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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acaagcattcggccatagagaccacttatgttttcaccgcggttcatgtttacaatgcctgtagtacgcttacctctggttttgtgtttgaatgccgcagTCTCTTGAGCTGTGGGACATGTCGGAGAACAGAACGATGACGCTCGCAGCTCATGACAGCCTCATCACAGCCCTGGCGTCGTCAAGCTCCGGTTTGGTCG

Basic information

species Oryza sativa
transcript LOC_Os01g08190.1
intron # 17
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|88960225|gb|CI382103.1|CI382103
EST:     CTTCATATTCATCTATGCTTATCATTGGTTGTTACCAG                         TCTCTTGAGCTGT-GGACATGTCGGAGAGCAGAACGATGACGCTCGCAGCT
genomic: CTTCATATTCATCTATGCTTATCATTGGTTGTTACCAGgcaagtactt ... aatgccgcagTCTCTTGAGCTGTGGGACATGTCGGAGAACAGAACGATGACGCTCGCAGCT
EST: gi|58662863|gb|CK051549.1|CK051549
EST:     GTGCTTTCCACCCTTCATATTCATCTATGCTTATCATTGGTTGTTACCAG                         TCTCTTGAGCTGTGGGACATGTCGGAGAAC
genomic: GTGCTTTCCACCCTTCATATTCATCTATGCTTATCATTGGTTGTTACCAGgcaagtactt ... aatgccgcagTCTCTTGAGCTGTGGGACATGTCGGAGAAC
EST: gi|88259915|gb|CI363125.1|CI363125
EST:     TTGGTTGTTACCAG                         TCTCTTGAGCTGTTGGACATGTCGGAGAACAGAACGATGACGCTCGCAGCT
genomic: TTGGTTGTTACCAGgcaagtactt ... aatgccgcagTCTCTTGAGCTGTGGGACATGTCGGAGAACAGAACGATGACGCTCGCAGCT
EST: gi|89185317|gb|CI051051.1|CI051051
EST:     GTGCTTTCCACCCTTCATATTCATCTATGCTTATCATTGGTTGTTACCAG                         TCTCTTGAGCTGTGGGACATGTCGGAGAACAGAACGATGACGCTCGCAGCT
genomic: GTGCTTTCCACCCTTCATATTCATCTATGCTTATCATTGGTTGTTACCAGgcaagtactt ... aatgccgcagTCTCTTGAGCTGTGGGACATGTCGGAGAACAGAACGATGACGCTCGCAGCT
EST: gi|25804243|gb|CA760204.1|CA760204
EST:     GTGCTTTCCACCCTTCATATTCATCTATGCTTATCATTGGTTGTTACCAG                         TCTCTTGAGCTGTGGGACATGTCGGAGAACAGAACGATGACGCTCGCAGCT
genomic: GTGCTTTCCACCCTTCATATTCATCTATGCTTATCATTGGTTGTTACCAGgcaagtactt ... aatgccgcagTCTCTTGAGCTGTGGGACATGTCGGAGAACAGAACGATGACGCTCGCAGCT
EST: gi|86482202|gb|CI124835.1|CI124835
EST:     GTGCTTTCCACCCTTCATATTCATCTATGCTTATCATTGGTTGTTACCAG                         TCTCTTGAGCTGTGGGACATGTCGGAGAACAGAACGATGACGCTCGCAGCT
genomic: GTGCTTTCCACCCTTCATATTCATCTATGCTTATCATTGGTTGTTACCAGgcaagtactt ... aatgccgcagTCTCTTGAGCTGTGGGACATGTCGGAGAACAGAACGATGACGCTCGCAGCT
EST: gi|86478759|gb|CI121392.1|CI121392
EST:     GTGCTTTCCACCCTTCATATTCATCTATGCTTATCATTGGTTGTTACCAG                         TCTCTTGAGCTGTGGGACATGTCGGAGAACAGAACGATGACGCTCGCAGCT
genomic: GTGCTTTCCACCCTTCATATTCATCTATGCTTATCATTGGTTGTTACCAGgcaagtactt ... aatgccgcagTCTCTTGAGCTGTGGGACATGTCGGAGAACAGAACGATGACGCTCGCAGCT
EST: gi|87029813|gb|CI274494.1|CI274494
EST:     ATTGGTTGTTACCAG                         TCTCTTGAGCTGTGGAACATGTCGGAGAACAGAACGATGACGCTCGCAGCT
genomic: ATTGGTTGTTACCAGgcaagtactt ... aatgccgcagTCTCTTGAGCTGTGGGACATGTCGGAGAACAGAACGATGACGCTCGCAGCT
EST: gi|66913391|gb|CX100239.1|CX100239
EST:     GTGCTTTCCACCCTTCATATTCATCTATGCTTATCATTGGTTGTTACCAG                         TCTCTTGAGCTGTGGGACATGTCGGAGAACAGAACGATGACGCTCGCAGCT
genomic: GTGCTTTCCACCCTTCATATTCATCTATGCTTATCATTGGTTGTTACCAGgcaagtactt ... aatgccgcagTCTCTTGAGCTGTGGGACATGTCGGAGAACAGAACGATGACGCTCGCAGCT
EST: gi|58680898|gb|CK069585.1|CK069585
EST:     GTGCTTTCCACCCTTCATATTCATCTATGCTTATCATTGGTTGTTACCAG                         TCTCTTGAGCTGTGGGACATGTCGGAGAACAGAACGATGACGCTCGCAGCT
genomic: GTGCTTTCCACCCTTCATATTCATCTATGCTTATCATTGGTTGTTACCAGgcaagtactt ... aatgccgcagTCTCTTGAGCTGTGGGACATGTCGGAGAACAGAACGATGACGCTCGCAGCT

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), 48 (downstream exon)
Score: 2

TGATCGCTGCGTGCAAGAGCTTAGCTGTACCGGGAGCAAGTTTCACTCGTGTGCTTTCCACCCTTCATATTCATCTATGCTTATCATTGGTTGTTACCAGgcaagtactt ... aatgccgcagTCTCTTGAGCTGTGGGACATGTCGGAGAACAGAACGATGACGCTCGCAGCTCATGACAGCCTCATCACAGCCCTGGCGTCGTCAAGCTCCGGTTTGGTCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgtttacaatgcctgtagtacgcttacctctggttttgtgtttgaatgccgcagTCTCTTGAGCTGTGGGACATGTCGGAGAACAGAACGATGACGCTCGCAGCTCATGACAGCCTCATCACAGCCCTGGCGTCGTCAAGCTCCGGTTTGGTCG
                     cgcttac  putative branch site (score: 2)
                                         tttgaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acaagcattcggccatagagaccacttatgttttcaccgcggttcatgtttacaatgcctgtagtacgcttacctctggttttgtgtttgaatgccgcagTCTCTTGAGCTGTGGGACATGTCGGAGAACAGAACGATGACGCTCGCAGCTCATGACAGCCTCATCACAGCCCTGGCGTCGTCAAGCTCCGGTTTGGTCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- -agcattc
- - - - - - - - - - - - -ttatgtt
- - - - - - - - - - - - - - - - ttcaccg
- - - - - - - - - - - - - - - - - - - - -gttcatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - atgcctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgtgtt