Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAACTCACACCATATTATTGAGGCAACTTTCAAAGCATTTGCTAGAGCCCTTCGACAAGCAACAGAATATGACTTGCGCCGACGCGGCACTGTCCCCAGgttcgttttagcttattgcaaatagcgtttaggaaattctatgttgtgcccaactacactgttgatgcctgattcaaaaacttcacacctgctaagcatatggtttatctctgacctttgctgatattgaaacattaacgtatctttcttgacttgatcgcag

Basic information

species Oryza sativa
transcript LOC_Os04g52710.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g52710.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G094255_T01 (Zea mays), 5'ss of exon 7
AAAACTCACACCATATTATTGAGGCAACTTTCAAAGCATTTGCTAGAGCCCTTCGACAAGCAACAGAATATGACTTGCGCCGACGCGGCACTGTCCCCAGgttcgttttagcttattgcaaa----tagcgtttaggaaattctatgttgtgcccaactacactgttgatgc---ctga---ttcaaaaac---ttcacacctgcta-----agcatatggtttatctctgacctttgctga--tattgaaacatta-acgtatctttcttgacttgatcgcag
|||||||||||||||| || |||||| |||||||||| |||||| | ||||||||||| |||||||| |||||| ||||||| |  ||||||||||||||||  || ||  |||| |   ||    |  || ||    | |  ||| | |  ||  || |  |||| ||||      ||   ||| |       || | | |||  |     ||   ||   |    |  ||  ||| |     | | |   | | | | || ||||  ||| ||  || ||||
AAAACTCACACCATATCATCGAGGCATCTTTCAAAGCGTTTGCTCGGGCCCTTCGACAGGCAACAGAGTATGACCTGCGCCGTCAAGGCACTGTCCCCAGgtctgtctttccttactcagaacttttgtcggttttctagtgttatttcgatccacaccattctgtagatgtagttcgagttttctagtgtcgattgatatctgacattggtagaggataactgggtttagaagtttacaaccctgtcgtctcctgatatgtttcttggttgtctcaatggcag

upper sequence: LOC_Os04g52710.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA20G28420.2 (Glycine max), 5'ss of exon 7
AAAACTCACACCATATTATTGAGGCAACTTTCAAAGCATTTGCTAGAGCCCTTCGACAAGCAACAGAATATGACTTGCGCCGACGCGGCACTGTCCCCAGgttcgttttagcttattgcaaatagcgtttaggaaattctatgttgtgcccaactacactgttgatgcctgattcaaaaacttcacacctgctaagcatatggtttatctctgacctttgctgatattgaaacattaacgtatctttcttgacttgatcgcag
|||| || || ||||||||||||||||| |||||||| |||||| | || ||||||||||||||||| |||||    || || || || ||| | || |||     | | |  | ||  |||| || ||| | |  || |  || |     || || | | |     | | |||     | ||    |  |     | |       || |                                                     
AAAATTCTCATCATATTATTGAGGCAACCTTCAAAGCTTTTGCTCGGGCTCTTCGACAAGCAACAGAGTATGATCCACGTCGCCGTGGAACTATACCAAGg-----tatggtatctttgaaattgccttttg-attttgtgggtagacgagaattagattttattcactttatt-----atttgctgctagtattacttgaaaaccatttt----------------------------------------------------

upper sequence: LOC_Os04g52710.1 (Oryza sativa), 5'ss of exon 7
lower sequence: Vv05s0020g03430.t01 (Vitis vinifera), 5'ss of exon 7
AAAACTCACACCATATTATTGAGGCAACTTTCAAAGCATTTGCTAGAGCCCTTCGACAAGCAACAGAATATGACTTGCGCCGACGCGGCACTGTCCCCAGgttcgtt-ttagcttattgcaaatagcgtttaggaaattctatgttgtgcccaactacactgttgatgcctgattcaaaaacttcacacctgctaagcatatggtttatctctgacctttgctgatattgaaacattaacgtatctttcttgacttgatcgcag
|||| || || ||||||||||||||||||||||| || || |||| ||| |||||||||||    |||||||||   ||||| |  |||||||| || ||||| |   ||  ||| ||  |||| |   |    ||  |||   |||  | |       || || || |||    ||||   ||   |  | | || | |      ||  | |||   |                                             
AAAATTCTCATCATATTATTGAGGCAACTTTCAAGGCTTTCGCTAAAGCTCTTCGACAAGCTGTGGAATATGACCCACGCCGTCATGGCACTGTGCCAAGgtttggaattttcttgttttaaattgacat----aacatctcctttgaacac-------ctattaatccctag--caaagggtttcta--tacaaatcctga----tacttttgagtct---------------------------------------------

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|88846550|gb|CI373318.1|CI373318
EST:     CTTCGACAAGCAACAGAATATGACTTGCGCCGACGCGGCACTGTCCCCAG                         CTCAAAAGGTGTGTTGTCAAGGTCATAGTGTTGCAGGTTTGGAAAACAAGG
genomic: CTTCGACAAGCAACAGAATATGACTTGCGCCGACGCGGCACTGTCCCCAGgttcgtttta ... ttgatcgcagCTCAAAAGGTGTGTTGTCAAGGTCATAGTGTTGCAGGTTTGGAAAACAAGG
EST: gi|89186200|gb|CI048069.1|CI048069
EST:     CTTCGACAAGCAACAGAATATGACTTGCGCCGACGCGGCACTGTCCCCAG                         CTCAAAAGGTGTGTTGTCAAGGTCATAGTGTTGCAGGTTTGGAAAACAAGG
genomic: CTTCGACAAGCAACAGAATATGACTTGCGCCGACGCGGCACTGTCCCCAGgttcgtttta ... ttgatcgcagCTCAAAAGGTGTGTTGTCAAGGTCATAGTGTTGCAGGTTTGGAAAACAAGG
EST: gi|86538064|gb|CI178270.1|CI178270
EST:     CGCGGCACTGTCCCCAG                         CTCAAAAGGTGTGTTGTCAAGGTCATAGTGTTGCAGGTTTGGAAAACAAGG
genomic: CGCGGCACTGTCCCCAGgttcgtttta ... ttgatcgcagCTCAAAAGGTGTGTTGTCAAGGTCATAGTGTTGCAGGTTTGGAAAACAAGG
EST: gi|29658247|gb|CB654522.1|CB654522
EST:     CTTCGACAAGCAACAGAATATGACTTGCGCCGACGCGGCACTGTCCCCAG                         CTCAAAAGGTGTGTTGTCAAGGTCATAGTGTTGCAGGTTTGGAAAACAAGG
genomic: CTTCGACAAGCAACAGAATATGACTTGCGCCGACGCGGCACTGTCCCCAGgttcgtttta ... ttgatcgcagCTCAAAAGGTGTGTTGTCAAGGTCATAGTGTTGCAGGTTTGGAAAACAAGG
EST: gi|86832686|gb|CI345101.1|CI345101
EST:     GCAACAGAATATGACTTGCGCCGACGCGGCACTGTCCCCAG                         CTCAAAAGGTGTGTTGTCAAGGTCATAGTGTTGCAGGTTTGGAAAACAAGG
genomic: GCAACAGAATATGACTTGCGCCGACGCGGCACTGTCCCCAGgttcgtttta ... ttgatcgcagCTCAAAAGGTGTGTTGTCAAGGTCATAGTGTTGCAGGTTTGGAAAACAAGG
EST: gi|88219830|gb|CI219390.1|CI219390
EST:     ACTGTCCCCAG                         CTCAAAAGGTGTGTTGTCAAGGTCATAGTGTTGCAGGTTTGGAAAACAATG
genomic: ACTGTCCCCAGgttcgtttta ... ttgatcgcagCTCAAAAGGTGTGTTGTCAAGGTCATAGTGTTGCAGGTTTGGAAAACAAGG
EST: gi|33798600|gb|CF325158.1|CF325158
EST:     GCAACAGAATATGACTTGCGCCGACGCGGCACTGTCCCCAG                         CTCAAAAGGTGTGTTGTCAAGGTCATAGTGTTGCAGGTTTGGAAAACAAGG
genomic: GCAACAGAATATGACTTGCGCCGACGCGGCACTGTCCCCAGgttcgtttta ... ttgatcgcagCTCAAAAGGTGTGTTGTCAAGGTCATAGTGTTGCAGGTTTGGAAAACAAGG
EST: gi|86862816|gb|CI331677.1|CI331677
EST:     GCGCCGACGCGGCACTGTCCCCAG                         CTCAAAAGGTGTGTTGTCAAGGTCATAGTGTTGCAGGTTTGGAAAACAAGG
genomic: GCGCCGACGCGGCACTGTCCCCAGgttcgtttta ... ttgatcgcagCTCAAAAGGTGTGTTGTCAAGGTCATAGTGTTGCAGGTTTGGAAAACAAGG
EST: gi|86853631|gb|CI330482.1|CI330482
EST:     CAGAATATGACTTGCGCCGACGCGGCACTGTCCCCAG                         CTCAAAAGGTGTGTTGTCAAGGTCATAGTGTTGCAGGTTTGGAAAACAAGG
genomic: CAGAATATGACTTGCGCCGACGCGGCACTGTCCCCAGgttcgtttta ... ttgatcgcagCTCAAAAGGTGTGTTGTCAAGGTCATAGTGTTGCAGGTTTGGAAAACAAGG
EST: gi|58666132|gb|CK054818.1|CK054818
EST:     CTTCGACAAGCAACAGAATATGACTTGCGCCGACGCGGCACTGTCCCCAG                         CTCAAAAGGTGTGTTGTCAAGGTCATAGTGTTGCAGGTTTGGAAAACAAGG
genomic: CTTCGACAAGCAACAGAATATGACTTGCGCCGACGCGGCACTGTCCCCAGgttcgtttta ... ttgatcgcagCTCAAAAGGTGTGTTGTCAAGGTCATAGTGTTGCAGGTTTGGAAAACAAGG
EST: gi|86504503|gb|CI147136.1|CI147136
EST:     CTTCGACAAGCAACAGAATATGACTTGCGCCGACGCGGCACTGTCCCCAG                         CTCAAAAGGTGTGTTGTCAAGGTCATAGTGTTGCAGGTTTGGAAAACAAGG
genomic: CTTCGACAAGCAACAGAATATGACTTGCGCCGACGCGGCACTGTCCCCAGgttcgtttta ... ttgatcgcagCTCAAAAGGTGTGTTGTCAAGGTCATAGTGTTGCAGGTTTGGAAAACAAGG
EST: gi|89182904|gb|CI045662.1|CI045662
EST:     CTTCGACAAGCAACAGAATATGACTTGCGCCGACGCGGCACTGTCCCCAG                         CTCAAAAGGTGTGTTGTCAAGGTCATAGTGTTGCAGGTTTGGAAAACAAGG
genomic: CTTCGACAAGCAACAGAATATGACTTGCGCCGACGCGGCACTGTCCCCAGgttcgtttta ... ttgatcgcagCTCAAAAGGTGTGTTGTCAAGGTCATAGTGTTGCAGGTTTGGAAAACAAGG
EST: gi|86527139|gb|CI167345.1|CI167345
EST:     CTTCGACAAGCAACAGAGTATGACTTGCGCCGACGCGGCACTGTCCCCAG                         CTCAAAAGGTGTGTTGTCAAGGTCATAGTGTTGCAGGTTTGGAAAACAAGG
genomic: CTTCGACAAGCAACAGAATATGACTTGCGCCGACGCGGCACTGTCCCCAGgttcgtttta ... ttgatcgcagCTCAAAAGGTGTGTTGTCAAGGTCATAGTGTTGCAGGTTTGGAAAACAAGG

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: 68 (upstream exon), 51 (downstream exon)
Score: 20

AAAACTCACACCATATTATTGAGGCAACTTTCAAAGCATTTGCTAGAGCCCTTCGACAAGCAACAGAATATGACTTGCGCCGACGCGGCACTGTCCCCAGgttcgtttta ... ttgatcgcagCTCAAAAGGTGTGTTGTCAAGGTCATAGTGTTGCAGGTTTGGAAAACAAGGGGTGCATGCTACTGTTCCTTGTAGATTGCAATATTCAAAGGAAACAAAT




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAAACTCACACCATATTATTGAGGCAACTTTCAAAGCATTTGCTAGAGCCCTTCGACAAGCAACAGAATATGACTTGCGCCGACGCGGCACTGTCCCCAGgttcgttttagcttattgcaaatagcgtttaggaaattctatgttgtgcccaactacactgttgatgcctgattcaaaaacttcacacctgctaagcatatggtttatctctgacctttgctgatattgaaacattaacgtatctttcttgacttgatcgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA