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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgctatttgaggttttaagtagtaccagcggtacttaaaatctttcacatttatgattgcaatattacttttctatgttcttatgctcaatttttttcagGCCGCAGATATATTGTCCAAAGAAGGAATCAGTGCTGAG

Basic information

species Oryza sativa
transcript LOC_Os09g33500.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g33500.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G128121_T01 (Zea mays), 3'ss of exon 4
tgctatttgaggttttaagtagtaccagcggtacttaaaatctttcacattt-atgattgcaa--tattacttttctatgttcttatgctcaatttttttcagGCCGCAGATATATTGTCCAAAGAAGGAATCAGTGCTGAG
   |    || | ||| |||||| |    |  ||||       || |  ||| || || |     | ||| |||  |   |||| ||||| | |||  ||||||| ||||| ||| ||||||| ||||||||||||||||||
---tgacagatggttttagtagtgctcatgtcacttgtctgtcttaatttttcatcatagtgggctgttattttggtgcattctcatgctaagtttgcttcagGCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG

upper sequence: LOC_Os09g33500.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G097226_T01 (Zea mays), 3'ss of exon 10
tgctatttgaggttttaagtagtacc-agcggtacttaaaatctttcacatttatgattgcaatattacttttctatgttcttatgctcaattt-ttttcagGCCGCAGATATATTGTCCAAAGAAGGAATCAGTGCTGAG
 | |    || | ||| ||||||||  |  |  || |    || ||     | || | ||   | ||| ||| ||   |||| ||||| | ||| | ||||||| ||||| ||| ||||||| ||||||||||||||||||
-ggtgaaagatggttttagtagtacttaatgtcacctctcttcatttttcgtcat-agtgggctgttattttgctgcattctcatgcttagtttgtcttcagGCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG
















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|86600093|gb|CI258433.1|CI258433
EST:     AAGATGTTACAATTACTGCATACTCCAAGATGGTTGGATATGCTCTTCAG                         GCCGCAGATATATTGTCCAAAGAAGGAATCAGTGCTGAG
genomic: AAGATGTTACAATTACTGCATACTCCAAGATGGTTGGATATGCTCTTCAGgtgcgtcatt ... tttttttcagGCCGCAGATATATTGTCCAAAGAAGGAATCAGTGCTGAG
EST: gi|88241310|gb|CI241159.1|CI241159
EST:     ACTGCATACTCCAAGATGGTTGGATATGCTCTTCAG                         GCCGCAGATATATTGTCCAAAGAAGGAATCAGTGCTGAG
genomic: ACTGCATACTCCAAGATGGTTGGATATGCTCTTCAGgtgcgtcatt ... tttttttcagGCCGCAGATATATTGTCCAAAGAAGGAATCAGTGCTGAG
EST: gi|87032949|gb|CI187573.1|CI187573
EST:     AAGATGTTACAATTACTGCATACTCCAAGATGGTTGGATATGCTCTTCAG                         GCCGCAGATATATTGTCCAAAGAAGGAATCAGTGCTGAG
genomic: AAGATGTTACAATTACTGCATACTCCAAGATGGTTGGATATGCTCTTCAGgtgcgtcatt ... tttttttcagGCCGCAGATATATTGTCCAAAGAAGGAATCAGTGCTGAG
EST: gi|88219808|gb|CI219368.1|CI219368
EST:     AAGATGTTACAATTACTGCATACTCCAAGATGGTTGGATATGCTCTTCAG                         GCCGCAGATATATTGTCCAAAGAAGGAATCAGTGCTGAG
genomic: AAGATGTTACAATTACTGCATACTCCAAGATGGTTGGATATGCTCTTCAGgtgcgtcatt ... tttttttcagGCCGCAGATATATTGTCCAAAGAAGGAATCAGTGCTGAG
EST: gi|86494245|gb|CI136878.1|CI136878
EST:     AAGATGTTACAATTACTGCATACTCCAAGATGGTTGGATATGCTCTTCAG                         GCCGCAGATATATTGTCCAAAGAAGGAATCAGTGCTGAG
genomic: AAGATGTTACAATTACTGCATACTCCAAGATGGTTGGATATGCTCTTCAGgtgcgtcatt ... tttttttcagGCCGCAGATATATTGTCCAAAGAAGGAATCAGTGCTGAG
EST: gi|29637529|gb|CB642538.1|CB642538
EST:     AAGATGTTACAATTACTGCATACTCCAAGATGGTTGGATATGCTCTTCAG                         GCCGCAGATATATTGTCCAAAGAAGGAATCAGTGCTGAG
genomic: AAGATGTTACAATTACTGCATACTCCAAGATGGTTGGATATGCTCTTCAGgtgcgtcatt ... tttttttcagGCCGCAGATATATTGTCCAAAGAAGGAATCAGTGCTGAG
EST: gi|33800162|gb|CF325945.1|CF325945
EST:     AAGATGTTACAATTACTGCATACTCCAAGATGGTTGGATATGCTCTTCAG                         GCCGCAGATATATTGTCCAAAGAAGGAATCAGTGCTGAG
genomic: AAGATGTTACAATTACTGCATACTCCAAGATGGTTGGATATGCTCTTCAGgtgcgtcatt ... tttttttcagGCCGCAGATATATTGTCCAAAGAAGGAATCAGTGCTGAG
EST: gi|2796459|gb|AA749753.1|AA749753
EST:     AAGATGTTACAATTACTGCATACTCCAAGATGGTTGGATATGCTCTTCAG                         GCCGCAGATATATTGTCCAAAGAAGGAATCAGTGCTGAG
genomic: AAGATGTTACAATTACTGCATACTCCAAGATGGTTGGATATGCTCTTCAGgtgcgtcatt ... tttttttcagGCCGCAGATATATTGTCCAAAGAAGGAATCAGTGCTGAG
EST: gi|33380822|gb|CF196165.1|CF196165
EST:     AAGATGTTACAATTACTGCATACTCCAAGATGGTTGGATATGCTCTTCNN                         NCCGCAGATATATTGTCCAAAGNNNNAATCAGTGCTGNN
genomic: AAGATGTTACAATTACTGCATACTCCAAGATGGTTGGATATGCTCTTCAGgtgcgtcatt ... tttttttcagGCCGCAGATATATTGTCCAAAGAAGGAATCAGTGCTGAG
EST: gi|86844834|gb|CI338720.1|CI338720
EST:     ACTCCAAGATGGTTGGATATGCTCTTCAG                         GCCGCAGATATATTGTCCAAATAAGGAATCAGGGCTGAG
genomic: ACTCCAAGATGGTTGGATATGCTCTTCAGgtgcgtcatt ... tttttttcagGCCGCAGATATATTGTCCAAAGAAGGAATCAGTGCTGAG
EST: gi|86542747|gb|CI182953.1|CI182953
EST:     AAGATGTTACAATTACTGCATACTCCAAGATGGTTGGATATGCTCTTCAG                         GCCGCAGATATATTGTCCAAAGAAGGAATCAGTGCTGAG
genomic: AAGATGTTACAATTACTGCATACTCCAAGATGGTTGGATATGCTCTTCAGgtgcgtcatt ... tttttttcagGCCGCAGATATATTGTCCAAAGAAGGAATCAGTGCTGAG
EST: gi|157649975|gb|EX449609.1|EX449609
EST:     AAGATGTTACAATTACTGCATACTCCAAGATGGTTGGATATGCTCTTCAG                         GCCGCAGATATATTGTCCAAAGAAGGAATCAGTGCTGAG
genomic: AAGATGTTACAATTACTGCATACTCCAAGATGGTTGGATATGCTCTTCAGgtgcgtcatt ... tttttttcagGCCGCAGATATATTGTCCAAAGAAGGAATCAGTGCTGAG
EST: gi|87022122|gb|CI259194.1|CI259194
EST:     AAGATGTTACAATTACTGCATACTCCAAGATGGTTGAATATGCTCTTCAG                         GCCGCAGATATATTGTCCAAAGAAGGAATCAGTGCTGAG
genomic: AAGATGTTACAATTACTGCATACTCCAAGATGGTTGGATATGCTCTTCAGgtgcgtcatt ... tttttttcagGCCGCAGATATATTGTCCAAAGAAGGAATCAGTGCTGAG
EST: gi|88828484|gb|CI073354.1|CI073354
EST:     AAGATGTTACAATTACTGCATACTCCAAGATGGTTGGATATGCTCTTCAG                         GCCGCAGATATATTGTCCAAAGAAGGAATCAGTGCTGAG
genomic: AAGATGTTACAATTACTGCATACTCCAAGATGGTTGGATATGCTCTTCAGgtgcgtcatt ... tttttttcagGCCGCAGATATATTGTCCAAAGAAGGAATCAGTGCTGAG
EST: gi|2312022|gb|C28177.1|C28177
EST:     AAGATGTTACAATTACTGCATACTCCAAGATGGTTGGATATGCTCTTCAG                         GCCGCAGATATATTGTCCAAAGAAGGAATCAGTGCTGAG
genomic: AAGATGTTACAATTACTGCATACTCCAAGATGGTTGGATATGCTCTTCAGgtgcgtcatt ... tttttttcagGCCGCAGATATATTGTCCAAAGAAGGAATCAGTGCTGAG
EST: gi|29645720|gb|CB650727.1|CB650727
EST:     AAGATGTTACAATTACTGCATACTCCAAGATGGTTGGATATGCTCTTCAG                         GCCGCAGATATATTGTCCAAAGAAGGAATCAGTGCTGAG
genomic: AAGATGTTACAATTACTGCATACTCCAAGATGGTTGGATATGCTCTTCAGgtgcgtcatt ... tttttttcagGCCGCAGATATATTGTCCAAAGAAGGAATCAGTGCTGAG
EST: gi|89169219|gb|CI038726.1|CI038726
EST:     AAGATGTTACAATTACTGCATACTCCAAGATGGTTGGATATGCTCTTCAG                         GCCGCAGATATATTGTCCAAAGAAGGAATCAGTGCTGAG
genomic: AAGATGTTACAATTACTGCATACTCCAAGATGGTTGGATATGCTCTTCAGgtgcgtcatt ... tttttttcagGCCGCAGATATATTGTCCAAAGAAGGAATCAGTGCTGAG
EST: gi|87034409|gb|CI189033.1|CI189033
EST:     AAGATGTTACAATTACTGCATACTCCAAGATGGTTGGATATGCTCTTCAG                         GCCGCAGATATATTGTCCAAAGAAGGAATCAGTGCTGAG
genomic: AAGATGTTACAATTACTGCATACTCCAAGATGGTTGGATATGCTCTTCAGgtgcgtcatt ... tttttttcagGCCGCAGATATATTGTCCAAAGAAGGAATCAGTGCTGAG
EST: gi|33666828|gb|CF297795.1|CF297795
EST:     AAGATGTTACAATTACTGCATACTCCAAGATGGTTGGATATGCTCTTCAG                         GCCGCAGATATATTGTCCAAAGAAGGAATCAGTGCTGAG
genomic: AAGATGTTACAATTACTGCATACTCCAAGATGGTTGGATATGCTCTTCAGgtgcgtcatt ... tttttttcagGCCGCAGATATATTGTCCAAAGAAGGAATCAGTGCTGAG
EST: gi|29657623|gb|CB653898.1|CB653898
EST:     AAGATGTTACAATTACTGCATACTCCAAGATGGTTGGATATGCTCTTCAG                         GCCGCAGATATATTGTCCAAAGAAGGAATCAGTGCTGAG
genomic: AAGATGTTACAATTACTGCATACTCCAAGATGGTTGGATATGCTCTTCAGgtgcgtcatt ... tttttttcagGCCGCAGATATATTGTCCAAAGAAGGAATCAGTGCTGAG
EST: gi|86497317|gb|CI139950.1|CI139950
EST:     AGATGTTACAATTACTGCATACTCCCAAGATGGTTGGATATGCTCTTCAG                         GCCGCAGATATATTGTCCAAAGAAGGAATCAGTGCTGAG
genomic: AGATGTTACAATTACTGCATACT-CCAAGATGGTTGGATATGCTCTTCAGgtgcgtcatt ... tttttttcagGCCGCAGATATATTGTCCAAAGAAGGAATCAGTGCTGAG

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: 66 (upstream exon), 39 (downstream exon)
Score: 104

ATAGAGCGTGAGGGTAAAGATGTTACAATTACTGCATACTCCAAGATGGTTGGATATGCTCTTCAGgtgcgtcatt ... tttttttcagGCCGCAGATATATTGTCCAAAGAAGGAATCAGTGCTGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacatttatgattgcaatattacttttctatgttcttatgctcaatttttttcagGCCGCAGATATATTGTCCAAAGAAGGAATCAGTGCTGAG
                                             tttttttc  CT-rich tract
               aatattacttttctat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgctatttgaggttttaagtagtaccagcggtacttaaaatctttcacatttatgattgcaatattacttttctatgttcttatgctcaatttttttcagGCCGCAGATATATTGTCCAAAGAAGGAATCAGTGCTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
tgctatt
- - - - - - - - - - - taccagc
- - - - - - - - - - - - - - - - - - - - - - - - - - -tgattgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgctcaa