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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattatttttagtctcctctctgcttgtctgcttttttgcattagacattagacatcaaatatgattatttgttcaagtgaagtgatgattattctctgggcaatccagGGGCCATGTCCGAATTGTGGCGCTGAAAACCTTTCCTTCTTCGGGACTATCCTGTCAGTGTCTAGTGGCGGTGAAACAAACAAAGTGAAATGTGCAGA

Basic information

species Oryza sativa
transcript LOC_Os03g64020.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g64020.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM5G896082_T03 (Zea mays), 3'ss of exon 8
gtattatttttagtctcctctctgcttgtctgcttttttgcattagacatta-gacatcaaatatgattatttgttcaagtgaag-tgatgatt--attctctgggcaatccagGGGCCATGTCCGAATTGTGGCGCTGAAAACCTTTCCTTCTTCGGGACTATCCTGTCAGTGTCTAGTGGCGGTGAAACAAACAAAGTGAAATGTGCAGA
                  | | || | |||   |    | ||||   | ||| ||||   ||| |   |    ||  ||| |||  ||||||||  ||| |   ||  ||| ||||||||||||| ||||||||  ||||||||||||||||||| |||||||| |||||||| || |||||||||  |||||||||||||||||||||| |
-----------------gtatgtgttggtc--gtgccatccattgttctttatgacagagaatgtatattgaagtagaagggaaactgatgattttatttttctggggatc-agGGGCCATGTCCTAATTGTGGTACTGAAAACCTTTCCTTCTTTGGGACTATACTGTCAGTCTCCAGTGGCGGTACAACAAACAAAGTGAAATGTGCAAA

upper sequence: LOC_Os03g64020.1 (Oryza sativa), 3'ss of exon 5
lower sequence: AC203966.5_FGT002 (Zea mays), 3'ss of exon 7
gtattatttttagtctcctctctgcttgtctgcttttttgcattagacattagacatcaaatatgattatttgttcaagtgaagtgatgattattctctgggcaatccagGGGCCATGTCCGAATTGTGGCGCTGAAAACCTTTCCTTCTTCGGGACTATCCTGTCAGTGT-CTAGTGGCGGTGAAACAAACAAAGTGAAATGTG---CAGA------
             |  | ||| ||    | | || |    |   ||       ||| |||| |   | |  ||| |||    ||| |||    ||        |         | |  | ||  |     | ||  |     ||  ||||   | |  | |||  || ||| ||| |  | ||   |    | |  || | | ||   || |      
------------tttccttctttgggactatactgtcagtctccagtggcggtacaacaaacaaagtgaaatgtgcaa----agt-atgtccctttatcatagatcatgttatctagATTCGTGTCTACCCTCTTGATGTGCTTATTTCTA-AGAAGCACCCTTCCAATGTTCTATTTCCAGTTGCAGTGCCGAGCTGGAGTATGACTCAAAATCTCG
















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|86884857|gb|CI314433.1|CI314433
EST:     TAGCACAGTCGATAACTAATGCCATAGTGAACGACTTCTTAATCCTCAAG                         GGGCCATGTCCGAATTGTGGCGCTGAAAACCTTTCCTTCTTCGGGACTATC
genomic: TAGCACAGTCGATAACTAATGCCATAGTGAACGACTTCTTAATCCTCAAGgtattatttt ... ggcaatccagGGGCCATGTCCGAATTGTGGCGCTGAAAACCTTTCCTTCTTCGGGACTATC
EST: gi|88518624|gb|CI446278.1|CI446278
EST:     CTAATGCCATAGTGAACGACTTCTTAATCCTCAAG                         GGGCCATGTCCGAATTGTGGCGCTGAAAACCTTTCCTTCTTCGGGACTATC
genomic: CTAATGCCATAGTGAACGACTTCTTAATCCTCAAGgtattatttt ... ggcaatccagGGGCCATGTCCGAATTGTGGCGCTGAAAACCTTTCCTTCTTCGGGACTATC
EST: gi|86882127|gb|CI325663.1|CI325663
EST:     TAGCACAGTCGATAAATAATGCCATAGTGAAAGACTTGTTAATCCTCAAG                         GGCCCATGTCCGAATTGTGGCGCTGAAAACCTTTCCTTCTTCGGGACTATC
genomic: TAGCACAGTCGATAACTAATGCCATAGTGAACGACTTCTTAATCCTCAAGgtattatttt ... ggcaatccagGGGCCATGTCCGAATTGTGGCGCTGAAAACCTTTCCTTCTTCGGGACTATC
EST: gi|88965747|gb|CI006624.1|CI006624
EST:     TAGCACAGTCGATAACTAATGCCATAGTGAACGACTTCTTAATCCTCAAG                         GGGCCATGTCCGAATTGTGGCGCTGAAAACCTTTCCTTCTTCGGGACTATC
genomic: TAGCACAGTCGATAACTAATGCCATAGTGAACGACTTCTTAATCCTCAAGgtattatttt ... ggcaatccagGGGCCATGTCCGAATTGTGGCGCTGAAAACCTTTCCTTCTTCGGGACTATC
EST: gi|33822703|gb|CF337158.1|CF337158
EST:     TAGCACAGTCGATAACTAATGCCATAGTGAACGACTTCTTAATCCTCAAG                         GGGCCATGTCCGAATTGTGGCGCTGAAAACCTTTCCTTCTTCGGGACTATC
genomic: TAGCACAGTCGATAACTAATGCCATAGTGAACGACTTCTTAATCCTCAAGgtattatttt ... ggcaatccagGGGCCATGTCCGAATTGTGGCGCTGAAAACCTTTCCTTCTTCGGGACTATC
EST: gi|86865586|gb|CI330994.1|CI330994
EST:     TAGCACACTCGATAACTAATGCCATAGTGAACGACTTCTTAATCCTCAAG                         GGGCCATGTCCGAATTGTGGCGCTGAAAACCTTTCCTTCTTCGGGACTATC
genomic: TAGCACAGTCGATAACTAATGCCATAGTGAACGACTTCTTAATCCTCAAGgtattatttt ... ggcaatccagGGGCCATGTCCGAATTGTGGCGCTGAAAACCTTTCCTTCTTCGGGACTATC
EST: gi|3763560|gb|AU030312.1|AU030312
EST:     TAGCACAGTCGATAACTAATGCCATAGTGAACGACTTCTTAATCCTCAAG                         GGGCCATGTCCGAATTGTGGCGCTGAAAACCTTTCCTTCTTCGGGACTATC
genomic: TAGCACAGTCGATAACTAATGCCATAGTGAACGACTTCTTAATCCTCAAGgtattatttt ... ggcaatccagGGGCCATGTCCGAATTGTGGCGCTGAAAACCTTTCCTTCTTCGGGACTATC
EST: gi|29684429|gb|CB680704.1|CB680704
EST:     TAGCACAGTCGATAACTAATGCCATAGTGAACGACTTCTTAATCCTCAAG                         GGGCCATGTCCGAATTGTGGCGCTGAAAACCTTTCCTTCTTCGGGACTATC
genomic: TAGCACAGTCGATAACTAATGCCATAGTGAACGACTTCTTAATCCTCAAGgtattatttt ... ggcaatccagGGGCCATGTCCGAATTGTGGCGCTGAAAACCTTTCCTTCTTCGGGACTATC
EST: gi|86861130|gb|CI326610.1|CI326610
EST:     TAGCACAGTCGATAACTAATGCCATAATGAACGACTTCTTAATCCTC-AG                         GGGCCATGTCCGAATTGTGGCGCTGAAAACCTTTCCTTCTTCGGGACTATC
genomic: TAGCACAGTCGATAACTAATGCCATAGTGAACGACTTCTTAATCCTCAAGgtattatttt ... ggcaatccagGGGCCATGTCCGAATTGTGGCGCTGAAAACCTTTCCTTCTTCGGGACTATC
EST: gi|33821393|gb|CF336509.1|CF336509
EST:     TAGCACAGTCGATAACTAATGCCATAGTGAACGACTTCTTAATCCTCAAG                         GGGCCATGTCCGAATTGTGGCGCTGAAAACCTTTCCTTCTTCGGGACTATC
genomic: TAGCACAGTCGATAACTAATGCCATAGTGAACGACTTCTTAATCCTCAAGgtattatttt ... ggcaatccagGGGCCATGTCCGAATTGTGGCGCTGAAAACCTTTCCTTCTTCGGGACTATC
EST: gi|86477381|gb|CI120014.1|CI120014
EST:     TAGCACAGTCGATAACTAATGCCATAGTGAACGACTTCTTAATCCTCAAG                         GGGCCATGTCCGAATTGTGGCGCTGAAAACCTTTCCTTCTTCGGGACTATC
genomic: TAGCACAGTCGATAACTAATGCCATAGTGAACGACTTCTTAATCCTCAAGgtattatttt ... ggcaatccagGGGCCATGTCCGAATTGTGGCGCTGAAAACCTTTCCTTCTTCGGGACTATC
EST: gi|86890101|gb|CI320090.1|CI320090
EST:     TAGCACAGTCGATAACTAATCCCATAGTGAACGACTTCTTAATCCTC-AG                         GGGCCATGTCCGAATTGTGGCTCTGAAAACCTTTCCTTCTTC-GGACTATC
genomic: TAGCACAGTCGATAACTAATGCCATAGTGAACGACTTCTTAATCCTCAAGgtattatttt ... ggcaatccagGGGCCATGTCCGAATTGTGGCGCTGAAAACCTTTCCTTCTTCGGGACTATC
EST: gi|88904001|gb|CI006234.1|CI006234
EST:     TAGCACAGTCGATAACTAATGCCATAGTGAACGACTTCTTAATCCTCAAG                         GGGCCATGTCCGAATTGTGGCGCTGAAAACCTTTCCTTCTTCGGGACTATC
genomic: TAGCACAGTCGATAACTAATGCCATAGTGAACGACTTCTTAATCCTCAAGgtattatttt ... ggcaatccagGGGCCATGTCCGAATTGTGGCGCTGAAAACCTTTCCTTCTTCGGGACTATC
EST: gi|88319547|gb|CI518391.1|CI518391
EST:     ACGACTTCTTAATCCTCAAGG                         GGGCCATGTCCGAATTGTGGCGCTGAAAACCTTTCCTTCTTCGGGACTAT
genomic: ACGACTTCTTAATCCTCAA-Ggtattatttt ... ggcaatccagGGGCCATGTCCGAATTGTGGCGCTGAAAACCTTTCCTTCTTCGGGACTAT
EST: gi|86896793|gb|CI317331.1|CI317331
EST:     AGGCACAGTCGATAACTAATGCCATAGTGAACGACTTCTTAATCCTCAAG                         GGGCCATGTCCGAATTGTGGCGCTGAAAACCTTTCCTTCTTCGGGACTATC
genomic: A-GCACAGTCGATAACTAATGCCATAGTGAACGACTTCTTAATCCTCAAGgtattatttt ... ggcaatccagGGGCCATGTCCGAATTGTGGCGCTGAAAACCTTTCCTTCTTCGGGACTATC
EST: gi|88844776|gb|CI021351.1|CI021351
EST:     TAGCACAGTCGATAACTAATGCCATAGTGAACGACTTCTTAATCCTCAAG                         GGGCCATGTCCGAATTGTGGCGCTGAAAACCTTTCCTTCTTCGGGACTATC
genomic: TAGCACAGTCGATAACTAATGCCATAGTGAACGACTTCTTAATCCTCAAGgtattatttt ... ggcaatccagGGGCCATGTCCGAATTGTGGCGCTGAAAACCTTTCCTTCTTCGGGACTATC
EST: gi|33679890|gb|CF308129.1|CF308129
EST:     TAGCACAGTCGATAACTAATGCCATAGTGAACGACTTCTTAATCCTCAAG                         GGGCCATGTCCGAATTGTGGCGCTGAAAACCTTTCCTTCTTCGGGACTATC
genomic: TAGCACAGTCGATAACTAATGCCATAGTGAACGACTTCTTAATCCTCAAGgtattatttt ... ggcaatccagGGGCCATGTCCGAATTGTGGCGCTGAAAACCTTTCCTTCTTCGGGACTATC
EST: gi|88484444|gb|CI421715.1|CI421715
EST:     GACTTCTTAATCCTCAAG                         GGGCCATGTCCGAATTGTGGCGCTGAAAACCTTTCCTTCTTCGGGACTATC
genomic: GACTTCTTAATCCTCAAGgtattatttt ... ggcaatccagGGGCCATGTCCGAATTGTGGCGCTGAAAACCTTTCCTTCTTCGGGACTATC
EST: gi|86862773|gb|CI331653.1|CI331653
EST:     TAGCACAGTCGATAACTAATGCCATAGTGAACGACTTCTTAATCCTCAAG                         GGGCCATGTCCGAATTGTGGCGCTGAAAACCTTTCCTTCTTCGGGACTATC
genomic: TAGCACAGTCGATAACTAATGCCATAGTGAACGACTTCTTAATCCTCAAGgtattatttt ... ggcaatccagGGGCCATGTCCGAATTGTGGCGCTGAAAACCTTTCCTTCTTCGGGACTATC
EST: gi|88995899|gb|CI037190.1|CI037190
EST:     TAGCACAGTCGATAACTAATGCCATAGTGAACGACTTCTTAATCCTCAAG                         GGGCCATGTCCGAATTGTGGCGCTGAAAACCTTTCCTTCTTCGGGACTATC
genomic: TAGCACAGTCGATAACTAATGCCATAGTGAACGACTTCTTAATCCTCAAGgtattatttt ... ggcaatccagGGGCCATGTCCGAATTGTGGCGCTGAAAACCTTTCCTTCTTCGGGACTATC
EST: gi|86860511|gb|CI323436.1|CI323436
EST:     GCACAGTCGATAACTAATGCCATAGTGGACGACTTCTTAATCCTCAAG                         GGGCAATGTCCGGAATTGTGGCGCTGAAAACCTTTCCTTCTTC-GGACTAT
genomic: GCACAGTCGATAACTAATGCCATAGTGAACGACTTCTTAATCCTCAAGgtattatttt ... ggcaatccagGGGCCATGTCC-GAATTGTGGCGCTGAAAACCTTTCCTTCTTCGGGACTAT

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: 57 (upstream exon), 74 (downstream exon)
Score: 71

TTTCGGTTTCATTTTCACATGGTTTGCTGCTTTGCCTCTAATATTGTTCATAGCACAGTCGATAACTAATGCCATAGTGAACGACTTCTTAATCCTCAAGgtattatttt ... ggcaatccagGGGCCATGTCCGAATTGTGGCGCTGAAAACCTTTCCTTCTTCGGGACTATCCTGTCAGTGTCTAGTGGCGGTGAAACAAACAAAGTGAAATGTGCAGA




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcaaatatgattatttgttcaagtgaagtgatgattattctctgggcaatccagGGGCCATGTCCGAATTGTGGCGCTGAAAACCTTTCCTTCTTCGGGACTATCCTGTCAGTGTCTAGTGGCGGTGAAACAAACAAAGTGAAATGTGCAGA
     atatgattatttgtt  TA-rich tract