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

GATGAGGGTGTCAACATAACTGCAAATTCTCTTCATCCTGGATCTATCATCACGAACCTTCTTCGTCACCACAGTATCCTAGATGgtaaaatatacttgaattgaactctaggagatatttagtattcctgcttttgtaagctaaagggatctttcactcatgaactcaaaataattgaactgaa...

Basic information

species Oryza sativa
transcript LOC_Os09g39670.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g39670.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G009940_T02 (Zea mays), 5'ss of exon 6
GATGAGGGTGTCAACATAACTGCAAATTCTCTTCATCCTGGATCTATCATCACGAACCTTCTTCGTCACCACAGTATCCTAGATGgtaaaatatacttgaattgaactctaggagatatttagtattcctgcttttgtaagctaaagggatctttcactcatgaactcaaaataattgaactgaa---
|| ||   ||||||||||||||||||||||||||||||||| || || |||||||||||||||||  ||||||||||||||||||||||  |||| |||  |    || |     | |||||    ||||| | || ||| ||||| ||    ||  ||  |  | |  || | | ||||||      
GAAGATAATGTCAACATAACTGCAAATTCTCTTCATCCTGGTTCCATTATCACGAACCTTCTTCGCTACCACAGTATCCTAGATGgtaag-tataattg--tcattctttccacaacatttacctctcctggtcttataaactaaaagggaaattggctagtttaatagaacttactgaactatgtta
















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|14192202|gb|AU184413.1|AU184413
EST:     CTATCATCACGAACCTTCTTCGTCACCACAGTATCCTAGATG                         TTCTCCATCGGACACTTGGTAAATTGGTGCTTAAAAATGCTCAGCAG
genomic: CTATCATCACGAACCTTCTTCGTCACCACAGTATCCTAGATGgtaaaatata ... ttatatgcagTTCTCCATCGGACACTTGGTAAATTGGTGCTTAAAAATGCTCAGCAG
EST: gi|86828431|gb|CI278560.1|CI278560
EST:     TCCTGGATCTATCATCACGAACCTTCTTCGTCACCACAGTATCCTAGATG                         TTCTCCATCGGACACTTGGTAAATTGGTGCTTAAAAATGCTCAGCAG
genomic: TCCTGGATCTATCATCACGAACCTTCTTCGTCACCACAGTATCCTAGATGgtaaaatata ... ttatatgcagTTCTCCATCGGACACTTGGTAAATTGGTGCTTAAAAATGCTCAGCAG
EST: gi|88972231|gb|CI018674.1|CI018674
EST:     TCCTGGATCTATCATCACGAACCTTCTTCGTCACCACAGTATCCTAGATG                         TTCTCCATCGGACACTTGGTAAATTGGTGCTTAAAAATGCTCAGCAG
genomic: TCCTGGATCTATCATCACGAACCTTCTTCGTCACCACAGTATCCTAGATGgtaaaatata ... ttatatgcagTTCTCCATCGGACACTTGGTAAATTGGTGCTTAAAAATGCTCAGCAG
EST: gi|88977035|gb|CI024772.1|CI024772
EST:     TCCTGGATCTATCATCACGAACCTTCTTCGTCACCACAGTATCCTAGATG                         TTCTCCATCGGACACTTGGTAAATTGGTGCTTAAAAATGCTCAGCAG
genomic: TCCTGGATCTATCATCACGAACCTTCTTCGTCACCACAGTATCCTAGATGgtaaaatata ... ttatatgcagTTCTCCATCGGACACTTGGTAAATTGGTGCTTAAAAATGCTCAGCAG
EST: gi|88206217|gb|CI206066.1|CI206066
EST:     TCCTGGATCTATCATCACGAACCTTCTTCGTCACCACAGTATCCTAGACG                         TTCTCCATCGGACACTTGGTAAATTGGTGCTTAGAAATGCTCAGCAG
genomic: TCCTGGATCTATCATCACGAACCTTCTTCGTCACCACAGTATCCTAGATGgtaaaatata ... ttatatgcagTTCTCCATCGGACACTTGGTAAATTGGTGCTTAAAAATGCTCAGCAG
EST: gi|88206151|gb|CI206000.1|CI206000
EST:     TCCTGGATCTATCATCACGAACCTTCTTCGTCACCACAGTATCCTAGATG                         TTCTCCATCGGACACTTGGTAAATTGGTGCTTAAAAATGCTCAGCAG
genomic: TCCTGGATCTATCATCACGAACCTTCTTCGTCACCACAGTATCCTAGATGgtaaaatata ... ttatatgcagTTCTCCATCGGACACTTGGTAAATTGGTGCTTAAAAATGCTCAGCAG
EST: gi|12623120|gb|AU173333.1|AU173333
EST:     ATCTATCATCACGAACCTTCTTCGTCACCNCAGTATCCTAGATG                         TTCTCCATCGGACACTTGGTAAATTGGTGCTTAAAAATGCTCAGCAG
genomic: ATCTATCATCACGAACCTTCTTCGTCACCACAGTATCCTAGATGgtaaaatata ... ttatatgcagTTCTCCATCGGACACTTGGTAAATTGGTGCTTAAAAATGCTCAGCAG
EST: gi|58677683|gb|CK066370.1|CK066370
EST:     TCCTGGATCTATCATCACGAACCTTCTTCGTCACCACAGTATCCTAGATG                         TTCTCCATCGAACACTTGGTAAATTGGTGCTTAAAAATGCTCAGCAG
genomic: TCCTGGATCTATCATCACGAACCTTCTTCGTCACCACAGTATCCTAGATGgtaaaatata ... ttatatgcagTTCTCCATCGGACACTTGGTAAATTGGTGCTTAAAAATGCTCAGCAG
EST: gi|5003515|gb|AU068664.1|AU068664
EST:     TCCTGGATCTATCATCACGAACCTTCTTCGTCACCACAGTATCCTAGATG                         TTCTCCATCGGACACTTGGTAAATTGGTGCTTAAAAATGCTCAGCAG
genomic: TCCTGGATCTATCATCACGAACCTTCTTCGTCACCACAGTATCCTAGATGgtaaaatata ... ttatatgcagTTCTCCATCGGACACTTGGTAAATTGGTGCTTAAAAATGCTCAGCAG
EST: gi|88204335|gb|CI204184.1|CI204184
EST:     TCCTGGATCTATCATCACGTACCTTTTTCGTCACCACAGTATCCTAGATG                         TTCTCCATCGGACACTTGGTAAATTGGTGCTTAAAAATGCTCAGCAG
genomic: TCCTGGATCTATCATCACGAACCTTCTTCGTCACCACAGTATCCTAGATGgtaaaatata ... ttatatgcagTTCTCCATCGGACACTTGGTAAATTGGTGCTTAAAAATGCTCAGCAG
EST: gi|5002903|gb|AU068012.1|AU068012
EST:     TCCTGGATCTATCATCACGAACCTTCTTCGTCACCACAGTATCCTAGATG                         TTCTCCATCGGACACTTGGTAAATTGGTGCTTAAAAATGCTCAGCAG
genomic: TCCTGGATCTATCATCACGAACCTTCTTCGTCACCACAGTATCCTAGATGgtaaaatata ... ttatatgcagTTCTCCATCGGACACTTGGTAAATTGGTGCTTAAAAATGCTCAGCAG
EST: gi|88202309|gb|CI201171.1|CI201171
EST:     TCCTGGATCTATCATCACGAACCTTCTTCGTCACCACAGTATCCTAGATG                         TTCTCCATCGGACACTTGGTAAATTGGTGCTTAAAAATGCTCAGCAG
genomic: TCCTGGATCTATCATCACGAACCTTCTTCGTCACCACAGTATCCTAGATGgtaaaatata ... ttatatgcagTTCTCCATCGGACACTTGGTAAATTGGTGCTTAAAAATGCTCAGCAG

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: 70 (upstream exon), 47 (downstream exon)
Score: 56

GATGAGGGTGTCAACATAACTGCAAATTCTCTTCATCCTGGATCTATCATCACGAACCTTCTTCGTCACCACAGTATCCTAGATGgtaaaatata ... ttatatgcagTTCTCCATCGGACACTTGGTAAATTGGTGCTTAAAAATGCTCAGCAG




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATGAGGGTGTCAACATAACTGCAAATTCTCTTCATCCTGGATCTATCATCACGAACCTTCTTCGTCACCACAGTATCCTAGATGgtaaaatatacttgaattgaactctaggagatatttagtattcctgcttttgtaagctaaagggatctttcactcatgaactcaaaataattgaactgaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaataa