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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTAGAATTGTCATTGGCCTTTATGGAGATGTTGTGCCAAAAACAGTTGgtaatcttacgcccattcttttcttcatcatatttatttacaaacttgagattaatcctttggagacagtggcatagcagattgtggaattcttatgttt...

Basic information

species Oryza sativa
transcript LOC_Os09g36670.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g36670.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G158237_T01 (Zea mays), 5'ss of exon 3
GTAGAATTGTCATTGGCCTTTATGGAGATGTTGTGCCAAAAACAGTTGgtaatcttacgcccattcttttcttc-atcatatttatttacaaactt-gagattaatcctttggagacagtggcatagcagattgtggaattcttatgttt-
|||||||||| ||||| || ||||| || || || |||||||||||||||| ||||| |||| || ||| | ||| || |||| | || || || |||| || | | ||| | ||| | | ||
GTAGAATTGTTATTGGTCTCTATGGGGAGGTCGTTCCAAAAACAGTTGgtattcttattatacttctctttttccagcatgttcttttattgattttgattttcgaagtttgtgtactc---ctttgcacgcctggtgcttcctgcgcttc
















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|44665422|gb|CR278856.1|CR278856
EST:     GTCGAATTGTCATTGGCCTT-ATGGAGATGTTGTGCCAAAAACAGTTG                         CAAATTTTAGGGCTCTTTGTACAG
genomic: GTAGAATTGTCATTGGCCTTTATGGAGATGTTGTGCCAAAAACAGTTGgtaatcttac ... cattttgcagCAAATTTTAGGGCTCTTTGTACAG
EST: gi|88570043|gb|CI661218.1|CI661218
EST:     GTAGAATTGTCATTGGCCTTTATGGAGATGTTGTGCCACAAACAGTTG                         CAAATTTTAGGGCTCTTTGTACAG
genomic: GTAGAATTGTCATTGGCCTTTATGGAGATGTTGTGCCAAAAACAGTTGgtaatcttac ... cattttgcagCAAATTTTAGGGCTCTTTGTACAG
EST: gi|88328504|gb|CI676714.1|CI676714
EST:     GTAGAATTGTCATTGGCCTTTATGGAGATGTTGTGCCAAAAACAGTTG                         CAAATTTTAGGGCTCTTTGTACAG
genomic: GTAGAATTGTCATTGGCCTTTATGGAGATGTTGTGCCAAAAACAGTTGgtaatcttac ... cattttgcagCAAATTTTAGGGCTCTTTGTACAG
EST: gi|88580780|gb|CI697732.1|CI697732
EST:     GTAGAATTGTCATTGGCCTTTATGGAGATGTNGTGCCAAAAACAGTTG                         CAAATTTTAGGGCTCTTTGTACAG
genomic: GTAGAATTGTCATTGGCCTTTATGGAGATGTTGTGCCAAAAACAGTTGgtaatcttac ... cattttgcagCAAATTTTAGGGCTCTTTGTACAG
EST: gi|58597588|gb|CK008116.1|CK008116
EST:     GTAGAATTGTCATTGGCCTTTATGGAGATGTTGTGCCAAAAACAGTTG                         CAAATTTTAGGG
genomic: GTAGAATTGTCATTGGCCTTTATGGAGATGTTGTGCCAAAAACAGTTGgtaatcttac ... cattttgcagCAAATTTTAGGG
EST: gi|58601241|gb|CK011769.1|CK011769
EST:     GTAGAATTGTCATTGGCCTTTATGGAGATGTTGTGCCAAAAACAGTTG                         CAAATTTTAGGGCTCTTTGTACAG
genomic: GTAGAATTGTCATTGGCCTTTATGGAGATGTTGTGCCAAAAACAGTTGgtaatcttac ... cattttgcagCAAATTTTAGGGCTCTTTGTACAG
EST: gi|87005928|gb|CI289345.1|CI289345
EST:     GTAGAATTGTCATTGGCCTTTATGGAGATGTTGTGCCAAAAACAGTTG                         CAAATTTTAGGGCTCTTTGTACAG
genomic: GTAGAATTGTCATTGGCCTTTATGGAGATGTTGTGCCAAAAACAGTTGgtaatcttac ... cattttgcagCAAATTTTAGGGCTCTTTGTACAG
EST: gi|88419577|gb|CI686794.1|CI686794
EST:     GTAGAATTGTCATTGGCCTTTATGGAGATGTTGTGCCAAAAACAGTTG                         CAAATTTTAGGGCTCTTTGTACAGGAGAAG
genomic: GTAGAATTGTCATTGGCCTTTATGGAGATGTTGTGCCAAAAACAGTTGgtaatcttac ... cattttgcagCAAATTTTAGGGCTCTTTGTACAGGAGAAG
EST: gi|88307256|gb|CI641892.1|CI641892
EST:     GTAGAATTGTCATTGGCCTTTATGGAGATGTTGTGCCACAAACAGTGG                         CCAATTTTAGGGCTCTTTGTACAG
genomic: GTAGAATTGTCATTGGCCTTTATGGAGATGTTGTGCCAAAAACAGTTGgtaatcttac ... cattttgcagCAAATTTTAGGGCTCTTTGTACAG
EST: gi|88580485|gb|CI697419.1|CI697419
EST:     GTAGAATTGTCATTGGCCTTTATGGAGATGTTGTGCCAAAAACAGTTG                         CAAATTTTAGGGCTCTTTGTACAG
genomic: GTAGAATTGTCATTGGCCTTTATGGAGATGTTGTGCCAAAAACAGTTGgtaatcttac ... cattttgcagCAAATTTTAGGGCTCTTTGTACAG
EST: gi|88581910|gb|CI699127.1|CI699127
EST:     GTAGAATTGTCATTGGCCTTTATGGAGATGTTGTGCCAAAAACAGTTG                         CAAATTTTAGGGCTCTTTGTACAG
genomic: GTAGAATTGTCATTGGCCTTTATGGAGATGTTGTGCCAAAAACAGTTGgtaatcttac ... cattttgcagCAAATTTTAGGGCTCTTTGTACAG
EST: gi|88335390|gb|CI650355.1|CI650355
EST:     GTAGAATTGTCATTGGCCTTTATGGAGATGTTGTGCCAAAAACAGTTG                         CAAATTTTAGGGCTCTTTGTACAG
genomic: GTAGAATTGTCATTGGCCTTTATGGAGATGTTGTGCCAAAAACAGTTGgtaatcttac ... cattttgcagCAAATTTTAGGGCTCTTTGTACAG
EST: gi|58691487|gb|CK080174.1|CK080174
EST:     GTAGAATTGTCATTGGCCTTTATGGAGATGTTGTGCCAAAAACAGTTG                         CAAATTTTAGGGCTCTTTGTACAG
genomic: GTAGAATTGTCATTGGCCTTTATGGAGATGTTGTGCCAAAAACAGTTGgtaatcttac ... cattttgcagCAAATTTTAGGGCTCTTTGTACAG

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: 48 (upstream exon), 24 (downstream exon)
Score: 10

GTAGAATTGTCATTGGCCTTTATGGAGATGTTGTGCCAAAAACAGTTGgtaatcttac ... cattttgcagCAAATTTTAGGGCTCTTTGTACAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTAGAATTGTCATTGGCCTTTATGGAGATGTTGTGCCAAAAACAGTTGgtaatcttacgcccattcttttcttcatcatatttatttacaaacttgagattaatcctttggagacagtggcatagcagattgtggaattcttatgttt

- - - - - - - - - - - TGGAGA
- - - - - - - - - - - GGAGAT
- - - - - - - - - - - - GAGATG