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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttaatgactttaattgagaaatgatgttcttgaatatttgccgctttgtacctatgtttgacctgtcatgtgttactgacactctgctgttgttgtgcagGAAGCGCCTGTTTGGTATGATTAATGATCTTCCCACGATTTTTGAAGTTGTTAGTGGGAAGAGTAAAGCCAAGCCACCGAGTGCTAATAACCACAGCAAT

Basic information

species Oryza sativa
transcript LOC_Os07g41740.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g41740.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G038066_T02 (Zea mays), 3'ss of exon 4
ttaatgactttaatt---gagaaatgatgttcttga-atatttgccgctttgtacctatgtttgacctgtcatgtgttactgacactctgctgttgttgtgcagGAAGCGCCTGTTTGGTATGATTAATGATCTTCCCACGATTTTTGAAGTTGTTAGTGGGAAGAGTAAAGCCAAGCCACCGAGTGCTAATAACCA-CAGCAAT
 || |||| |   ||   || ||    | ||  ||   | |||  |  ||||||||  |||||| |     |||  | ||| | |||   |||||||| |||||||||||||| |   || ||||| |||||||||||| |  ||||||| ||||||||||||||||| || ||||| |||| ||  | |  || ||  || || 
-tagtgacatatcttcaagaaaaccattatttctggcgtttttctcagtttgtaccactgtttggc--agtatggttcactaa-acttacctgttgttatgcagGAAGCGCCTCTACAGTTTGATTGATGATCTTCCCATGGCTTTTGAAATTGTTAGTGGGAAGAGTGAAACCAAGGCACC-AGCACCACCAAGCAGTAGTAAC
















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|66916026|gb|CX102874.1|CX102874
EST:     TCTGTTGCATTTTACTTTGGTGCTCGGTTCGGATTTGATAAAAATGACAG                         GAAGCGCCTGTTTGGTATGATTAATGATCTTCCCACGATTTTTGAAGTTGT
genomic: TCTGTTGCATTTTACTTTGGTGCTCGGTTCGGATTTGATAAAAATGACAGgtatctcatc ... tgttgtgcagGAAGCGCCTGTTTGGTATGATTAATGATCTTCCCACGATTTTTGAAGTTGT
EST: gi|58673430|gb|CK062116.1|CK062116
EST:     TCTGTTGCATTTTACTTTGGTGCTCGGTTCGGATTTGATAAAAATGACAG                         GAAGCGCCTGTTTGGTATGATTAATGATCTTCCCACGATTTTTGAAG
genomic: TCTGTTGCATTTTACTTTGGTGCTCGGTTCGGATTTGATAAAAATGACAGgtatctcatc ... tgttgtgcagGAAGCGCCTGTTTGGTATGATTAATGATCTTCCCACGATTTTTGAAG
EST: gi|58593299|gb|CF991607.1|CF991607
EST:     TCTGTTGCATTTTACTTTGGTGCTCGGTTCGGATTTGATAAAAATGACAG                         GAAGCGCCTGTTTGGTATGATTAATGATCTTCCCACGATTTTTGAAGTTGT
genomic: TCTGTTGCATTTTACTTTGGTGCTCGGTTCGGATTTGATAAAAATGACAGgtatctcatc ... tgttgtgcagGAAGCGCCTGTTTGGTATGATTAATGATCTTCCCACGATTTTTGAAGTTGT
EST: gi|58679144|gb|CK067831.1|CK067831
EST:     TCTGTTGCATTTTACTTTGGTGCTCGGTTCGGATTTGATAAAAATGACAG                         GAAGCGCCTGTTTGGTATGATTAATG
genomic: TCTGTTGCATTTTACTTTGGTGCTCGGTTCGGATTTGATAAAAATGACAGgtatctcatc ... tgttgtgcagGAAGCGCCTGTTTGGTATGATTAATG
EST: gi|58681410|gb|CK070097.1|CK070097
EST:     TCTGTTGCATTTTACTTTGGTGCTCGGTTCGGATTTGATAAAAATGACAG                         GAAGCGCCTGTTTGGTATGATTAATGATCTTCCCACGATTTTTGAAGTTGT
genomic: TCTGTTGCATTTTACTTTGGTGCTCGGTTCGGATTTGATAAAAATGACAGgtatctcatc ... tgttgtgcagGAAGCGCCTGTTTGGTATGATTAATGATCTTCCCACGATTTTTGAAGTTGT
EST: gi|58653321|gb|CK042001.1|CK042001
EST:     TCTGTTGCATTTTACTTTGGTGCTCGGTTCGGATTTGATAAAAATGACAG                         GAAGCGCCTGTTTGGTATGATTAATGATCTTCCCACGATTTTTGAAGTTGT
genomic: TCTGTTGCATTTTACTTTGGTGCTCGGTTCGGATTTGATAAAAATGACAGgtatctcatc ... tgttgtgcagGAAGCGCCTGTTTGGTATGATTAATGATCTTCCCACGATTTTTGAAGTTGT
EST: gi|38479958|gb|CF964047.1|CF964047
EST:     TCTGTTGCATTTTACTTTGGTGCTCGGTTCGGATTTGATAAAAATGACAG                         GAAGCGCCTGTTTGGTATGATTAATGATCTTCCCACGATTTTTGAAGTTGT
genomic: TCTGTTGCATTTTACTTTGGTGCTCGGTTCGGATTTGATAAAAATGACAGgtatctcatc ... tgttgtgcagGAAGCGCCTGTTTGGTATGATTAATGATCTTCCCACGATTTTTGAAGTTGT
EST: gi|58657324|gb|CK046004.1|CK046004
EST:     TCTGTTGCATTTTACTTTGGTGCTCGGTTCGGATTTGATAAAAATGACAG                         GAAGCGCCTGTTTGGTATGATTAATGATCTTCCCACGATTTTTGAAGTTGT
genomic: TCTGTTGCATTTTACTTTGGTGCTCGGTTCGGATTTGATAAAAATGACAGgtatctcatc ... tgttgtgcagGAAGCGCCTGTTTGGTATGATTAATGATCTTCCCACGATTTTTGAAGTTGT
EST: gi|58600404|gb|CK010932.1|CK010932
EST:     TCTGTTGCATTTTACTTTGGTGCTCGGTTCGGATTTGATAAAAATGACAG                         GAAGCGCCTGTTTGGTATGATTAATGATCTTCCCACGATTTTTGAAGTTGT
genomic: TCTGTTGCATTTTACTTTGGTGCTCGGTTCGGATTTGATAAAAATGACAGgtatctcatc ... tgttgtgcagGAAGCGCCTGTTTGGTATGATTAATGATCTTCCCACGATTTTTGAAGTTGT
EST: gi|58682916|gb|CK071603.1|CK071603
EST:     TCTGTTGCATTTTACTTTGGTGCTCGGTTCGGATTTGATAAAAATGACAG                         GAAGCGCCTGTTTGGTATGATTAATGATCTTCCCACGATTTTTGAAGTTGT
genomic: TCTGTTGCATTTTACTTTGGTGCTCGGTTCGGATTTGATAAAAATGACAGgtatctcatc ... tgttgtgcagGAAGCGCCTGTTTGGTATGATTAATGATCTTCCCACGATTTTTGAAGTTGT
EST: gi|58683778|gb|CK072465.1|CK072465
EST:     TCTGTTGCATTTTACTTTGGTGCTCGGTTCGGATTTGATAAAAATGACAG                         GAAGCGCCTGTTTGGTATGATTAATGATCTTCCCACGATTTTTGAAGTTGT
genomic: TCTGTTGCATTTTACTTTGGTGCTCGGTTCGGATTTGATAAAAATGACAGgtatctcatc ... tgttgtgcagGAAGCGCCTGTTTGGTATGATTAATGATCTTCCCACGATTTTTGAAGTTGT

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: 72 (upstream exon), 73 (downstream exon)
Score: 28

AAAAAGATTGGCTGTCCATGGTTGCAGTGCACAGTGATGCATGGTTACTTTCTGTTGCATTTTACTTTGGTGCTCGGTTCGGATTTGATAAAAATGACAGgtatctcatc ... tgttgtgcagGAAGCGCCTGTTTGGTATGATTAATGATCTTCCCACGATTTTTGAAGTTGTTAGTGGGAAGAGTAAAGCCAAGCCACCGAGTGCTAATAACCACAGCAAT




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtacctatgtttgacctgtcatgtgttactgacactctgctgttgttgtgcagGAAGCGCCTGTTTGGTATGATTAATGATCTTCCCACGATTTTTGAAGTTGTTAGTGGGAAGAGTAAAGCCAAGCCACCGAGTGCTAATAACCACAGCAAT
                            tactgac  putative branch site (score: 28)
       tatgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttaatgactttaattgagaaatgatgttcttgaatatttgccgctttgtacctatgtttgacctgtcatgtgttactgacactctgctgttgttgtgcagGAAGCGCCTGTTTGGTATGATTAATGATCTTCCCACGATTTTTGAAGTTGTTAGTGGGAAGAGTAAAGCCAAGCCACCGAGTGCTAATAACCACAGCAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - atgatgt
- - - - - - - - - - - - - -tcttgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - tgtttga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgtgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgacac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tctgctg