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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactacccacttcacttgctcctccttcaattcaattattactcctatttacgaaagcctgcactaccagGTATCCAATGACCCACAAGGAAGAAATATTCTCAAGGAGCTGCAAGATGATGGGGTCGACACCTCTCATATCCTG

Basic information

species Oryza sativa
transcript LOC_Os08g45180.1
intron # 2
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|58691834|gb|CK080521.1|CK080521
EST:     CCTTGACCGCCGCTGCTCGTTTGGGCCTTCGCCCAAGGATCATATCCAAG                         GTATCCAATGACCCACAAGGAAGAAATATTCTCAAGGAGCTGCAAGATGAT
genomic: CCTTGACCGCCGCTGCTCGTTTGGGCCTTCGCCCAAGGATCATATCCAAGgtactaccca ... gcactaccagGTATCCAATGACCCACAAGGAAGAAATATTCTCAAGGAGCTGCAAGATGAT
EST: gi|29659991|gb|CB656266.1|CB656266
EST:     CCTTGACCGCCGCTGCTCGTTTGGGCCTTCGCCCAAGGATCATATCCAAG                         GTATCCAATGACCCACAAGGAAGAAATATTCTCAAGGAGCTGCAAGATGAT
genomic: CCTTGACCGCCGCTGCTCGTTTGGGCCTTCGCCCAAGGATCATATCCAAGgtactaccca ... gcactaccagGTATCCAATGACCCACAAGGAAGAAATATTCTCAAGGAGCTGCAAGATGAT
EST: gi|88406865|gb|CI578393.1|CI578393
EST:     CCTTGACCGCCGCTGCTCGTTTGGGCCTTCGCCCAAGGATCATATCCAAG                         GTATCCAATGACCCACAAGGAAGAAATATTCTCAAGGAGCTGCAAGATGAT
genomic: CCTTGACCGCCGCTGCTCGTTTGGGCCTTCGCCCAAGGATCATATCCAAGgtactaccca ... gcactaccagGTATCCAATGACCCACAAGGAAGAAATATTCTCAAGGAGCTGCAAGATGAT
EST: gi|58674585|gb|CK063272.1|CK063272
EST:     CCTTGACCGCCGCTGCTCGTTTGGGCCTTCGCCCAAGGATCATATCCAAG                         GTATCCAATGACCCACAAGGAAGAAATATTCTCAAGGAGCTGCAAGATGAT
genomic: CCTTGACCGCCGCTGCTCGTTTGGGCCTTCGCCCAAGGATCATATCCAAGgtactaccca ... gcactaccagGTATCCAATGACCCACAAGGAAGAAATATTCTCAAGGAGCTGCAAGATGAT
EST: gi|88410251|gb|CI575849.1|CI575849
EST:     CCTTGACCGCCGCTGCTCGTTTGGGCCTTCGCCCAAGGATCATATCCAAG                         GTATCCAATGACCCACAAGGAAGAAATATTCTCAAGGAGCTGCAAGATGAT
genomic: CCTTGACCGCCGCTGCTCGTTTGGGCCTTCGCCCAAGGATCATATCCAAGgtactaccca ... gcactaccagGTATCCAATGACCCACAAGGAAGAAATATTCTCAAGGAGCTGCAAGATGAT
EST: gi|88403626|gb|CI575510.1|CI575510
EST:     CCTTGACCGCCGCTGCTCGTTTGGGCCTTCGCCCAAGGATCATATCCAAG                         GTATCCAATGACCCACAAGGAAGAAATATTCTCAAGGAGCTGCAAGATGAT
genomic: CCTTGACCGCCGCTGCTCGTTTGGGCCTTCGCCCAAGGATCATATCCAAGgtactaccca ... gcactaccagGTATCCAATGACCCACAAGGAAGAAATATTCTCAAGGAGCTGCAAGATGAT
EST: gi|88423490|gb|CI579202.1|CI579202
EST:     CCTTGACCGCCGCTGCTCGTTTGGGCCTTCGCCCAAGGATCATATCCAAG                         GTATCCAATGACCCACAAGGAAGAAATATTCTCAAGGAGCTGGAAGATGAT
genomic: CCTTGACCGCCGCTGCTCGTTTGGGCCTTCGCCCAAGGATCATATCCAAGgtactaccca ... gcactaccagGTATCCAATGACCCACAAGGAAGAAATATTCTCAAGGAGCTGCAAGATGAT
EST: gi|88447757|gb|CI579833.1|CI579833
EST:     CCTTGACCGCCGCTGCTCGTTTGGGCCTTCGCCCAAGGATCATATCCAAG                         GTATCCAATGACCCACAAGGAAGAAATATTCTCAAGGAGCTGCAAGATGAT
genomic: CCTTGACCGCCGCTGCTCGTTTGGGCCTTCGCCCAAGGATCATATCCAAGgtactaccca ... gcactaccagGTATCCAATGACCCACAAGGAAGAAATATTCTCAAGGAGCTGCAAGATGAT
EST: gi|29672289|gb|CB668564.1|CB668564
EST:     CCTTGACCGCCGCTGCTCGTTTGGGCCTTCGCCCAAGGATCATATCCAAG                         GTATCCAATGACCCACAAGGAAGAAATATTCTCAAGGAGCTGCAAGATGAT
genomic: CCTTGACCGCCGCTGCTCGTTTGGGCCTTCGCCCAAGGATCATATCCAAGgtactaccca ... gcactaccagGTATCCAATGACCCACAAGGAAGAAATATTCTCAAGGAGCTGCAAGATGAT
EST: gi|88409812|gb|CI571069.1|CI571069
EST:     CCTTGACCGCCGCTGCTCGTTTGGGCCTTCGCCCAAGGATCATATCCAAG                         GTATCCAATGACCCACAAGGAAGAAATATTCTCAAGGAGCTGCAAGATGAT
genomic: CCTTGACCGCCGCTGCTCGTTTGGGCCTTCGCCCAAGGATCATATCCAAGgtactaccca ... gcactaccagGTATCCAATGACCCACAAGGAAGAAATATTCTCAAGGAGCTGCAAGATGAT
EST: gi|88729957|gb|CI753572.1|CI753572
EST:     CCTTGACCGCCGCTGCTCGTTTGGGCCTTCGCCCAAGGATCATATCCAAG                         GTATCCAATGACCCACAAGGAAGAAATATTCTCAAGGAGCTGCAAGATGAT
genomic: CCTTGACCGCCGCTGCTCGTTTGGGCCTTCGCCCAAGGATCATATCCAAGgtactaccca ... gcactaccagGTATCCAATGACCCACAAGGAAGAAATATTCTCAAGGAGCTGCAAGATGAT
EST: gi|88422711|gb|CI573873.1|CI573873
EST:     CCTTGACCGCCGCTGCTCGTTTGGGCCTTCGCCCAAGGATCATATCCAAG                         GTATCCAATGACCCACAAGGAAGAAATATTCTCAAGGAGCTGCAAGATGAT
genomic: CCTTGACCGCCGCTGCTCGTTTGGGCCTTCGCCCAAGGATCATATCCAAGgtactaccca ... gcactaccagGTATCCAATGACCCACAAGGAAGAAATATTCTCAAGGAGCTGCAAGATGAT
EST: gi|58690473|gb|CK079160.1|CK079160
EST:     CCTTGACCGCCGCTGCTCGTTTGGGCCTTCGCCCAAGGATCATATCCAAG                         GTATCCAATGACCCACAAGGAAGAAATATTCTCAAGGAGCTGCAAGATGAT
genomic: CCTTGACCGCCGCTGCTCGTTTGGGCCTTCGCCCAAGGATCATATCCAAGgtactaccca ... gcactaccagGTATCCAATGACCCACAAGGAAGAAATATTCTCAAGGAGCTGCAAGATGAT
EST: gi|87023595|gb|CI286346.1|CI286346
EST:     CCTTGACCGCCGCTGCTCGTTTGGGCCTTCGCCCAAGGATCATATCCAAG                         GTATCCAATGACCCACAAGGAAGAAATATTCTCAAGGAGCTGCAAGATGAT
genomic: CCTTGACCGCCGCTGCTCGTTTGGGCCTTCGCCCAAGGATCATATCCAAGgtactaccca ... gcactaccagGTATCCAATGACCCACAAGGAAGAAATATTCTCAAGGAGCTGCAAGATGAT
EST: gi|58611246|gb|CK038958.1|CK038958
EST:     CCTTGACCGCCGCTGCTCGTTTGGGCCTTCGCCCAAGGATCATATCCAAG                         GTATCCAATGACCCACAAGGAAGAAATATTCTCAAGGAGCTGCAAGATGAT
genomic: CCTTGACCGCCGCTGCTCGTTTGGGCCTTCGCCCAAGGATCATATCCAAGgtactaccca ... gcactaccagGTATCCAATGACCCACAAGGAAGAAATATTCTCAAGGAGCTGCAAGATGAT
EST: gi|29656464|gb|CB652739.1|CB652739
EST:     CCTTGACCGCCGCTGCTCGTTTGGGCCTTCGCCCAAGGATCATATCCAAG                         GTATCCAATGACCCACAAGGAAGAAATATTCTCAAGGAGCTGCAAGATGAT
genomic: CCTTGACCGCCGCTGCTCGTTTGGGCCTTCGCCCAAGGATCATATCCAAGgtactaccca ... gcactaccagGTATCCAATGACCCACAAGGAAGAAATATTCTCAAGGAGCTGCAAGATGAT
EST: gi|29664341|gb|CB660616.1|CB660616
EST:     CCTTGACCGCCGCTGCTCGTTTGGGCCTTCGCCCAAGGATCATATCCAAG                         GTATCCAATGACCCACAAGGAAGAAATATTCTCAAGGAGCTGCAAGATGAT
genomic: CCTTGACCGCCGCTGCTCGTTTGGGCCTTCGCCCAAGGATCATATCCAAGgtactaccca ... gcactaccagGTATCCAATGACCCACAAGGAAGAAATATTCTCAAGGAGCTGCAAGATGAT
EST: gi|88413351|gb|CI581366.1|CI581366
EST:     CCTTGACCGCCGCTACTCGTTTGGGCCTTCGCCCAAGGATCATATCCAAG                         GTATCCAATGACCCACAAGGAAGAAATATTCTCAAGGAGCTGCAAGATGAT
genomic: CCTTGACCGCCGCTGCTCGTTTGGGCCTTCGCCCAAGGATCATATCCAAGgtactaccca ... gcactaccagGTATCCAATGACCCACAAGGAAGAAATATTCTCAAGGAGCTGCAAGATGAT

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: 58 (upstream exon), 72 (downstream exon)
Score: 6

GATCCGAAGCCTAACGCTCAAGGTCCAGGGAGGCGGCAACACTGGCAATGCCTTGACCGCCGCTGCTCGTTTGGGCCTTCGCCCAAGGATCATATCCAAGgtactaccca ... gcactaccagGTATCCAATGACCCACAAGGAAGAAATATTCTCAAGGAGCTGCAAGATGATGGGGTCGACACCTCTCATATCCTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgctcctccttcaattcaattattactcctatttacgaaagcctgcactaccagGTATCCAATGACCCACAAGGAAGAAATATTCTCAAGGAGCTGCAAGATGATGGGGTCGACACCTCTCATATCCTG
          ttcaattcaattatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactacccacttcacttgctcctccttcaattcaattattactcctatttacgaaagcctgcactaccagGTATCCAATGACCCACAAGGAAGAAATATTCTCAAGGAGCTGCAAGATGATGGGGTCGACACCTCTCATATCCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG