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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAACTACTGGGCCTCAAGAATCAGAAGGATGAACACTTCTCCAATCTCATTATGGAGCAGAAGGACACACTAAAGAGTCGTGCTGACCACTTGATAAAGgttaccttctcataacattctgaatgatacttccaattaagctttcattcacaattctgatccctttggaagtaagatcaacggcagggcttaaaatatg...

Basic information

species Oryza sativa
transcript LOC_Os05g01470.1
intron # 11
splice site 5'
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|88236169|gb|CI235371.1|CI235371
EST:     TCGTGCTGACCACTTGATAAAG                         ACACTTGAGGGCTGTGGCTGGGATGTTGCTGGCAGTCATGGTGGCATATCG
genomic: TCGTGCTGACCACTTGATAAAGgttaccttct ... ctatgaacagACACTTGAGGGCTGTGGCTGGGATGTTGCTGGCAGTCATGGTGGCATATCG
EST: gi|25807221|gb|CA763182.1|CA763182
EST:     TGGAGCAGCAGGGCCTCCCTATAGGGGTCGTGCTGTCCACCTTGATAAAG                         ACACCTGAGGGCTGTGGTTGGGATGTTGCTGGCAGTCATGGTGGCATATCG
genomic: TGGAGCAG-AAGGACACACTA-AAGAGTCGTGCTGACCA-CTTGATAAAGgttaccttct ... ctatgaacagACACTTGAGGGCTGTGGCTGGGATGTTGCTGGCAGTCATGGTGGCATATCG
EST: gi|29624031|gb|CB629042.1|CB629042
EST:     TTATGGAGCAGAAGGACACACTAAAGAGTCGTGCTGACCACTTGATAAAG                         ACACTTGAGGGCTGTGGCTGGGATGTTGCTGGCAGTCATGGTGGCATATCG
genomic: TTATGGAGCAGAAGGACACACTAAAGAGTCGTGCTGACCACTTGATAAAGgttaccttct ... ctatgaacagACACTTGAGGGCTGTGGCTGGGATGTTGCTGGCAGTCATGGTGGCATATCG
EST: gi|87036975|gb|CI191597.1|CI191597
EST:     TTATGGAGCAGAAGGACACATTAAAGAGTCGTGCTGACCACTTGATAAAG                         ACACTTGAGGGCTGTGGCTGGGATGTTGCTGGCAGTCATGGTGGCATATCG
genomic: TTATGGAGCAGAAGGACACACTAAAGAGTCGTGCTGACCACTTGATAAAGgttaccttct ... ctatgaacagACACTTGAGGGCTGTGGCTGGGATGTTGCTGGCAGTCATGGTGGCATATCG
EST: gi|86437307|gb|CI119029.1|CI119029
EST:     TTATGGAGCAGAAGGACACACTAAAGAGTCGTGCTGACCACTTGATAAAG                         ACACTTGAGGTCTGTGTCTGGGATGTTGCTGGCAGTCATGGTGGCATATCG
genomic: TTATGGAGCAGAAGGACACACTAAAGAGTCGTGCTGACCACTTGATAAAGgttaccttct ... ctatgaacagACACTTGAGGGCTGTGGCTGGGATGTTGCTGGCAGTCATGGTGGCATATCG
EST: gi|4715443|gb|AU056560.1|AU056560
EST:     CACTAAAGAGTCGTGCTGACCACTTGATAAAG                         CCACTTGAGGGCTGTGGCTGGGATGTTGCTGGCAGTCATGGTGNCATATCG
genomic: CACTAAAGAGTCGTGCTGACCACTTGATAAAGgttaccttct ... ctatgaacagACACTTGAGGGCTGTGGCTGGGATGTTGCTGGCAGTCATGGTGGCATATCG
EST: gi|29627786|gb|CB632797.1|CB632797
EST:     TTATGGAGCAGAAGGACACACTAAAGAGTCGTGCTGACCACTTGATAAAG                         ACACTTGAGGGCTGTGGCTGGGATGTTGCTGGCAGTCATGGTGGCATATCG
genomic: TTATGGAGCAGAAGGACACACTAAAGAGTCGTGCTGACCACTTGATAAAGgttaccttct ... ctatgaacagACACTTGAGGGCTGTGGCTGGGATGTTGCTGGCAGTCATGGTGGCATATCG
EST: gi|29688962|gb|CB685237.1|CB685237
EST:     TTATGGAGCAGAAGGACACACTAAAGAGTCGTGCTGACCACTTGATAAAG                         ACACTTGAGGGCTGTGGCTGGGATGTTGCTGGCAGTCATGGTGGCATATCG
genomic: TTATGGAGCAGAAGGACACACTAAAGAGTCGTGCTGACCACTTGATAAAGgttaccttct ... ctatgaacagACACTTGAGGGCTGTGGCTGGGATGTTGCTGGCAGTCATGGTGGCATATCG
EST: gi|87042024|gb|CI194648.1|CI194648
EST:     TTATGGAGCAGAAGGACACACTAAAGAGTCGTGCTGACCACTTGATAAAG                         ACACTTGAGGGCTGTGGCTGGGATGTTGCTGGCAGTCATGGTGGCATATCG
genomic: TTATGGAGCAGAAGGACACACTAAAGAGTCGTGCTGACCACTTGATAAAGgttaccttct ... ctatgaacagACACTTGAGGGCTGTGGCTGGGATGTTGCTGGCAGTCATGGTGGCATATCG
EST: gi|87036972|gb|CI191594.1|CI191594
EST:     TTATGGAGCAGAAGGACACACTAAAGAGTCGTGCTGACCACTTGATAAAG                         ACACTTGAGGGCTGTGGCTGGGATGTTGCTGGCAGTCATGGTGGCATATCG
genomic: TTATGGAGCAGAAGGACACACTAAAGAGTCGTGCTGACCACTTGATAAAGgttaccttct ... ctatgaacagACACTTGAGGGCTGTGGCTGGGATGTTGCTGGCAGTCATGGTGGCATATCG
EST: gi|29630291|gb|CB635300.1|CB635300
EST:     TTATGGAGCAGAAGGACACACTAAAGAGTCGTGCTGACCACTTGATAAAG                         ACACTTGAGGGCTGTGGCTGGGATGTTGCTGGCAGTCATGGTGGCATATCG
genomic: TTATGGAGCAGAAGGACACACTAAAGAGTCGTGCTGACCACTTGATAAAGgttaccttct ... ctatgaacagACACTTGAGGGCTGTGGCTGGGATGTTGCTGGCAGTCATGGTGGCATATCG
EST: gi|87036168|gb|CI190642.1|CI190642
EST:     TTATGGAGCAGAAGGACACACTAAAGAGTCGTGCTGACCACTTGATAAAA                         ACACTTGAGGGCTGTGGCTGGGATGTTGCTGGCAGTCATGGTGGCATATCG
genomic: TTATGGAGCAGAAGGACACACTAAAGAGTCGTGCTGACCACTTGATAAAGgttaccttct ... ctatgaacagACACTTGAGGGCTGTGGCTGGGATGTTGCTGGCAGTCATGGTGGCATATCG
EST: gi|86479496|gb|CI122129.1|CI122129
EST:     TTATGGAGCAGAAGGACACACTAAAGAGTCGTGCTGACCACTTGATAAAG                         ACACTTGAGGGCTGTGGCTGGGATGTTGCTGCCAGTCATGGTGGCATATCG
genomic: TTATGGAGCAGAAGGACACACTAAAGAGTCGTGCTGACCACTTGATAAAGgttaccttct ... ctatgaacagACACTTGAGGGCTGTGGCTGGGATGTTGCTGGCAGTCATGGTGGCATATCG
EST: gi|22305551|gb|BQ906773.1|BQ906773
EST:     TATGGAGCAGAAGGACACACTAAAGA-TCGTGCTGACCACTTGATAANAG                         ACACTTGAGGGCTGTGGCTGGGATGTTGCTGGCAGTCATGGTGGCATATC
genomic: TATGGAGCAGAAGGACACACTAAAGAGTCGTGCTGACCACTTGATAA-AGgttaccttct ... ctatgaacagACACTTGAGGGCTGTGGCTGGGATGTTGCTGGCAGTCATGGTGGCATATC
EST: gi|29688961|gb|CB685236.1|CB685236
EST:     TTATGGAGCAGAAGGACACACTAAAGAGTCGTGCTGACCACTTGATAAAG                         ACACTTGAGGGCTGTGGCTGGGATGTTGCTGGCAGTCATGGTGGCATATCG
genomic: TTATGGAGCAGAAGGACACACTAAAGAGTCGTGCTGACCACTTGATAAAGgttaccttct ... ctatgaacagACACTTGAGGGCTGTGGCTGGGATGTTGCTGGCAGTCATGGTGGCATATCG
EST: gi|86519901|gb|CI160107.1|CI160107
EST:     TTATGGAGCAGAAGGACACACTAAAGAGTCGTGCTGACCACTTGATAAAG                         ACACTTGAGGGCTGTGGCTGGGATGTTGCTGCCAGTCATGGTGGCATATCG
genomic: TTATGGAGCAGAAGGACACACTAAAGAGTCGTGCTGACCACTTGATAAAGgttaccttct ... ctatgaacagACACTTGAGGGCTGTGGCTGGGATGTTGCTGGCAGTCATGGTGGCATATCG
EST: gi|29620990|gb|CB626001.1|CB626001
EST:     TTATGGAGCAGAAGGACACACTAAAGAGTCGTGCTGACCACTTGATAAAG                         ACACTTGAGGGCTGTGGCTGGGATGTTGCTGGCAGTCATGGTGGCATATCG
genomic: TTATGGAGCAGAAGGACACACTAAAGAGTCGTGCTGACCACTTGATAAAGgttaccttct ... ctatgaacagACACTTGAGGGCTGTGGCTGGGATGTTGCTGGCAGTCATGGTGGCATATCG
EST: gi|27578356|gb|CB001051.1|CB001051
EST:     TTATGGAGCAGAAGGACACACTAAAGAGTCGTGCTGACCACTTGATAAAG                         ACACTTGAGGGCTGTGGCTGGGATGTTGCTGGCAGTCATGGTGGCATATCG
genomic: TTATGGAGCAGAAGGACACACTAAAGAGTCGTGCTGACCACTTGATAAAGgttaccttct ... ctatgaacagACACTTGAGGGCTGTGGCTGGGATGTTGCTGGCAGTCATGGTGGCATATCG
EST: gi|27577198|gb|CA999892.1|CA999892
EST:     TTATGGAGCAGAAGGACACACTANAGAGTCGTGCTGACCACTTGATAAAG                         ACACTTGAGGGCTGTGGCTGGGATGTTGCTGGCAGTCATGGTGGCATATCG
genomic: TTATGGAGCAGAAGGACACACTAAAGAGTCGTGCTGACCACTTGATAAAGgttaccttct ... ctatgaacagACACTTGAGGGCTGTGGCTGGGATGTTGCTGGCAGTCATGGTGGCATATCG

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: 66 (upstream exon), 68 (downstream exon)
Score: 20

AAAACTACTGGGCCTCAAGAATCAGAAGGATGAACACTTCTCCAATCTCATTATGGAGCAGAAGGACACACTAAAGAGTCGTGCTGACCACTTGATAAAGgttaccttct ... ctatgaacagACACTTGAGGGCTGTGGCTGGGATGTTGCTGGCAGTCATGGTGGCATATCGATGCTGGCGAAACCGACTGCCTACATCGGCAAAATAATCAAGGTGGATG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAAACTACTGGGCCTCAAGAATCAGAAGGATGAACACTTCTCCAATCTCATTATGGAGCAGAAGGACACACTAAAGAGTCGTGCTGACCACTTGATAAAGgttaccttctcataacattctgaatgatacttccaattaagctttcattcacaattctgatccctttggaagtaagatcaacggcagggcttaaaatatg

- - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggcaggg