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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagccattgatttttacctctcaaatgatacacaaaactaaatttctgcttgaggttcttatggcaacaccttcccttaataaacacagATCGACAGCCCATCTGCACACGGTGGGCGGGGTTTTGTTACAGGGCGAATGTTCAACCGACAAGGAGAG

Basic information

species Oryza sativa
transcript LOC_Os04g47120.1
intron # 15
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|88974436|gb|CI021977.1|CI021977
EST:     GATTTGGTTCCACAAGCCTGTGAAAGCTGATGATTGGCTTTTATATGTG                         ATCGACAGCCCATCTGCACACGGTGGGCGGGGTTTTGTTACACGGGCGAAT
genomic: GATTTGGTTCCACAAGCCTGTGAAAGCTGATGATTGGCTTTTATATGTGgtaagccatt ... ataaacacagATCGACAGCCCATCTGCACACGGTGGGCGGGGTTTTGTTACA-GGGCGAAT
EST: gi|86430173|gb|CI082596.1|CI082596
EST:     GATTTGGTTCCACAAGCCTGTGAAAGCTGATGATTGGCTTTTATATGTG                         ATCGACAGCCCATCTGCACACGGTGGGCGGGGTTTTGTTACAGGGCGAATG
genomic: GATTTGGTTCCACAAGCCTGTGAAAGCTGATGATTGGCTTTTATATGTGgtaagccatt ... ataaacacagATCGACAGCCCATCTGCACACGGTGGGCGGGGTTTTGTTACAGGGCGAATG
EST: gi|87005717|gb|CI316136.1|CI316136
EST:     GATTTGGTTCCACAAGCCTGTGAAAGCTGATGATTGGCTTTTATATGTG                         ATCGACAGCCCATCTGCACACGGTGGGCGGGGTTTTGTTACAGGGCGAATG
genomic: GATTTGGTTCCACAAGCCTGTGAAAGCTGATGATTGGCTTTTATATGTGgtaagccatt ... ataaacacagATCGACAGCCCATCTGCACACGGTGGGCGGGGTTTTGTTACAGGGCGAATG
EST: gi|163927283|gb|EG710270.1|EG710270
EST:     GATTTGGTTCCACAAGCCTGTGAAAGCTGATGATTGGCTTTTATATGTG                         ATCGACAGCCCATCTGCACAC
genomic: GATTTGGTTCCACAAGCCTGTGAAAGCTGATGATTGGCTTTTATATGTGgtaagccatt ... ataaacacagATCGACAGCCCATCTGCACAC
EST: gi|88254772|gb|CI353596.1|CI353596
EST:     GTGAAAGCTGATGATTGGCTTTTATATGTG                         ATCGACAGCCCATCTGCACACGGTGGGCGGGGTTTTGTTACAGGGCGAATG
genomic: GTGAAAGCTGATGATTGGCTTTTATATGTGgtaagccatt ... ataaacacagATCGACAGCCCATCTGCACACGGTGGGCGGGGTTTTGTTACAGGGCGAATG
EST: gi|86863469|gb|CI345210.1|CI345210
EST:     CGATTTGGTTCCACAAGCCTGTGAAAGCTGATGATTGGCTTTTATATGTG                         ATCGACAGCCCATCTGCACACGGTGGGCGGGGTTTTGTTACAGGGCGAATG
genomic: CGATTTGGTTCCACAAGCCTGTGAAAGCTGATGATTGGCTTTTATATGTGgtaagccatt ... ataaacacagATCGACAGCCCATCTGCACACGGTGGGCGGGGTTTTGTTACAGGGCGAATG
EST: gi|89177316|gb|CI250765.1|CI250765
EST:     GATTTGGTTCCACAAGCCTGTGAAAGCTGATGATTGGCTTTTATATGTG                         ATCGACAGCCCATCTGCACACGGTGGGCGGGGTTTTGTTACAGGGCGAATG
genomic: GATTTGGTTCCACAAGCCTGTGAAAGCTGATGATTGGCTTTTATATGTGgtaagccatt ... ataaacacagATCGACAGCCCATCTGCACACGGTGGGCGGGGTTTTGTTACAGGGCGAATG
EST: gi|58609050|gb|CK037083.1|CK037083
EST:     GATTTGGTTCCACAAGCCTGTGAAAGCTGATGATTGGCTTTTATATGTG                         ATCGACAGCCCATCTGCACACGGTGGGCGGGGTTTTGTTACAGGGCGAATG
genomic: GATTTGGTTCCACAAGCCTGTGAAAGCTGATGATTGGCTTTTATATGTGgtaagccatt ... ataaacacagATCGACAGCCCATCTGCACACGGTGGGCGGGGTTTTGTTACAGGGCGAATG
EST: gi|88255678|gb|CI354502.1|CI354502
EST:     GCTGATGATTGGCTTTTATATGTG                         ATCGACAGCCCATCTGCACACGGTGGGCGGGGTTTTGTTACAGGGCGAATG
genomic: GCTGATGATTGGCTTTTATATGTGgtaagccatt ... ataaacacagATCGACAGCCCATCTGCACACGGTGGGCGGGGTTTTGTTACAGGGCGAATG
EST: gi|88506400|gb|CI433906.1|CI433906
EST:     GATTTGGTTCCACAAGCCTGTGAAAGCTGATGATTGGCTTTTATATGTG                         ATCGACAGCCCATCTGCACACGGTGGGCGGGGTTTTGTTACAGGGCGAATG
genomic: GATTTGGTTCCACAAGCCTGTGAAAGCTGATGATTGGCTTTTATATGTGgtaagccatt ... ataaacacagATCGACAGCCCATCTGCACACGGTGGGCGGGGTTTTGTTACAGGGCGAATG
EST: gi|86844554|gb|CI338574.1|CI338574
EST:     CGATTTGGTTCCACAAGCCTGTGAAAGCTGATGATT-GCTTTTATATGTG                         ATCGACAGCCCATCTGCACACGGTGGGCGGGGTTTTGTTACAGGGCGAATG
genomic: CGATTTGGTTCCACAAGCCTGTGAAAGCTGATGATTGGCTTTTATATGTGgtaagccatt ... ataaacacagATCGACAGCCCATCTGCACACGGTGGGCGGGGTTTTGTTACAGGGCGAATG
EST: gi|88829709|gb|CI074579.1|CI074579
EST:     GATTTGGTTCCACAAGCCTGTGAAAGCTGATGATTGGCTTTTATATGTG                         ATCGACAGCCTATCTGCACACGGTGGGCGGGGTTTTGTTACAGGGCGAATG
genomic: GATTTGGTTCCACAAGCCTGTGAAAGCTGATGATTGGCTTTTATATGTGgtaagccatt ... ataaacacagATCGACAGCCCATCTGCACACGGTGGGCGGGGTTTTGTTACAGGGCGAATG
EST: gi|88267559|gb|CI379494.1|CI379494
EST:     TTGGCTTTTATATGTG                         ATCGACAGCCCATCTGCACACGGTGGGCGGGGTTTTGTTACAGGGCGAATG
genomic: TTGGCTTTTATATGTGgtaagccatt ... ataaacacagATCGACAGCCCATCTGCACACGGTGGGCGGGGTTTTGTTACAGGGCGAATG
EST: gi|88250752|gb|CI348982.1|CI348982
EST:     GATTTGGTTCCACAAGCCTGTGAAAGCTGATGATTGGCTTTTATATGTG                         ATCGACAGCCCATCTGCACACGGTGGGCGGGGTTTTGTTACAGGGCGAATG
genomic: GATTTGGTTCCACAAGCCTGTGAAAGCTGATGATTGGCTTTTATATGTGgtaagccatt ... ataaacacagATCGACAGCCCATCTGCACACGGTGGGCGGGGTTTTGTTACAGGGCGAATG
EST: gi|88218896|gb|CI216894.1|CI216894
EST:     GATTTGGTTCCACAAGCCTGTGAAAGCTGATGATTGGCTTTTATATGTG                         ATCGACAGCCCATCTGCACACGGTGGGCGGGGTTTTGTTACAGGGCGAATG
genomic: GATTTGGTTCCACAAGCCTGTGAAAGCTGATGATTGGCTTTTATATGTGgtaagccatt ... ataaacacagATCGACAGCCCATCTGCACACGGTGGGCGGGGTTTTGTTACAGGGCGAATG
EST: gi|87026186|gb|CI278310.1|CI278310
EST:     GATTTGGTTCCACAAGCCTGTGAAAGCTGATGATTGGCTTTTATATGTG                         ATCGACAGCCCATCTGCACACGGTGGGCGGGGTTTTGTTACAGGGCGAATG
genomic: GATTTGGTTCCACAAGCCTGTGAAAGCTGATGATTGGCTTTTATATGTGgtaagccatt ... ataaacacagATCGACAGCCCATCTGCACACGGTGGGCGGGGTTTTGTTACAGGGCGAATG
EST: gi|86429359|gb|CI076040.1|CI076040
EST:     GATTTGGTTCCACAAGCCTGTGAAAGCTGATGATTGGCTTTTATATGTG                         ATCGACAGCCCATCTGCACACGGTGGGCGGGGTTTTGTTACAGGGCGAATG
genomic: GATTTGGTTCCACAAGCCTGTGAAAGCTGATGATTGGCTTTTATATGTGgtaagccatt ... ataaacacagATCGACAGCCCATCTGCACACGGTGGGCGGGGTTTTGTTACAGGGCGAATG
EST: gi|86878942|gb|CI315384.1|CI315384
EST:     GATTTGGTTCCACAAGCCTGTGAAAGCTGATGATTGGCTTTTATATGTG                         ATCGACAGCCCATCTGCACACGGTGGGCGGGGTTTTGTTACAGGGCGAATG
genomic: GATTTGGTTCCACAAGCCTGTGAAAGCTGATGATTGGCTTTTATATGTGgtaagccatt ... ataaacacagATCGACAGCCCATCTGCACACGGTGGGCGGGGTTTTGTTACAGGGCGAATG
EST: gi|29670926|gb|CB667201.1|CB667201
EST:     GATTTGGTTCCACAAGCCTGTGAAAGCTGATGATTGGCTTTTATATGTG                         ATCGACAGCCCATCTGCACACGGTGGGCGGGGTTTTGTTACAGGGCGAATG
genomic: GATTTGGTTCCACAAGCCTGTGAAAGCTGATGATTGGCTTTTATATGTGgtaagccatt ... ataaacacagATCGACAGCCCATCTGCACACGGTGGGCGGGGTTTTGTTACAGGGCGAATG
EST: gi|86434548|gb|CI105781.1|CI105781
EST:     GATTTGGTTCCACAAGCCTGTGAAAGCTGATGGTTGGCTTTTATATGTG                         ATCGACAGCCTATCTGCACACGGTGGGCGGGGTTTTGTTACAGGGCGAATG
genomic: GATTTGGTTCCACAAGCCTGTGAAAGCTGATGATTGGCTTTTATATGTGgtaagccatt ... ataaacacagATCGACAGCCCATCTGCACACGGTGGGCGGGGTTTTGTTACAGGGCGAATG
EST: gi|88843985|gb|CI008566.1|CI008566
EST:     GATTTGGTTCCACAAGCCTGTGAAAGCTGATGATTGGCTTTTATATGTG                         ATCGACAGCCCATCTGCACACGGTGGGCGGGGTTTTGTTACAGGGCGAATG
genomic: GATTTGGTTCCACAAGCCTGTGAAAGCTGATGATTGGCTTTTATATGTGgtaagccatt ... ataaacacagATCGACAGCCCATCTGCACACGGTGGGCGGGGTTTTGTTACAGGGCGAATG
EST: gi|86487750|gb|CI130383.1|CI130383
EST:     CTGTGAAAGCTGATGATTGGCTTTAATATGTG                         ATCGACAGCCCATCTGCACACGGTGGGCGGGTTTTTGTTACAGGGCGAATG
genomic: CTGTGAAAGCTGATGATTGGCTTTTATATGTGgtaagccatt ... ataaacacagATCGACAGCCCATCTGCACACGGTGGGCGGGGTTTTGTTACAGGGCGAATG
EST: gi|33681707|gb|CF309946.1|CF309946
EST:     GATTTGGTTCCACAAGCCTGTGAAAGCTGATGATTGGCTTTTATATGTG                         ATCGACAGCCCATCTGCACACGGTGGGCGGGGGTTTTGTCACAGGGCGAAT
genomic: GATTTGGTTCCACAAGCCTGTGAAAGCTGATGATTGGCTTTTATATGTGgtaagccatt ... ataaacacagATCGACAGCCCATCTGCACACGGTGGGCGGGG-TTTTGTTACAGGGCGAAT
EST: gi|88971423|gb|CI017737.1|CI017737
EST:     GATTTGGTTCCACAAGCCTGTGAAAGCTGATGATTGGCTTTTATATGTG                         ATCGACAGCCCATCTGCACACGGTGGGCGGGGTTTTGTTACAGGGCGAATG
genomic: GATTTGGTTCCACAAGCCTGTGAAAGCTGATGATTGGCTTTTATATGTGgtaagccatt ... ataaacacagATCGACAGCCCATCTGCACACGGTGGGCGGGGTTTTGTTACAGGGCGAATG
EST: gi|86426203|gb|CI071300.1|CI071300
EST:     GATTTGGTTCCACAAGCCTGTGAAAGCTGATGATTGGCTTTTATATGTG                         ATCGACAGCCCATCTGCACACGGTGGGCGGGGTTTTGTTACAGGGCGAATG
genomic: GATTTGGTTCCACAAGCCTGTGAAAGCTGATGATTGGCTTTTATATGTGgtaagccatt ... ataaacacagATCGACAGCCCATCTGCACACGGTGGGCGGGGTTTTGTTACAGGGCGAATG
EST: gi|88489955|gb|CI427227.1|CI427227
EST:     AAGCTGATGATTGGCTTTTATATGTG                         ATCGACAGCCCATCTGCACACGGTGGGCGGGGTTTTGTTACAGGGCGAATG
genomic: AAGCTGATGATTGGCTTTTATATGTGgtaagccatt ... ataaacacagATCGACAGCCCATCTGCACACGGTGGGCGGGGTTTTGTTACAGGGCGAATG
EST: gi|22304837|gb|BQ906059.1|BQ906059
EST:     GAAAGCTGATGATTGGCTTTTATATGTG                         ATCGACAGCCCATCTGCACACGGTGGGCGGGGTTTTGTTACAGGGCGAATG
genomic: GAAAGCTGATGATTGGCTTTTATATGTGgtaagccatt ... ataaacacagATCGACAGCCCATCTGCACACGGTGGGCGGGGTTTTGTTACAGGGCGAATG
EST: gi|86490744|gb|CI133377.1|CI133377
EST:     GATTTGGTTCCACAAGCCTGTGAAAGCTGATGATTGGCTTTAATATGTG                         ATCGACAGCCCATCTGCACACGGTGGGCGGGGTTTTGTTACAGGGCGAATG
genomic: GATTTGGTTCCACAAGCCTGTGAAAGCTGATGATTGGCTTTTATATGTGgtaagccatt ... ataaacacagATCGACAGCCCATCTGCACACGGTGGGCGGGGTTTTGTTACAGGGCGAATG
EST: gi|88959770|gb|CI002380.1|CI002380
EST:     GATTTGGTTCCACAAGCCTGTGAAAGCTGATGATTGGCTTTTATATGTG                         ATCGACAGCCCATCTGCACACGGTGGGCGGGGTTTTGTTACAGGGCGAATG
genomic: GATTTGGTTCCACAAGCCTGTGAAAGCTGATGATTGGCTTTTATATGTGgtaagccatt ... ataaacacagATCGACAGCCCATCTGCACACGGTGGGCGGGGTTTTGTTACAGGGCGAATG
EST: gi|86844461|gb|CI337736.1|CI337736
EST:     CGATTTGGTTCCACAAGCCTGTGAAAGCTGATGATTGGCTTTTATATGTG                         ATCGACAGCCCATCTGCACACGGTGGGCGGGGTTTTGTTACAGGGCGAATG
genomic: CGATTTGGTTCCACAAGCCTGTGAAAGCTGATGATTGGCTTTTATATGTGgtaagccatt ... ataaacacagATCGACAGCCCATCTGCACACGGTGGGCGGGGTTTTGTTACAGGGCGAATG

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

GATTTGGTTCCACAAGCCTGTGAAAGCTGATGATTGGCTTTTATATGTGgtaagccatt ... ataaacacagATCGACAGCCCATCTGCACACGGTGGGCGGGGTTTTGTTACAGGGCGAATGTTCAACCGACAAGGAGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaactaaatttctgcttgaggttcttatggcaacaccttcccttaataaacacagATCGACAGCCCATCTGCACACGGTGGGCGGGGTTTTGTTACAGGGCGAATGTTCAACCGACAAGGAGAG
                                          ttaataaaca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagccattgatttttacctctcaaatgatacacaaaactaaatttctgcttgaggttcttatggcaacaccttcccttaataaacacagATCGACAGCCCATCTGCACACGGTGGGCGGGGTTTTGTTACAGGGCGAATGTTCAACCGACAAGGAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA