||||||| ||||||||||||||  |||||||||||||||   ||           |||||  ||| |||||  | ||| |||| ||    || |  |  ||||   | || |  |      |   | || ||||| |    
TATAAGTACTTTAAAGTTTGCTGAAAGGGTGTCTGGAGTAGAGTTAGGTGCTGCTAGAAGTAACAAGGAGGGAAAAGATATAAAAGAGCTATTGGAACAGgttcttgtacttc---------ttgacttgtcactaactagagtttatttgtttccaattctgtagcaattttggttggaaaaacagtatactgaaaaaagggcaaact

upper sequence: LOC_Os05g44560.1 (Oryza sativa), 5'ss of exon 18
lower sequence: GRMZM5G845682_T02 (Zea mays), 5'ss of exon 5
TATAAGCACTCTAAAGTTTGCTGAAAGGGTTTCTGGAGTTGAGTTAGGTGCTGCAAGAAGTAATAAAGAGGGAAAGGATATAAAAGAGCTGCTGGAACAGgttcttgctttttatgttctgtctgactcatcattaactgaaatttctttgctttt-gttttacataattg-ctgaactatttagttctaggaagaagggga--------
|||||||||| ||||||||||||||||||| |||||||| |||||||||||||||||||| || || ||||||||||||||||||||||| ||||||||||||||||   |||          |||||  ||| |||||| | ||| |||| || |  || ||  | |||  |||| | ||||   | |   |  ||  | |        
TATAAGCACTTTAAAGTTTGCTGAAAGGGTGTCTGGAGTAGAGTTAGGTGCTGCAAGAAGCAACAAGGAGGGAAAGGATATAAAAGAGCTACTGGAACAGgttcttgtacttt---------ttgactt-tcactaactggagtttgtttgtttctcattctatttgattatctgagcaattttagtttttaataaatagtatgctgaaa

upper sequence: LOC_Os05g44560.1 (Oryza sativa), 5'ss of exon 18
lower sequence: GLYMA07G10190.1 (Glycine max), 5'ss of exon 20
TATAAGCACTCTAAAGTTTGCTGAAAGGGTTTCTGGAGTTGAGTTAGGTGCTGCAAGAAGTAATAAAGAGGGAAAGGATATAAAAGAGCTGCTGGAACAGgttcttgctttttatgttctgtctgactcatcattaactgaaatttctt---tgcttttgttttacataattgctgaactatttagttctaggaagaagggga
| |||| ||| | ||||||| ||  ||||||| ||||||||||||||||||||| | |||||  ||||| || |  ||| | |||||  |  |||| || || |||   ||   |  | ||  |   | |   ||||   | ||||  |   ||| |   | |    || ||| |  | ||| ||  | |             
TTTAAGTACTTTGAAGTTTGTTGGGAGGGTTTTTGGAGTTGAGTTAGGTGCTGCTAAAAGTACCAAAGATGGTAGAGATGTCAAAGAATTAATGGAGCATgtgcttaacttgattaatatggttatgttacttttaataaatattttatgaatgcatcaatgtcttttagttgatctagtatctacctttcttttttttt---

upper sequence: LOC_Os05g44560.1 (Oryza sativa), 5'ss of exon 18
lower sequence: GLYMA05G37800.1 (Glycine max), 5'ss of exon 18
TATAAGCACTCTAAAGTTTGCTGAAAGGGTTTCTGGAGTTGAGTTAGGTGCTGCAAGAAGTAATAAAGAGGGAAAGGATATAAAAGAGCTGCTGGAACAGgttcttgctttttatg------ttctgtctga-----ctcatcattaactgaaatttctttgcttttgttttacataattgctgaactatttagttctaggaagaagggga
| |||||||  | |||||||||||| |||||||||| || |||||||| |||||  | || || |||||||| | |||| | | ||| ||  |||| |||||| || || ||| ||      || |   ||       |  | || | | |||    |     || ||  ||  |   ||  | |   |||| ||| |             
TGTAAGCACCTTGAAGTTTGCTGAACGGGTTTCTGGCGTGGAGTTAGGCGCTGCTCGTAGCAACAAAGAGGGGAGGGATGTGAGAGAACTTATGGAGCAGgttatttctatttttgaatgcattttacttggatgttttagttatcagc-gaagcaccaaatgttatgaattggaattttagttattcattttgtttttta----------

upper sequence: LOC_Os05g44560.1 (Oryza sativa), 5'ss of exon 18
lower sequence: GLYMA05G35130.1 (Glycine max), 5'ss of exon 16
TATAAGCACTCTAAAGTTTGCTGAAAGGGTTTCTGGAGTTGAGTTAGGTGCTGCAAGAAGTAATAAAGAGGGAAAGGATATAAAAGAGCTGCTGGAACAGgttcttgctttttatgttctgtctgactcatcattaactgaaatttctttgcttttgttttacataattgctgaactatttagttctaggaagaagggga-
  | |||||| ||||||||||||||||||||||||||||||| ||||| |||||| ||||||  |||||| | || ||| | | |||  |  |||||||||| ||  | |||| | | |    | |        | |||| | |   ||   ||  | |||    |    |  || | | |     | |     |      
ACTGAGCACTTTAAAGTTTGCTGAAAGGGTTTCTGGAGTTGAATTAGGAGCTGCACGAAGTAGCAAAGAGAGCAAAGATGTGAGAGAATTAATGGAACAGgtact-accttttgtctaccaaattatgttggcatgactgtattacattcttttcagctttgtgaatgaaccaaaatgtctttcagttgatcttatatctg

upper sequence: LOC_Os05g44560.1 (Oryza sativa), 5'ss of exon 18
lower sequence: AT1G63640.1 (Arabidopsis thaliana), 5'ss of exon 18
TATAAGCACTCTAAAGTTTGCTGAAAGGGTTTCTGGAGTTGAGTTAGGTGCTGCAAGAAGTAATAAAGAGGGAAAGGATATAAAAGAGCTGCTGGAACAGgttcttgctttttatgttctgtctgactcatcattaactgaaatttctttgcttttgttt------tacataattgctgaactatt--tagttctaggaagaagggga
  |||||||| | || || || |||||||||||||| || |||||||||||||| | ||||| |||||||||    ||| ||| | | ||  |||||||||||  |  | | | |  ||| |||  |||       | | || |||   |  |     ||       ||| |  |  |    ||||  || | || |  | ||  |  
AGTAAGCACTTTGAAATTCGCCGAAAGGGTTTCTGGTGTGGAGTTAGGTGCTGCCAAAAGTAGTAAAGAGGGTCGAGATGTAAGACAACTCATGGAACAGgtttgtattctcttt-ctctctctatctctctcaagatttaattttggctattgaaagttaaagagcacaaaggtattcgtatattgatattgcttgatataacag--

upper sequence: LOC_Os05g44560.1 (Oryza sativa), 5'ss of exon 18
lower sequence: Vv17s0000g03700.t01 (Vitis vinifera), 5'ss of exon 18
TATAAGCACTCTAAAGTTTGCTGAAAGGGTTTCTGGAGTTGAGTTAGGTGCTGCAAGAAGTAATAAAGAGGGAAAGGATATAAAAGAGCTGCTGGAACAGgttcttgctttttatgttctgtctgactcatcattaactgaa-atttctttgcttttgttttacata-attgctgaactatttag------ttctaggaagaagggga
|  ||| ||| | || |||||||| |||||||||||||| ||| ||||||||||| | ||||  |||||||| | |||  | || ||  |  |||| ||||||||        || |||  | | | |     ||   |||| ||||  | ||  | ||  || ||| | |  |   || || |       ||  | | |  |  | |
TGCAAGTACTTTGAAATTTGCTGAGAGGGTTTCTGGAGTCGAGCTAGGTGCTGCACGGAGTAGCAAAGAGGGCAGGGACGTTAAGGAATTAATGGATCAGgttct-------catattc-atttaagtagcagtttgttgaatatttactagccatggtgctaaatagaattttatgcttttcaagacgtattgcaagcactatagaa

upper sequence: LOC_Os05g44560.1 (Oryza sativa), 5'ss of exon 18
lower sequence: Vv02s0025g03480.t01 (Vitis vinifera), 5'ss of exon 19
TATAAGCACTCTAAAGTTTGCTGAAAGGGTTTCTGGAGTTGAGTTAGGTGCTGCAAGAAGTAATAAAGAGGGAAAGGATATAAAAGAGCTGCTGGAACAGgttcttgctttt--tatgttct-----gtctgactcatcattaactgaaatttctt----tgcttttgttttacataattgctgaactatttagttctaggaagaagggga--
|||||| ||  | |||||||| || || || ||||| |||||||||||||||||||| || || |||||||||| |||| | | ||| ||  |||| |||||  || | |||  |||  | |     || |||||  | ||  | | | ||||  |    |||| ||   ||   |  |||||  |   | |  |||   |  ||    ||  
TATAAGTACCTTGAAGTTTGCCGAGAGAGTCTCTGGTGTTGAGTTAGGTGCTGCAAGGAGCAACAAAGAGGGAAGGGATGTTAGAGAACTTATGGAGCAGgtcattacgtttattataattttcattgtttgacttct-atgcattaagattttatgaagtgctgttcccttgtgt--ttgct--atcttctgattccctgttgatcttgaag

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|66914991|gb|CX101839.1|CX101839
EST:     CTGCAAGAAGTAATAAAGAGGGAAAGGATATAAAAGAGCTGCTGGAACAG                         GTTGCATCTTTGAAAGACACTATTGTACGAAAAGATACGGAAATTGAGCAG
genomic: CTGCAAGAAGTAATAAAGAGGGAAAGGATATAAAAGAGCTGCTGGAACAGgttcttgctt ... ttttgtccagGTTGCATCTTTGAAAGACACTATTGTACGAAAAGATACGGAAATTGAGCAG
EST: gi|58657012|gb|CK045692.1|CK045692
EST:     GCAAGAAGTAATAAAGAGGGAAAGGATATAAAAGAGCTGCTGGAACAG                         GTTGCATCTTTGAAAGACACTATTGTACGAAAAGATACGGAAATTGAGCAG
genomic: GCAAGAAGTAATAAAGAGGGAAAGGATATAAAAGAGCTGCTGGAACAGgttcttgctt ... ttttgtccagGTTGCATCTTTGAAAGACACTATTGTACGAAAAGATACGGAAATTGAGCAG

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), 64 (downstream exon)
Score: 12

TATAAGCACTCTAAAGTTTGCTGAAAGGGTTTCTGGAGTTGAGTTAGGTGCTGCAAGAAGTAATAAAGAGGGAAAGGATATAAAAGAGCTGCTGGAACAGgttcttgctt ... ttttgtccagGTTGCATCTTTGAAAGACACTATTGTACGAAAAGATACGGAAATTGAGCAGCTCCAACTCATGAAAGACAAAGTCAAATCGCCAAGTTTTGCAGTCGATA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TATAAGCACTCTAAAGTTTGCTGAAAGGGTTTCTGGAGTTGAGTTAGGTGCTGCAAGAAGTAATAAAGAGGGAAAGGATATAAAAGAGCTGCTGGAACAGgttcttgctttttatgttctgtctgactcatcattaactgaaatttctttgcttttgttttacataattgctgaactatttagttctaggaagaagggga

- - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaagggg