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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgaccttgatttctctatgccttgcgaatttaaaggatagctactagcttgtttggtagtgttgcttctgtgtgttaatttacttacctctaatatttgttgtcattcagGCCAAGACAACAAAGAAGATCGTTCTGAAGCTGCAGTGCCAGAGCTGCAAGCACTACTCTCAGCACCCGATCAAG

Basic information

species Oryza sativa
transcript LOC_Os07g26740.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g26740.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G160351_T01 (Zea mays), 3'ss of exon 2
gtttgaccttgatttctctatgccttgcgaatttaaaggatagctactagcttgtttggtagtg-ttgcttctgtgtgttaatttacttacctc-taatatttgttgtc------attcagGCCAAGACAACAAAGAAGATCGTTCTGAAGCTGCAGTGCCAGAGCTGCAAGCACTACTCTCAGCACCCGATCAAG
|||  ||    | |||||||    ||||      ||       ||    |||  ||| | |||  ||  | | |    || |||||||| | || ||| |||   | |       |||||||| || |||||||||||||| || |||||||||||||||||||||||||||||||||||||| ||||||||||||
gttcaacac-aaattctctactgtttgcagtaccaattacatactgaaggctgcttttggagttcttaatgcggatcctttatttacttgcttcctaacattaactcttcggtctattcagGCAAAAACAACAAAGAAGATTGTGCTGAAGCTGCAGTGCCAGAGCTGCAAGCACTACTCTCAACACCCGATCAAG
















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|58599599|gb|CK010127.1|CK010127
EST:     GCAAGCAGTCAGGATATGGTGGGCAGACAAAGCCTGTTTTTCACAAGAAG                         GCCAAGACAACAAAGAAGATCGTTCTGAAGCTGCAGTGCCAGAGCTGCAAG
genomic: GCAAGCAGTCAGGATATGGTGGGCAGACAAAGCCTGTTTTTCACAAGAAGgtttgacctt ... tgtcattcagGCCAAGACAACAAAGAAGATCGTTCTGAAGCTGCAGTGCCAGAGCTGCAAG
EST: gi|88330761|gb|CI636769.1|CI636769
EST:     GCAAGCAGTCAGGATATGGTGGGCAGACAAAGCCTGTTTTTCACAAGAAG                         GCCAAGACAACAAAGAAGATCGTTCTGAAGCTGCAGTGCCAGAGCTGCAAG
genomic: GCAAGCAGTCAGGATATGGTGGGCAGACAAAGCCTGTTTTTCACAAGAAGgtttgacctt ... tgtcattcagGCCAAGACAACAAAGAAGATCGTTCTGAAGCTGCAGTGCCAGAGCTGCAAG
EST: gi|88742622|gb|CI766130.1|CI766130
EST:     GCAAGCAGTCAGGATATGGTGGGCAGACAAAGCCTGTTTTTCACAAGAAG                         GCCAAGACAACAAAGAAGATCGTTCTGAAGCTGCAGTGCCAGAGCTGCAAG
genomic: GCAAGCAGTCAGGATATGGTGGGCAGACAAAGCCTGTTTTTCACAAGAAGgtttgacctt ... tgtcattcagGCCAAGACAACAAAGAAGATCGTTCTGAAGCTGCAGTGCCAGAGCTGCAAG
EST: gi|88906166|gb|CI375238.1|CI375238
EST:     GCAGACAAAGCCTGTTTTTCACAAGAAG                         GCCAAGACAACAAAGAAGATCGTTCTGAAGCTGCAGTGCCAGAGCTGCAAG
genomic: GCAGACAAAGCCTGTTTTTCACAAGAAGgtttgacctt ... tgtcattcagGCCAAGACAACAAAGAAGATCGTTCTGAAGCTGCAGTGCCAGAGCTGCAAG
EST: gi|88505133|gb|CI432639.1|CI432639
EST:     AGGATATGGTGGGCAGACAAAGCCTGTTTTTCACAAGAAG                         GCCAAGACGACAAAGAAGATCGTTCTGAAGCTGCAGTGCCAGAGCTGCAAG
genomic: AGGATATGGTGGGCAGACAAAGCCTGTTTTTCACAAGAAGgtttgacctt ... tgtcattcagGCCAAGACAACAAAGAAGATCGTTCTGAAGCTGCAGTGCCAGAGCTGCAAG
EST: gi|88310008|gb|CI657432.1|CI657432
EST:     GCAAGCAGTCAGGATATGGTGGGCAGACAAAGCCTGTTTTTCACAAGAAG                         GCCAAGACAACAAAGAAGATCGTTCTGAAGCTGCAGTGCCAGAGCTGCAAG
genomic: GCAAGCAGTCAGGATATGGTGGGCAGACAAAGCCTGTTTTTCACAAGAAGgtttgacctt ... tgtcattcagGCCAAGACAACAAAGAAGATCGTTCTGAAGCTGCAGTGCCAGAGCTGCAAG
EST: gi|88575814|gb|CI669959.1|CI669959
EST:     GCAAGCAGTCAGGATATGGTGGGCAGACAAAGCCTGTTTTTCACAAGAAG                         GCCAAGACAACAAAGAAGATCGTTCTGAAGCTGCAGTGCCAGAGCTGCAAG
genomic: GCAAGCAGTCAGGATATGGTGGGCAGACAAAGCCTGTTTTTCACAAGAAGgtttgacctt ... tgtcattcagGCCAAGACAACAAAGAAGATCGTTCTGAAGCTGCAGTGCCAGAGCTGCAAG
EST: gi|2311208|gb|C27363.1|C27363
EST:     GCAAGCAGTCAGGATATGGTGGGCAGACAAAGCCTGTTTTTCACAAGAAG                         GCCAAGACAACAAAGAAGATCGTTCTGAAGCTGCAGTGCCAGAGCTGCAAG
genomic: GCAAGCAGTCAGGATATGGTGGGCAGACAAAGCCTGTTTTTCACAAGAAGgtttgacctt ... tgtcattcagGCCAAGACAACAAAGAAGATCGTTCTGAAGCTGCAGTGCCAGAGCTGCAAG
EST: gi|88330344|gb|CI633550.1|CI633550
EST:     GCAAGCAGTCAGGATATGGTGGGCAGACAAAGCCTGTTTTTCACAAGAAG                         GCCAAGACAACAAAGAAGATCGTTCTGAAGCTGCAGTGCCAGAGCTGCAAG
genomic: GCAAGCAGTCAGGATATGGTGGGCAGACAAAGCCTGTTTTTCACAAGAAGgtttgacctt ... tgtcattcagGCCAAGACAACAAAGAAGATCGTTCTGAAGCTGCAGTGCCAGAGCTGCAAG
EST: gi|88336818|gb|CI644245.1|CI644245
EST:     GCAAGCAGTCAGGATATGGTGGGCAGACAAAGCCTGTTTTTCACAAGAAG                         GCCAAGACAACAAAGAAGATCGTTCTGAAGCTGCAGTGCCAGAGCTGCAAG
genomic: GCAAGCAGTCAGGATATGGTGGGCAGACAAAGCCTGTTTTTCACAAGAAGgtttgacctt ... tgtcattcagGCCAAGACAACAAAGAAGATCGTTCTGAAGCTGCAGTGCCAGAGCTGCAAG
EST: gi|88349588|gb|CI653867.1|CI653867
EST:     GCAAGCAGTCAGGATATGGTGGGCAGACAAAGCCTGTTTTTCACAAGAAG                         GCCAAGACAACAAAGAAGATCGTTCTGAAGCTGCAGTGCCAGAGCTGCAAG
genomic: GCAAGCAGTCAGGATATGGTGGGCAGACAAAGCCTGTTTTTCACAAGAAGgtttgacctt ... tgtcattcagGCCAAGACAACAAAGAAGATCGTTCTGAAGCTGCAGTGCCAGAGCTGCAAG
EST: gi|425966|gb|D22649.1|D22649
EST:     GCAAGCAGTCAGGATATGGTGGGCAGACAAAGCCTGTTTTTCACAAGAAG                         GCCAAGACAACAAAGAAGATCGTTCTGAAGCTGCAGTGCCAGAGCTGCAAG
genomic: GCAAGCAGTCAGGATATGGTGGGCAGACAAAGCCTGTTTTTCACAAGAAGgtttgacctt ... tgtcattcagGCCAAGACAACAAAGAAGATCGTTCTGAAGCTGCAGTGCCAGAGCTGCAAG
EST: gi|27576163|gb|CA998857.1|CA998857
EST:     GCAAGCAGTCAGGATATGGTGGGCAGACAAAGCCTGTTTTTCACAAGAAG                         GCCAAGACAACAAAGAAGATCGTTCTGAAGCTGCAGTGCCAGAGCTGCAAG
genomic: GCAAGCAGTCAGGATATGGTGGGCAGACAAAGCCTGTTTTTCACAAGAAGgtttgacctt ... tgtcattcagGCCAAGACAACAAAGAAGATCGTTCTGAAGCTGCAGTGCCAGAGCTGCAAG
EST: gi|88488152|gb|CI425423.1|CI425423
EST:     GCAAGCAGTCAGGATATGGTGGGCAGACAAAGCCTGTTTTTCACAAGAAG                         GCCAAGACAACAAAGAAGATCGTTCTGAAGCTGCAGTGCCAGAGCTGCAAG
genomic: GCAAGCAGTCAGGATATGGTGGGCAGACAAAGCCTGTTTTTCACAAGAAGgtttgacctt ... tgtcattcagGCCAAGACAACAAAGAAGATCGTTCTGAAGCTGCAGTGCCAGAGCTGCAAG
EST: gi|88479294|gb|CI416565.1|CI416565
EST:     GCAAGCAGTCAGGATATGGTGGGCAGACAAAGCCTGTTTTTCACAAGAAG                         GCCAAGACAACAAAGAAGATCGTTCTGAAGCTGCAGTGCCAGAGCTGCAAG
genomic: GCAAGCAGTCAGGATATGGTGGGCAGACAAAGCCTGTTTTTCACAAGAAGgtttgacctt ... tgtcattcagGCCAAGACAACAAAGAAGATCGTTCTGAAGCTGCAGTGCCAGAGCTGCAAG
EST: gi|88575707|gb|CI669852.1|CI669852
EST:     GCAAGCAGTCAGGATATGGTGGGCAGACAAAGCCTGTTTTTCACAAGAAG                         GCCAAGACAACAAAGAAGATCGTTCTGAAGCTGCAGTGCCAGAGCTGCAAG
genomic: GCAAGCAGTCAGGATATGGTGGGCAGACAAAGCCTGTTTTTCACAAGAAGgtttgacctt ... tgtcattcagGCCAAGACAACAAAGAAGATCGTTCTGAAGCTGCAGTGCCAGAGCTGCAAG
EST: gi|88423189|gb|CI613490.1|CI613490
EST:     GCAAGCAGTCAGGATATGGTGGGCAGACAAAGCCTGTTTTTCACAAGAAG                         GCCAAGACAACAAAGAAGATCGTTCTGAAGCTGGAGTGCCAGAGCTGCAAG
genomic: GCAAGCAGTCAGGATATGGTGGGCAGACAAAGCCTGTTTTTCACAAGAAGgtttgacctt ... tgtcattcagGCCAAGACAACAAAGAAGATCGTTCTGAAGCTGCAGTGCCAGAGCTGCAAG
EST: gi|88490932|gb|CI428204.1|CI428204
EST:     GCAAGCAGTCAGGATATGGTGGGCAGACAAAGCCTGTTTTTCACAAGAAG                         GCCAAGACAACAAAGAAGATCGTTCTGAAGCTGCAGTGCCAGAGCTGCAAG
genomic: GCAAGCAGTCAGGATATGGTGGGCAGACAAAGCCTGTTTTTCACAAGAAGgtttgacctt ... tgtcattcagGCCAAGACAACAAAGAAGATCGTTCTGAAGCTGCAGTGCCAGAGCTGCAAG
EST: gi|88427254|gb|CI586802.1|CI586802
EST:     GCAAGCAGTCAGGATATGGTGGGCAGACAAAGCCTGTTTTTCACAAGAAG                         GCCAAGACAACAAAGAAGATCGTTCTGAAGCTGCAGTGCCAGAGCTGCAAG
genomic: GCAAGCAGTCAGGATATGGTGGGCAGACAAAGCCTGTTTTTCACAAGAAGgtttgacctt ... tgtcattcagGCCAAGACAACAAAGAAGATCGTTCTGAAGCTGCAGTGCCAGAGCTGCAAG
EST: gi|88662682|gb|CI472142.1|CI472142
EST:     GCAAGCAGTCAGGATATGGTGGGCAGACAAAGCCTGTTTTTCACAAGAAG                         GCCAAGACAACAAAGAAGATCGTTCTGAAGCTGCAGTGCCAGAGCTGCAAG
genomic: GCAAGCAGTCAGGATATGGTGGGCAGACAAAGCCTGTTTTTCACAAGAAGgtttgacctt ... tgtcattcagGCCAAGACAACAAAGAAGATCGTTCTGAAGCTGCAGTGCCAGAGCTGCAAG
EST: gi|286577|gb|D15384.1|D15384
EST:     GCAAGCAGTCAGGATATGGTGGGCAGACAAAGCCTGTTTTTCACAAGAAG                         GCCAAGACAACAAAGAAGATCGTTCTGAAGCTGCAGTGCCAGAGCTGCAAG
genomic: GCAAGCAGTCAGGATATGGTGGGCAGACAAAGCCTGTTTTTCACAAGAAGgtttgacctt ... tgtcattcagGCCAAGACAACAAAGAAGATCGTTCTGAAGCTGCAGTGCCAGAGCTGCAAG
EST: gi|88479759|gb|CI417030.1|CI417030
EST:     GCAAGCAGTCAGGATATGGTGGGCAGACAAAGCCTGTTTTTCACAAGAAG                         GCCAAGACAACAAAGAAGATCGTTCTGAAGCTGCAGTGCCAGAGCTGCAAG
genomic: GCAAGCAGTCAGGATATGGTGGGCAGACAAAGCCTGTTTTTCACAAGAAGgtttgacctt ... tgtcattcagGCCAAGACAACAAAGAAGATCGTTCTGAAGCTGCAGTGCCAGAGCTGCAAG
EST: gi|88512222|gb|CI439728.1|CI439728
EST:     GCAAGCAGTCAGGATATGGTGGGCAGACAAAGCCTGTTTTTCACAAGAAG                         GCCAAGACAACAAAGAAGATCGTTCTGAAGCTGCAGTGCCAGAGCTGCAAG
genomic: GCAAGCAGTCAGGATATGGTGGGCAGACAAAGCCTGTTTTTCACAAGAAGgtttgacctt ... tgtcattcagGCCAAGACAACAAAGAAGATCGTTCTGAAGCTGCAGTGCCAGAGCTGCAAG
EST: gi|88963096|gb|CI026770.1|CI026770
EST:     GCAAGCAGTCAGGATATGGTGGGCAGACAAAGCCTGTTTTTCACAAGAAG                         GCCAAGACAACAAAGAAGATCGTTCTGAAGCTGCAGTGCCAGAGCTGCAAG
genomic: GCAAGCAGTCAGGATATGGTGGGCAGACAAAGCCTGTTTTTCACAAGAAGgtttgacctt ... tgtcattcagGCCAAGACAACAAAGAAGATCGTTCTGAAGCTGCAGTGCCAGAGCTGCAAG
EST: gi|88332629|gb|CI651789.1|CI651789
EST:     GCAAGCAGTCAGGATATGGTGGGCAGACAAAGCCTGTTTTTCACAAGAAG                         GCCAAGACAACAAAGAAGATCGTTCTGAAGCTGCAGTGCCAGAGCTGCAAG
genomic: GCAAGCAGTCAGGATATGGTGGGCAGACAAAGCCTGTTTTTCACAAGAAGgtttgacctt ... tgtcattcagGCCAAGACAACAAAGAAGATCGTTCTGAAGCTGCAGTGCCAGAGCTGCAAG
EST: gi|88512855|gb|CI440361.1|CI440361
EST:     GCAAGCAGTCAGGATATGGTGGGCAGACAAAGCCTGTTTTTCACAAGAAG                         GCCAAGACAACAAAGAAGATCGTTCTGAAGCTGCAGTGCCAGAGCTGCAAG
genomic: GCAAGCAGTCAGGATATGGTGGGCAGACAAAGCCTGTTTTTCACAAGAAGgtttgacctt ... tgtcattcagGCCAAGACAACAAAGAAGATCGTTCTGAAGCTGCAGTGCCAGAGCTGCAAG
EST: gi|88364533|gb|CI644611.1|CI644611
EST:     GCAAGCAGTCAGGATATGGTGGGCAGACAAAGCCTGTTTTTCACAAGAAG                         GCCAAGACAACAAAGAAGATCGTTCTGAAGCTGCAGTGCCAGAGCTGCAAG
genomic: GCAAGCAGTCAGGATATGGTGGGCAGACAAAGCCTGTTTTTCACAAGAAGgtttgacctt ... tgtcattcagGCCAAGACAACAAAGAAGATCGTTCTGAAGCTGCAGTGCCAGAGCTGCAAG
EST: gi|88519979|gb|CI447548.1|CI447548
EST:     GCAACCAGTCAGGATATGGTGGGCAGACAAAGCCTNTTTTTCACAAGAAG                         GCCAAGACAACAAAGAAGATCGTTCTGAAGCTGCAGTGCCAGAGCTGCAAG
genomic: GCAAGCAGTCAGGATATGGTGGGCAGACAAAGCCTGTTTTTCACAAGAAGgtttgacctt ... tgtcattcagGCCAAGACAACAAAGAAGATCGTTCTGAAGCTGCAGTGCCAGAGCTGCAAG
EST: gi|88519767|gb|CI447421.1|CI447421
EST:     TTTTTCACAAGAAG                         GCCAAGACAACAAAGAAGATCGTTCTGAAGCTGCAGTGCCAGAGCTGCAAG
genomic: TTTTTCACAAGAAGgtttgacctt ... tgtcattcagGCCAAGACAACAAAGAAGATCGTTCTGAAGCTGCAGTGCCAGAGCTGCAAG
EST: gi|88382288|gb|CI633146.1|CI633146
EST:     GCAAGCAGTCAGGATATGGTGGGCAGACAAAGCCTGTTTTTCANAAGAAG                         GCCAAGACAACAAAGAAGATCGTTCTGAACCTGCAGTGCCAGAGCTGCAAG
genomic: GCAAGCAGTCAGGATATGGTGGGCAGACAAAGCCTGTTTTTCACAAGAAGgtttgacctt ... tgtcattcagGCCAAGACAACAAAGAAGATCGTTCTGAAGCTGCAGTGCCAGAGCTGCAAG
EST: gi|88281752|gb|CI403148.1|CI403148
EST:     ATGGTGGGCAGACAAAGCCTGTTTTTCACAAGAAG                         GCCAAGACAACAAAGAAGATCGTTCTGAAGCTGCAGTGCCAGAGCTGCAAG
genomic: ATGGTGGGCAGACAAAGCCTGTTTTTCACAAGAAGgtttgacctt ... tgtcattcagGCCAAGACAACAAAGAAGATCGTTCTGAAGCTGCAGTGCCAGAGCTGCAAG
EST: gi|87012754|gb|CI295198.1|CI295198
EST:     GCAAGCAGTCAGGATATGGTGGGCAGACAAAGCCTGTTTTTCACAAGAAG                         GCCAAGACAACAAAGAAGATCGTTCTGAAGCTGCAGTGCCAGAGCTGCAAG
genomic: GCAAGCAGTCAGGATATGGTGGGCAGACAAAGCCTGTTTTTCACAAGAAGgtttgacctt ... tgtcattcagGCCAAGACAACAAAGAAGATCGTTCTGAAGCTGCAGTGCCAGAGCTGCAAG

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: 75 (upstream exon), 64 (downstream exon)
Score: 27

CAAGAAAGGAAAGGATAGCCTTTCTGCTCAGGGGAAGCGTCGTTATGACCGCAAGCAGTCAGGATATGGTGGGCAGACAAAGCCTGTTTTTCACAAGAAGgtttgacctt ... tgtcattcagGCCAAGACAACAAAGAAGATCGTTCTGAAGCTGCAGTGCCAGAGCTGCAAGCACTACTCTCAGCACCCGATCAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtagtgttgcttctgtgtgttaatttacttacctctaatatttgttgtcattcagGCCAAGACAACAAAGAAGATCGTTCTGAAGCTGCAGTGCCAGAGCTGCAAGCACTACTCTCAGCACCCGATCAAG
                 tgttaatttactta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgaccttgatttctctatgccttgcgaatttaaaggatagctactagcttgtttggtagtgttgcttctgtgtgttaatttacttacctctaatatttgttgtcattcagGCCAAGACAACAAAGAAGATCGTTCTGAAGCTGCAGTGCCAGAGCTGCAAGCACTACTCTCAGCACCCGATCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC