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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttttgctttatgtgaagactctttattcttatttgatttcattttgttgaaataaaacaatgattttattttccttttgttcatgatggcaactacttttcagAATCTGTGTGTAACTGCTGCACATTGCCCCATAAGGGAGATCCTTGAAAGAGAGAAGAAG

Basic information

species Oryza sativa
transcript LOC_Os07g47530.1
intron # 25
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g47530.1 (Oryza sativa), 3'ss of exon 25
lower sequence: GRMZM2G157621_T03 (Zea mays), 3'ss of exon 25
gtatttttgctttatgtgaagactctttattcttatttgatttcattttgttgaaataaaacaatgattttattttccttttgttcatgatggcaactactttt-cagAATCTGTGTGTAACTGCTGCACATTGCCCCATAAGGGAGATCCTTGAAAGAGAGAAGAAG
                       |   ||||||  |  ||| |   ||| ||    ||         |  |   ||| || ||||  ||  | || ||| |||| ||||| |||||| ||||||| |||||| | ||||||||||| || ||||||||||||||||||
----------------------gtaggtattctattaagatatttctttcttatcctatt-------tcctcgcttctttgtgttgttggcgacacctatttttgcagAACCTGTGTATAACTGCAGCACATCGTCCCATAAGGGAAATTCTTGAAAGAGAGAAGAAG
















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|27546551|gb|CA764668.2|CA764668
EST:     GTGATATGAAG                         AATCTGTGCGTAACTGCTGCACATTGCCCCATAAGGGAGATCCTTGAAAGA
genomic: GTGATATGAAGgtatttttgc ... tacttttcagAATCTGTGTGTAACTGCTGCACATTGCCCCATAAGGGAGATCCTTGAAAGA
EST: gi|66914068|gb|CX100916.1|CX100916
EST:     TGGAAGCTCTGGCTAACTTGACTGATGGTTACTCAGGCAGTGATATGAAG                         AATCTGTGTGTAACTGCTGCACATTGCCCCATAAGGGAGATCCTTGAAAGA
genomic: TGGAAGCTCTGGCTAACTTGACTGATGGTTATTCAGGCAGTGATATGAAGgtatttttgc ... tacttttcagAATCTGTGTGTAACTGCTGCACATTGCCCCATAAGGGAGATCCTTGAAAGA
EST: gi|29669557|gb|CB665832.1|CB665832
EST:     TGGAAGCTCTGGCTAACTTGACTGATGGTTATTCAGGCAGTGATATGAAG                         AATCTGTGTGTAACTGCTGCACATTGCCCCATAAGGGAGATCCTTGAAAGA
genomic: TGGAAGCTCTGGCTAACTTGACTGATGGTTATTCAGGCAGTGATATGAAGgtatttttgc ... tacttttcagAATCTGTGTGTAACTGCTGCACATTGCCCCATAAGGGAGATCCTTGAAAGA
EST: gi|29632466|gb|CB637475.1|CB637475
EST:     TGGAAGCTCTGGCTAACTTGACTGATGGTTATTCAGGCAGTGATATGAAG                         AATCTGTGTGTAACTGCTGCACATTGCCCCATAAGGGAGATCCTTGAAAGA
genomic: TGGAAGCTCTGGCTAACTTGACTGATGGTTATTCAGGCAGTGATATGAAGgtatttttgc ... tacttttcagAATCTGTGTGTAACTGCTGCACATTGCCCCATAAGGGAGATCCTTGAAAGA
EST: gi|428039|gb|D24187.1|D24187
EST:     TGGAAGCTCTGGCTAACTTGACTGATGGTTATTCAGGCAGTGATATGAAG                         AATCTGTGTGTAACTGCTGCACATTGCCCCATAAGGGAGATCCTTGAAAGA
genomic: TGGAAGCTCTGGCTAACTTGACTGATGGTTATTCAGGCAGTGATATGAAGgtatttttgc ... tacttttcagAATCTGTGTGTAACTGCTGCACATTGCCCCATAAGGGAGATCCTTGAAAGA
EST: gi|58688870|gb|CK077557.1|CK077557
EST:     TGGAAGCTCTGGCTAACTTGACCGATGGTTACTCAGGCAGTGATATGAAG                         AATCTGTGTGTAACTGCTGCACATTGCCCCATAAGGGAGATCCTTGAAAGA
genomic: TGGAAGCTCTGGCTAACTTGACTGATGGTTATTCAGGCAGTGATATGAAGgtatttttgc ... tacttttcagAATCTGTGTGTAACTGCTGCACATTGCCCCATAAGGGAGATCCTTGAAAGA
EST: gi|29685522|gb|CB681797.1|CB681797
EST:     TGGAAGCTCTGGCTAACTTGACTGATGGTTATTCAGGCAGTGATATGAAG                         AATCTGTGTGTAACTGCTGCACATTGCCCCATAAGGGAGATCCTTGAAAGA
genomic: TGGAAGCTCTGGCTAACTTGACTGATGGTTATTCAGGCAGTGATATGAAGgtatttttgc ... tacttttcagAATCTGTGTGTAACTGCTGCACATTGCCCCATAAGGGAGATCCTTGAAAGA
EST: gi|325493960|gb|JG458484.1|JG458484
EST:     TGGAAGCTCTGGCTAACTTGACTGATGGTTATTCAGGCAGCGATATGAAG                         AATCTGTGTGTAACTGCTGCACATTGCCCCATAAGGGAGATC
genomic: TGGAAGCTCTGGCTAACTTGACTGATGGTTATTCAGGCAGTGATATGAAGgtatttttgc ... tacttttcagAATCTGTGTGTAACTGCTGCACATTGCCCCATAAGGGAGATC
EST: gi|29632742|gb|CB637751.1|CB637751
EST:     GCTAACTTGACTGATGGTTATTCAGGCAGTGATATGAAG                         AATCTGTGTGTAACTGCTGCACATTGCCCCATAAGGGAGATCCTTGAAAGA
genomic: GCTAACTTGACTGATGGTTATTCAGGCAGTGATATGAAGgtatttttgc ... tacttttcagAATCTGTGTGTAACTGCTGCACATTGCCCCATAAGGGAGATCCTTGAAAGA
EST: gi|29669556|gb|CB665831.1|CB665831
EST:     TGGAAGCTCTGGCTAACTTGACTGATGGTTATTCAGGCAGTGATATGAAG                         AATCTGTGTGTAACTGCTGCACATTGCCCCA
genomic: TGGAAGCTCTGGCTAACTTGACTGATGGTTATTCAGGCAGTGATATGAAGgtatttttgc ... tacttttcagAATCTGTGTGTAACTGCTGCACATTGCCCCA

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: 68 (upstream exon), 60 (downstream exon)
Score: 29

GATTCTTAGCGTAATACTGGCCAAAGAAGATTTGGCTGATGATGTAGATCTGGAAGCTCTGGCTAACTTGACTGATGGTTATTCAGGCAGTGATATGAAGgtatttttgc ... tacttttcagAATCTGTGTGTAACTGCTGCACATTGCCCCATAAGGGAGATCCTTGAAAGAGAGAAGAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaataaaacaatgattttattttccttttgttcatgatggcaactacttttcagAATCTGTGTGTAACTGCTGCACATTGCCCCATAAGGGAGATCCTTGAAAGAGAGAAGAAG
                                            ctacttttc  CT-rich tract
     aaaacaatgattttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatttttgctttatgtgaagactctttattcttatttgatttcattttgttgaaataaaacaatgattttattttccttttgttcatgatggcaactacttttcagAATCTGTGTGTAACTGCTGCACATTGCCCCATAAGGGAGATCCTTGAAAGAGAGAAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG