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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtacctgtcgagtgccgtcgtcttacctatttgttttgcaagtaatcagggagtatcgatcgctgaacataatgtagcccttttgccccccaaatgtgtcatgtcgttccatgattttgtttggattgcagGTGTCGCTGGGGGTGCATCTTCAGGTAAAAGTACTGTATGCAAGATGATAATTGATCAGCTACGTGATCAGCGTGTGGTTGTTGTTACTCAG

Basic information

species Oryza sativa
transcript LOC_Os11g16370.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g16370.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G169462_T01 (Zea mays), 3'ss of exon 1
gttagtacctgtcgagtgccgtcgtcttacctatttgttttgcaagtaatcagggagtatcgatcgctgaacataatgtagcccttttgccccccaaatgtgtcatgtcgttccatgattttgtttggattgcagGTGTCGCTGGGGGTGCATCTTCAGGTAAAAGTACTGTATGCAAGATGATAATTGATCAGCTACGTGATCAGCGTGTGGTTGTTGTTACTCAG
                                  ||| | |  |  || |   |    || ||| | |||  ||   ||||||  || ||||    |||| | |||| | |    || |   |||| |   |||||||| |||||||||||||| ||||| || ||||| || ||||||||||| ||||||||||| ||||| |||||||| || |||||||| |||
---------------------------------gttggtatata--tacttttgattgattgattgatgagtatggcgtagcctgttggccc--tgaatgcggcatgccctaatgtggtg--gttttgggcgcagGTGTTGCTGGGGGTGCATCGTCAGGCAAGAGTACCGTGTGCAAGATGATCATTGATCAGCTCCGTGACCAGCGTGTCGTGGTTGTTACGCAG

upper sequence: LOC_Os11g16370.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G034143_T01 (Zea mays), 3'ss of exon 2
-----------------gttagtacctgtcgagtgccgtcgtcttacctatttgtttt----------gcaagtaatcagggagtat--cgatcgctgaacataatgtagcccttt-tgccccccaaatgtgtcatgtcgttccatgattttgtttggattgcagGTGTCGCTGGGGGTGCATCTTCAGGTAAAAGTACTGTATGCAAGATGATAATTGATCAGCTACGTGATCAGCGTGTGGTTGTTGTTACTCAG
                  || ||   || |  |  |  ||  | || || | ||               ||| | |  |||  ||||  | || | |||  |||  ||||  |  | |   |||  ||||   ||||     || | || | || | |  | |||| || |||||||||||||| ||||| |||||||| || ||||||||||| ||||||||||| ||||| ||||| || || | |||||| |||
gtccgtatatatacttgattggttgatgccatggactctctccctatctttctgcgcctagcctaatgacaattcagtaggatgtatgccaattgatgagtatagcgtagatcgatgttggccctgaatgcagcatg-----ccctaatgtggtattgggtacagGCGTTGCTGGGGGTGCATCGTCAGGCAAAAGTACCGTGTGCAAGATGATCATTGATCAGCTCCGTGACCAGCGCGTTGTGGCTGTTACACAG
















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|88696045|gb|CI739620.1|CI739620
EST:     ACCGACAACCTCGGGCGTGGAGAATGGGCACCAGGAGCCATTTGTCATTG                         GTGTCGNTGGGGGTGCATCTTCAGGTAAAAGTACTGTATGCAAGATGATAA
genomic: ACCGACAACCTCGGGCGTGGAGAATGGGCACCAGGAGCCATTTGTCATTGgttagtacct ... tggattgcagGTGTCGCTGGGGGTGCATCTTCAGGTAAAAGTACTGTATGCAAGATGATAA
EST: gi|88576240|gb|CI670385.1|CI670385
EST:     ACCGACAACCTCGGGCGTGGAGAATGGGCACCAGGAGCCATTTGTCATTG                         GTGTCGCTGGGGGTGCATCTTCAGGTAAAAGTACTGTATGCAAGATGATAA
genomic: ACCGACAACCTCGGGCGTGGAGAATGGGCACCAGGAGCCATTTGTCATTGgttagtacct ... tggattgcagGTGTCGCTGGGGGTGCATCTTCAGGTAAAAGTACTGTATGCAAGATGATAA
EST: gi|88301528|gb|CI597221.1|CI597221
EST:     ACCGACAACCTCGGGCGTGGAGAATGGGCACCAGGAGCCATTTGTCATTG                         GTGTCGCTGGGGGTGCATCTTCAGGTAAAAGTACTGTATGCAAGATGATAA
genomic: ACCGACAACCTCGGGCGTGGAGAATGGGCACCAGGAGCCATTTGTCATTGgttagtacct ... tggattgcagGTGTCGCTGGGGGTGCATCTTCAGGTAAAAGTACTGTATGCAAGATGATAA
EST: gi|58665119|gb|CK053805.1|CK053805
EST:     ACCGACAACCTCGGGCGTGGAGAATGGGCACCAGGAGCCATTTGTCATTG                         GTGTCGCTGGGGGTGCATCTTCAGGTAAAAGTACTGTATGCAAGATGATAA
genomic: ACCGACAACCTCGGGCGTGGAGAATGGGCACCAGGAGCCATTTGTCATTGgttagtacct ... tggattgcagGTGTCGCTGGGGGTGCATCTTCAGGTAAAAGTACTGTATGCAAGATGATAA
EST: gi|117233504|gb|CT842322.1|CT842322
EST:     ACCGACAACCTCGGGCGTGGAGAATGGGCACCAGGAGCCATTTGTCATTG                         GTGTCGCTGGGGGTGCATCTTCAGGTAAAAGTACTGTATGCAAGATGATAA
genomic: ACCGACAACCTCGGGCGTGGAGAATGGGCACCAGGAGCCATTTGTCATTGgttagtacct ... tggattgcagGTGTCGCTGGGGGTGCATCTTCAGGTAAAAGTACTGTATGCAAGATGATAA
EST: gi|88331762|gb|CI640793.1|CI640793
EST:     ACCGACAACCTCGGGCGTGGAGAATGGGCACCAGGAGCCATTTGTCATTG                         GTGTCGCTGGGGGTGCATCTTCAGGTAAAAGTACTGTATGCAAGATGATAA
genomic: ACCGACAACCTCGGGCGTGGAGAATGGGCACCAGGAGCCATTTGTCATTGgttagtacct ... tggattgcagGTGTCGCTGGGGGTGCATCTTCAGGTAAAAGTACTGTATGCAAGATGATAA
EST: gi|58684586|gb|CK073273.1|CK073273
EST:     ACCGACAACCTCGGGCGTGGAGAATGGGCACCAGGAGCCATTTGTCATTG                         GTGTCGCTGGGGGTGCATCTTCAGGTAAAAGTACTGTATGCAAGATGATAA
genomic: ACCGACAACCTCGGGCGTGGAGAATGGGCACCAGGAGCCATTTGTCATTGgttagtacct ... tggattgcagGTGTCGCTGGGGGTGCATCTTCAGGTAAAAGTACTGTATGCAAGATGATAA
EST: gi|58689975|gb|CK078662.1|CK078662
EST:     ACCGACAACCTCGGGCGTGGAGAATGGGCACCAGGAGCCATTTGTCATTG                         GTGTCGCTGGGGGTGCATCTTCAGGTAAAAGTACTGTATGCAAGATGATAA
genomic: ACCGACAACCTCGGGCGTGGAGAATGGGCACCAGGAGCCATTTGTCATTGgttagtacct ... tggattgcagGTGTCGCTGGGGGTGCATCTTCAGGTAAAAGTACTGTATGCAAGATGATAA
EST: gi|88346696|gb|CI656723.1|CI656723
EST:     ACCGACAACCTCGGGCGTGGAGAATGGGCACCAGGAGCCATTTGTCATTG                         GTGTCGCTGGGGGTGCATCTTCAGGTAAAAG
genomic: ACCGACAACCTCGGGCGTGGAGAATGGGCACCAGGAGCCATTTGTCATTGgttagtacct ... tggattgcagGTGTCGCTGGGGGTGCATCTTCAGGTAAAAG
EST: gi|58655184|gb|CK043864.1|CK043864
EST:     ACCGACAACCTCGGGCGTGGAGAATGGGCACCAGGAGCCATTTGTCATTG                         GTGTCGCTGGGGGTGCATCTTCAGGTAAAAGTACTGTATGCAAGATGATAA
genomic: ACCGACAACCTCGGGCGTGGAGAATGGGCACCAGGAGCCATTTGTCATTGgttagtacct ... tggattgcagGTGTCGCTGGGGGTGCATCTTCAGGTAAAAGTACTGTATGCAAGATGATAA
EST: gi|88398002|gb|CI585505.1|CI585505
EST:     ACCGACAACCTCGGGCGTGGAGAATGGGCACCAGGAGCCATTTGTCATTG                         GTGTCGCTGGGGGTGCATCTTCAGGTAAAAGTACTGTATGCAAGATGATAA
genomic: ACCGACAACCTCGGGCGTGGAGAATGGGCACCAGGAGCCATTTGTCATTGgttagtacct ... tggattgcagGTGTCGCTGGGGGTGCATCTTCAGGTAAAAGTACTGTATGCAAGATGATAA
EST: gi|58653267|gb|CK041947.1|CK041947
EST:     ACCGACAACCTCGGGCGTGGAGAATGGGCACCAGGAGCCATTTGTCATTG                         GTGTCGCTGGGGGTGCATCTTCAGGTAAAAGTACTGTATGCAAGATGATAA
genomic: ACCGACAACCTCGGGCGTGGAGAATGGGCACCAGGAGCCATTTGTCATTGgttagtacct ... tggattgcagGTGTCGCTGGGGGTGCATCTTCAGGTAAAAGTACTGTATGCAAGATGATAA
EST: gi|88718580|gb|CI742090.1|CI742090
EST:     ACCGACAACCTCGGGCGTGGAGAATGGGCACCAGGAGCCATTTGTCATTG                         GTGTCGCTGGGGGTGCATCTTCAGGTAAAAGTACTGTATGCAAGATGATAA
genomic: ACCGACAACCTCGGGCGTGGAGAATGGGCACCAGGAGCCATTTGTCATTGgttagtacct ... tggattgcagGTGTCGCTGGGGGTGCATCTTCAGGTAAAAGTACTGTATGCAAGATGATAA
EST: gi|88340276|gb|CI652625.1|CI652625
EST:     ACCGACAACCTCGGGCGTGGAGAATGGGCACCAGGAGCCATTTGTCATTG                         GTGTCGCTGGGGGTGCATCTTCAGGTAAAAGTACTGTATGCAAGATGATAA
genomic: ACCGACAACCTCGGGCGTGGAGAATGGGCACCAGGAGCCATTTGTCATTGgttagtacct ... tggattgcagGTGTCGCTGGGGGTGCATCTTCAGGTAAAAGTACTGTATGCAAGATGATAA
EST: gi|58693385|gb|CK082072.1|CK082072
EST:     ACCGACAACCTCGGGCGTGGAGAATGGGCACCAGGAGCCATTTGTCATTG                         GTGTCGCTGGGGGTGCATCTTCAGGTAAAAGTACTGTATGCAAGATGATAA
genomic: ACCGACAACCTCGGGCGTGGAGAATGGGCACCAGGAGCCATTTGTCATTGgttagtacct ... tggattgcagGTGTCGCTGGGGGTGCATCTTCAGGTAAAAGTACTGTATGCAAGATGATAA
EST: gi|88344812|gb|CI624463.1|CI624463
EST:     ACCGACAACCTCGGGGGTGGAGAATGGGCACCAGGAGCCATTTGTCATTG                         GTGTCGCTGGGGGTGCATCTTCAGGTAAAAGTACTGTATGCAAGATGATAA
genomic: ACCGACAACCTCGGGCGTGGAGAATGGGCACCAGGAGCCATTTGTCATTGgttagtacct ... tggattgcagGTGTCGCTGGGGGTGCATCTTCAGGTAAAAGTACTGTATGCAAGATGATAA
EST: gi|58662773|gb|CK051459.1|CK051459
EST:     ACCGACAACCTCGGGCGTGGAGAATGGGCACCAGGAGCCATTTGTCATTG                         GTGTCGCTGGGGGTGCATCTTCAGGTAAAAGTACTGTATGCAAGATGATAA
genomic: ACCGACAACCTCGGGCGTGGAGAATGGGCACCAGGAGCCATTTGTCATTGgttagtacct ... tggattgcagGTGTCGCTGGGGGTGCATCTTCAGGTAAAAGTACTGTATGCAAGATGATAA
EST: gi|88696044|gb|CI739619.1|CI739619
EST:     AC-GACCACCTCGGGCGTGGAGAATGGGCACCACGAGCCATTCGTCATTG                         GTGTCGCTGGGGGTGCATCTTCAGGTAAAAGTACTGTATGCAAGATGATAA
genomic: ACCGACAACCTCGGGCGTGGAGAATGGGCACCAGGAGCCATTTGTCATTGgttagtacct ... tggattgcagGTGTCGCTGGGGGTGCATCTTCAGGTAAAAGTACTGTATGCAAGATGATAA
EST: gi|58666921|gb|CK055607.1|CK055607
EST:     ACCGACAACCTCGGGCGTGGAGAATGGGCACCAGGAGCCATTTGTCATTG                         GTGTCGCTGGGGGTGCATCTTCAGGTAAAAGTACTGTATGCAAGATGATAA
genomic: ACCGACAACCTCGGGCGTGGAGAATGGGCACCAGGAGCCATTTGTCATTGgttagtacct ... tggattgcagGTGTCGCTGGGGGTGCATCTTCAGGTAAAAGTACTGTATGCAAGATGATAA

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), 54 (downstream exon)
Score: 5

CTCCGTTTGGAAGAGCTTAACATGAATGGCTCCGTGTCAGGGGAGGACCAACCGACAACCTCGGGCGTGGAGAATGGGCACCAGGAGCCATTTGTCATTGgttagtacct ... tggattgcagGTGTCGCTGGGGGTGCATCTTCAGGTAAAAGTACTGTATGCAAGATGATAATTGATCAGCTACGTGATCAGCGTGTGGTTGTTGTTACTCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcccttttgccccccaaatgtgtcatgtcgttccatgattttgtttggattgcagGTGTCGCTGGGGGTGCATCTTCAGGTAAAAGTACTGTATGCAAGATGATAATTGATCAGCTACGTGATCAGCGTGTGGTTGTTGTTACTCAG
                                      ttttgttt  CT-rich tract
                                     attttgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtacctgtcgagtgccgtcgtcttacctatttgttttgcaagtaatcagggagtatcgatcgctgaacataatgtagcccttttgccccccaaatgtgtcatgtcgttccatgattttgtttggattgcagGTGTCGCTGGGGGTGCATCTTCAGGTAAAAGTACTGTATGCAAGATGATAATTGATCAGCTACGTGATCAGCGTGTGGTTGTTGTTACTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT