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'   		8  
 5'  3'   		9  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtatttgtgatacaatcgttgctgctgttttgggaagaaaagtcttccaaaaacagaacaaagaaatgataagaaaacgtgcttcctttgatttcatcagACAGGAGACTGCAGGAGGCTAAAGCAGCATTTGACACAAGCATAGATAATGGGATGACCTTATTTGATACAGCAGAAGTTTATGGTACAGCG

Basic information

species Oryza sativa
transcript LOC_Os07g04990.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g04990.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G111954_T03 (Zea mays), 3'ss of exon 1
--gtatttgtg-atacaatcgttgct-gctgttttgggaagaaaagtcttccaaaaacagaacaaagaaatgataagaaaacgtgcttcctttgatttcatcagACAGGAGACTGCAGGAGGCTAAAGCAGCATTTGACACAAGCATAGATAATGGGATGACCTTATTTGATACAGCAGAAGTTTATGGTACAGCG
  |  || ||| || ||| |    ||   | | | |   |  ||  | || ||    |  ||   | |   | | |  |    |  || |||   ||    ||||||||||||||  ||| ||  | |  || || ||  | ||||| ||||| ||||||||||| || ||||| ||||||||||| |||||||| 
tagctttagtgtattcaaacaccccttagtatgtcgatgactaatatatttcatt--ccaaatgtacagtaggtgattagttttttttacttgagtt--gccagACAGGAGACTGAGGGAAGCACAGGACGCGTTCGATGCGAGCATCGATAACGGGATGACCTTCTTCGATACTGCAGAAGTTTACGGTACAGCA
















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|38478740|gb|CF962873.1|CF962873
EST:     CGCCTGGTCGTGGGGGGACACCACCTACTGGAACGAGTCCGAGTGGGACG                         ACAGGAGACTGCAGGAGGCTAAAGCAGCATTTGACACAAGCATAGATAATG
genomic: CGCCTGGTCGTGGGGGGACACCACCTACTGGAACGACTCCGAGTGGGACGgtacgcactg ... atttcatcagACAGGAGACTGCAGGAGGCTAAAGCAGCATTTGACACAAGCATAGATAATG
EST: gi|38477681|gb|CF961814.1|CF961814
EST:     GCCTGGTCGTGGGGGGACACACACCTACTGG-ACGACTCCGAGTGGGACG                         ACAGGAGACTGCAGGAGGCTAAAGCAGCATTTGACACAAGCATAGAT-ATG
genomic: GCCTGGTCGTGGGGGGACAC-CACCTACTGGAACGACTCCGAGTGGGACGgtacgcactg ... atttcatcagACAGGAGACTGCAGGAGGCTAAAGCAGCATTTGACACAAGCATAGATAATG
EST: gi|58586534|gb|CF984842.1|CF984842
EST:     AACGACTCCGAGTGGGACG                         ACAGGAGACTGCAGGAGGCTAAAGCAGCATTTGACACAAGCATAGATAATG
genomic: AACGACTCCGAGTGGGACGgtacgcactg ... atttcatcagACAGGAGACTGCAGGAGGCTAAAGCAGCATTTGACACAAGCATAGATAATG
EST: gi|58590950|gb|CF989258.1|CF989258
EST:     GCCTGGTCGTGGGGGGACGAACACCTACTGGAACGACTCCGAGTGGGACG                         ACAGGAGACTGCAGGAGGCTAAAGCAGCATTTGACACAAGCATAGATAATG
genomic: GCCTGGTCGTGGGGGGAC-ACCACCTACTGGAACGACTCCGAGTGGGACGgtacgcactg ... atttcatcagACAGGAGACTGCAGGAGGCTAAAGCAGCATTTGACACAAGCATAGATAATG
EST: gi|38469835|gb|CF953966.1|CF953966
EST:     CGCCTGGTCGTGGGGGGACACCACCTACTGGAACGACTCCGAGTGGGACG                         ACAGGAGACTGCAGGAGGCTAAAGCAGCATTTGACAGGGGCATAGATAATG
genomic: CGCCTGGTCGTGGGGGGACACCACCTACTGGAACGACTCCGAGTGGGACGgtacgcactg ... atttcatcagACAGGAGACTGCAGGAGGCTAAAGCAGCATTTGACACAAGCATAGATAATG
EST: gi|58589665|gb|CF987973.1|CF987973
EST:     CGCCTGGTCGTGGGGGGA-GGGGCCTACTGGAACGACTCCGAGTGGGACG                         ACAGGAGACTGCAGGAGGCTAAAGCAGCATTTGACACAAGCATAGATAATG
genomic: CGCCTGGTCGTGGGGGGACACCACCTACTGGAACGACTCCGAGTGGGACGgtacgcactg ... atttcatcagACAGGAGACTGCAGGAGGCTAAAGCAGCATTTGACACAAGCATAGATAATG
EST: gi|38480259|gb|CF964348.1|CF964348
EST:     CGCCTGGTCGTGGGGGGACACCACCTAGTGGAACGACTCCGAGTGGGACG                         ACAGGAGACTGCAGGAGGCTAAAGCAGCATTTGACACAAGCATAGATAATG
genomic: CGCCTGGTCGTGGGGGGACACCACCTACTGGAACGACTCCGAGTGGGACGgtacgcactg ... atttcatcagACAGGAGACTGCAGGAGGCTAAAGCAGCATTTGACACAAGCATAGATAATG

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: 73 (upstream exon), 75 (downstream exon)
Score: 61

AAGGTGAGGCTGGGTGGGTCGGAAGTGGCGGTGAGCAAGCTCGGCATCGGCGCCTGGTCGTGGGGGGACACCACCTACTGGAACGACTCCGAGTGGGACGgtacgcactg ... atttcatcagACAGGAGACTGCAGGAGGCTAAAGCAGCATTTGACACAAGCATAGATAATGGGATGACCTTATTTGATACAGCAGAAGTTTATGGTACAGCG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccaaaaacagaacaaagaaatgataagaaaacgtgcttcctttgatttcatcagACAGGAGACTGCAGGAGGCTAAAGCAGCATTTGACACAAGCATAGATAATGGGATGACCTTATTTGATACAGCAGAAGTTTATGGTACAGCG
                                        ctttgat  putative branch site (score: 61)
                                    cttcctttgatttc  CT-rich tract
                  aaatgataagaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatttgtgatacaatcgttgctgctgttttgggaagaaaagtcttccaaaaacagaacaaagaaatgataagaaaacgtgcttcctttgatttcatcagACAGGAGACTGCAGGAGGCTAAAGCAGCATTTGACACAAGCATAGATAATGGGATGACCTTATTTGATACAGCAGAAGTTTATGGTACAGCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT