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

gtaaaaaattataaaaacctacccggatttgttgttcagatatcaatcatcaccgtagttttttgcttaattaaaatggcctaaaatgttatcattctactttctttcaaccagGTTACATTGGGAATATCTACACTTTTGATGTATGTTCCTACTTCCTTGGGCTCAGCTCATCAAGCTGGGGCATTGACACTACTGTCACTGATGATCCTTC

Basic information

species Oryza sativa
transcript LOC_Os08g38720.1
intron # 6
splice site 3'
intron type U2

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|88849143|gb|CI087665.1|CI087665
EST:     CAGCAATCAAGTCTCTTATCGGAAGCACGCTTGGAATGGCTGCCCTTCAG                         GTTACATTGGGAATATCTACACTTTTGATGTATGTTCCTACTTCCTTGGGC
genomic: CAGCAATCAAGTCTCTTATCGGAAGCACGCTTGGAATGGCTGCCCTTCAGgtaaaaaatt ... tttcaaccagGTTACATTGGGAATATCTACACTTTTGATGTATGTTCCTACTTCCTTGGGC
EST: gi|88834383|gb|CI077666.1|CI077666
EST:     CAGCAATCAAGTCTCTTATCGGAAGCACGCTTGGAATGGCTGCCCTTCAG                         GTTACATTGGGAANATCTACACTTTTGATGTATGTTCCTACTTCCTTGGGC
genomic: CAGCAATCAAGTCTCTTATCGGAAGCACGCTTGGAATGGCTGCCCTTCAGgtaaaaaatt ... tttcaaccagGTTACATTGGGAATATCTACACTTTTGATGTATGTTCCTACTTCCTTGGGC
EST: gi|24468693|gb|CA305642.1|CA305642
EST:     CAGCAATCAAGTCTCTTATCGGAAGCACGCTTGGAATGGCTGCCCTTCAG                         GTTACATTGGGAATATCTACACTTTTGATGTATGTTCCTACTTCCTTGGGC
genomic: CAGCAATCAAGTCTCTTATCGGAAGCACGCTTGGAATGGCTGCCCTTCAGgtaaaaaatt ... tttcaaccagGTTACATTGGGAATATCTACACTTTTGATGTATGTTCCTACTTCCTTGGGC
EST: gi|86498969|gb|CI141602.1|CI141602
EST:     CAGCAATCAAGTCTCTTATCGGAAGCACGCTTGGAATGGCTGCCCTTCAG                         GTTACATTGGGAATATCTACACTTTTGATGTATGTTCCTACTTCCTTGGGC
genomic: CAGCAATCAAGTCTCTTATCGGAAGCACGCTTGGAATGGCTGCCCTTCAGgtaaaaaatt ... tttcaaccagGTTACATTGGGAATATCTACACTTTTGATGTATGTTCCTACTTCCTTGGGC
EST: gi|88225939|gb|CI225855.1|CI225855
EST:     CAGCAATCAAGTCTCTTATCGGAAGCACGCTTGGAATGGCTGCCCTTCAG                         GTTACATTGGGAATATCTACACTTTTGATGTATGTTCCTACTTCCTTGGGC
genomic: CAGCAATCAAGTCTCTTATCGGAAGCACGCTTGGAATGGCTGCCCTTCAGgtaaaaaatt ... tttcaaccagGTTACATTGGGAATATCTACACTTTTGATGTATGTTCCTACTTCCTTGGGC
EST: gi|86492395|gb|CI135028.1|CI135028
EST:     GGAAGCACGCTTGGAATGGCTGCCCTTCAG                         GTTACATTGGGAATATCTACACTTTTGATGTATGTTCCTACTTCCTTGGGC
genomic: GGAAGCACGCTTGGAATGGCTGCCCTTCAGgtaaaaaatt ... tttcaaccagGTTACATTGGGAATATCTACACTTTTGATGTATGTTCCTACTTCCTTGGGC
EST: gi|86412924|gb|CI067329.1|CI067329
EST:     GAAGCACGCTTGGAATGGCTGCCCTTCAG                         GTTACATTGGGAATATCTACACTTTTGATGTATGTTCCTACTTCCTTGGGC
genomic: GAAGCACGCTTGGAATGGCTGCCCTTCAGgtaaaaaatt ... tttcaaccagGTTACATTGGGAATATCTACACTTTTGATGTATGTTCCTACTTCCTTGGGC
EST: gi|86502600|gb|CI145233.1|CI145233
EST:     CAGCAATCAAGTCTCTTATCGGAAGCACGCTTGGAATGGCTGCCCTTCAG                         GTTACATTGGGAATATCTACACTTTTGATGTATGTTCCTACTTCCTTGGGC
genomic: CAGCAATCAAGTCTCTTATCGGAAGCACGCTTGGAATGGCTGCCCTTCAGgtaaaaaatt ... tttcaaccagGTTACATTGGGAATATCTACACTTTTGATGTATGTTCCTACTTCCTTGGGC
EST: gi|86496261|gb|CI138894.1|CI138894
EST:     CAGCAATCAAGTCTCTTATCGGAAGCACGCTTGGAATGGCTGCCCTTCAG                         GTTACATTGGGAATATCTACACTTTTGATGTATGTTCCTACTTCCTTGGGC
genomic: CAGCAATCAAGTCTCTTATCGGAAGCACGCTTGGAATGGCTGCCCTTCAGgtaaaaaatt ... tttcaaccagGTTACATTGGGAATATCTACACTTTTGATGTATGTTCCTACTTCCTTGGGC
EST: gi|88467522|gb|CI537164.1|CI537164
EST:     TCTCTTATCGGAAGCACGCTTGGAATGGCTGCCCTTCAG                         GTTACATTGGGAATATCTACACTTTTGATGTATNTTCCTACTTCCTTGGGC
genomic: TCTCTTATCGGAAGCACGCTTGGAATGGCTGCCCTTCAGgtaaaaaatt ... tttcaaccagGTTACATTGGGAATATCTACACTTTTGATGTATGTTCCTACTTCCTTGGGC
EST: gi|89173888|gb|CI041781.1|CI041781
EST:     AGTCTCTTATCGGAAGCACGCTTGGAATGCCTGCCCTTCAG                         GTTACATTGGGAATATCTACACTTTTGATGTATGTTCCTACTTCCTTGGGC
genomic: AGTCTCTTATCGGAAGCACGCTTGGAATGGCTGCCCTTCAGgtaaaaaatt ... tttcaaccagGTTACATTGGGAATATCTACACTTTTGATGTATGTTCCTACTTCCTTGGGC
EST: gi|86503382|gb|CI146015.1|CI146015
EST:     CAGCAATCAAGTCTCTTATCGGAAGCACGCTTGGAATGGCTGCCCTTCAG                         GTTACATTGGGAATATCTACACTTTTGATGTATGTTCCTACTTCCTTGGGC
genomic: CAGCAATCAAGTCTCTTATCGGAAGCACGCTTGGAATGGCTGCCCTTCAGgtaaaaaatt ... tttcaaccagGTTACATTGGGAATATCTACACTTTTGATGTATGTTCCTACTTCCTTGGGC
EST: gi|89173616|gb|CI041509.1|CI041509
EST:     CAGCAATCAAGTCTCTTATCGGAAGCACGCTTGGAATGGCTGCCCTTCAG                         GTTACATTGGGAATATCTACACTTTTGATGTATGTTCCTACTTCCTTGGGC
genomic: CAGCAATCAAGTCTCTTATCGGAAGCACGCTTGGAATGGCTGCCCTTCAGgtaaaaaatt ... tttcaaccagGTTACATTGGGAATATCTACACTTTTGATGTATGTTCCTACTTCCTTGGGC

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: 64 (upstream exon), 71 (downstream exon)
Score: 7

ATTGTCTGTGGGTGGCTTATGGTTGGCTGCAAGGAAAGTGGACATGCATCCAGCAATCAAGTCTCTTATCGGAAGCACGCTTGGAATGGCTGCCCTTCAGgtaaaaaatt ... tttcaaccagGTTACATTGGGAATATCTACACTTTTGATGTATGTTCCTACTTCCTTGGGCTCAGCTCATCAAGCTGGGGCATTGACACTACTGTCACTGATGATCCTTC




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttgcttaattaaaatggcctaaaatgttatcattctactttctttcaaccagGTTACATTGGGAATATCTACACTTTTGATGTATGTTCCTACTTCCTTGGGCTCAGCTCATCAAGCTGGGGCATTGACACTACTGTCACTGATGATCCTTC
                   gcctaaa  putative branch site (score: 7)
                                tcattctactttcttt  putative PPT
                      taaaatgttatcatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaaaattataaaaacctacccggatttgttgttcagatatcaatcatcaccgtagttttttgcttaattaaaatggcctaaaatgttatcattctactttctttcaaccagGTTACATTGGGAATATCTACACTTTTGATGTATGTTCCTACTTCCTTGGGCTCAGCTCATCAAGCTGGGGCATTGACACTACTGTCACTGATGATCCTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG