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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacattttttatgccattgttaagacatccacatctagtaagtcctacctatgaagtgttttcaagttaatctacaatttagaaatctccccagttattgacaactatggcatttcacattgcgtctcacttggctttattgtgtcgtctctcttcagTCGGTGTCTGCATTCTCTCCGGTTGTCAATCCAATCAACTGCCCTTGGGGTCAGAAAGCATTCTCAAACTATTTGGGCCCAGCTAAATCAGATTGGAAG

Basic information

species Oryza sativa
transcript LOC_Os01g71300.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g71300.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G046558_T01 (Zea mays), 3'ss of exon 4
gtacattttttatgccattgttaagacatccacatctagtaagtcctacctatgaagtgttttcaagttaatctac--aatttagaaatctccccagttattgacaactatggcatttcacattgcgtctcacttggctttattgtgtcgtctctc--ttcagTCGGTGTCTGCATTCTCTCCGGTTGTCAATCCAATCAACTGCCCTTGGGGTCAGAAAGCATTCTCAAACTATTTGGGCCCAGCTAAATCAGATTGGAAG
                                                     | | | ||  || |  | | ||   |   |||| | |||        ||| |    ||| |||||   ||||  ||||||   |  || | |  | || |  |  ||||||||||||| |||||  ||||  ||| |||||| || |||||||||||||||||||||||||||||||| ||  ||||| || |||||||||||||| ||
-----------------------------------------------------gtactcttagcatgccattttatttagcctagatagctctttcaa-gttgccgttcatgacattttgtattgaatctcaccctgaattttgggtttgtattacatttcagTCGGTGTCAGCATTTGCTCCAATTGCCAATCCGATAAACTGCCCTTGGGGTCAGAAAGCATTCTCAAATTACCTGGGCTCAACTAAATCAGATTGGGAG
















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|313081136|gb|HO213722.1|HO213722
EST:     GAGGGCACGGTGCACTAACAATCTACTTAAAGAACACTGATAAATACAAG                         TCGGTGTCTGCATTCTCTCCGGTTGTCAATCCAATCAACTGCCCTTGGGGT
genomic: GAGGGCACGGTGCACTAACAATCTACTTAAAGAACACTGATAAATACAAGgtacattttt ... ctctcttcagTCGGTGTCTGCATTCTCTCCGGTTGTCAATCCAATCAACTGCCCTTGGGGT
EST: gi|33793936|gb|CF322856.1|CF322856
EST:     AGGGCACGGTGCACTAACAATCTACTTAAAGAACACTGATAAATACAANG                         TCGGTGTCTGCATTCTCTCCGGTTGTCAATCCAATCAACTGCCCTTGGGG
genomic: AGGGCACGGTGCACTAACAATCTACTTAAAGAACACTGATAAATACAA-Ggtacattttt ... ctctcttcagTCGGTGTCTGCATTCTCTCCGGTTGTCAATCCAATCAACTGCCCTTGGGG
EST: gi|33793279|gb|CF322520.1|CF322520
EST:     AGGGCACGGTGCACTAACAATCTACTTAAAGAACACTGATAAATACCAAG                         TCGGTGTCTGCATTCTCTCCGGTTGTCAATCCAATCAACTGCCCTTGGGG
genomic: AGGGCACGGTGCACTAACAATCTACTTAAAGAACACTGATAAATAC-AAGgtacattttt ... ctctcttcagTCGGTGTCTGCATTCTCTCCGGTTGTCAATCCAATCAACTGCCCTTGGGG
EST: gi|29616411|gb|CB621423.1|CB621423
EST:     GAGGGCACGGTGCACTAACAATCTACTTAAAGAACACTGATAAATACAAG                         TCGGTGTCTGCATTCTCTCCGGTTGTCAATCCAATCAACTGCCCTTGGGGT
genomic: GAGGGCACGGTGCACTAACAATCTACTTAAAGAACACTGATAAATACAAGgtacattttt ... ctctcttcagTCGGTGTCTGCATTCTCTCCGGTTGTCAATCCAATCAACTGCCCTTGGGGT
EST: gi|88213104|gb|CI212768.1|CI212768
EST:     TCTACTTAAAGAACACTGATAAATACAAG                         TCGGTGTCTGCATTCTCTCCGGTTGTCAATCCAATCAACTGCCCTTGGGGT
genomic: TCTACTTAAAGAACACTGATAAATACAAGgtacattttt ... ctctcttcagTCGGTGTCTGCATTCTCTCCGGTTGTCAATCCAATCAACTGCCCTTGGGGT
EST: gi|163921069|gb|EG710132.1|EG710132
EST:     AATCTACTTAAAGATTACTGATAAATACAAG                         TCGGTGTCTGCATTCTCTCCGGTTGTCAATCCAATCAACTGGCCCTTGGGG
genomic: AATCTACTTAAAGAACACTGATAAATACAAGgtacattttt ... ctctcttcagTCGGTGTCTGCATTCTCTCCGGTTGTCAATCCAATCAACT-GCCCTTGGGG
EST: gi|86513942|gb|CI156575.1|CI156575
EST:     GAGGGCACGGTGCACTAACAATCTACTTAAAGAACACTGATAAATACAAG                         TCGGTGTCTGCATTCTCTCCGGTTGTCAATCCAATCAACTGCCCTTGGGGT
genomic: GAGGGCACGGTGCACTAACAATCTACTTAAAGAACACTGATAAATACAAGgtacattttt ... ctctcttcagTCGGTGTCTGCATTCTCTCCGGTTGTCAATCCAATCAACTGCCCTTGGGGT
EST: gi|88201927|gb|CI202282.1|CI202282
EST:     ACACTGATAAATACAAG                         TCGGTGTCTGCATTCTCTCCGGTTGTCAATCCAATCAACTGCCCTTGGGGT
genomic: ACACTGATAAATACAAGgtacattttt ... ctctcttcagTCGGTGTCTGCATTCTCTCCGGTTGTCAATCCAATCAACTGCCCTTGGGGT
EST: gi|218484537|gb|FG954358.1|FG954358
EST:     CACTGATAAATACAAG                         TCGGTGTCTGCATTCTCTCCGGTTGTCAATCCAATCAACTGCCCTTGTGGG
genomic: CACTGATAAATACAAGgtacattttt ... ctctcttcagTCGGTGTCTGCATTCTCTCCGGTTGTCAATCCAATCAACTGCCCTTG-GGG
EST: gi|88977256|gb|CI024993.1|CI024993
EST:     TACTTAAAGAACACTGATAAATACAAG                         TCGGTGTCTGCATTCTCTCCGGTTGTCAATCCAATCAACTGCCCTTGGGGT
genomic: TACTTAAAGAACACTGATAAATACAAGgtacattttt ... ctctcttcagTCGGTGTCTGCATTCTCTCCGGTTGTCAATCCAATCAACTGCCCTTGGGGT
EST: gi|86252680|gb|CI010162.1|CI010162
EST:     GAGGGCACGGTGCACTAACAATCTACTTAAAGAACACTGATAAATACAAG                         TCGGTGTCTGCATTCTCTCCGGTTGTCAATCCAATCAACTGCCCTTGGGGT
genomic: GAGGGCACGGTGCACTAACAATCTACTTAAAGAACACTGATAAATACAAGgtacattttt ... ctctcttcagTCGGTGTCTGCATTCTCTCCGGTTGTCAATCCAATCAACTGCCCTTGGGGT
EST: gi|2443065|gb|C74836.1|C74836
EST:     GAGGGCACGGTGCACTAACAATCTACTTAAAGAACACTGATAAATACAAG                         TCGGTGTCTGCATTCTCTCCGGTTGTCAATCCAATCAACTGCCCTTGGGGT
genomic: GAGGGCACGGTGCACTAACAATCTACTTAAAGAACACTGATAAATACAAGgtacattttt ... ctctcttcagTCGGTGTCTGCATTCTCTCCGGTTGTCAATCCAATCAACTGCCCTTGGGGT
EST: gi|86594394|gb|CI251266.1|CI251266
EST:     GAGGGCACGGTGCACTAACAATCTACTTAAAGAACACTGATAAATACAAG                         TCGGTGTCTGCATTCTCTCCGGTTGTCAATCCAATCAACTGCCCTTGGGGT
genomic: GAGGGCACGGTGCACTAACAATCTACTTAAAGAACACTGATAAATACAAGgtacattttt ... ctctcttcagTCGGTGTCTGCATTCTCTCCGGTTGTCAATCCAATCAACTGCCCTTGGGGT

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: 69 (upstream exon), 75 (downstream exon)
Score: 45

CTTTGAACAGCTGAACACTTCACGGGCATCTATTTTTGGGCACTCAATGGGAGGGCACGGTGCACTAACAATCTACTTAAAGAACACTGATAAATACAAGgtacattttt ... ctctcttcagTCGGTGTCTGCATTCTCTCCGGTTGTCAATCCAATCAACTGCCCTTGGGGTCAGAAAGCATTCTCAAACTATTTGGGCCCAGCTAAATCAGATTGGAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actatggcatttcacattgcgtctcacttggctttattgtgtcgtctctcttcagTCGGTGTCTGCATTCTCTCCGGTTGTCAATCCAATCAACTGCCCTTGGGGTCAGAAAGCATTCTCAAACTATTTGGGCCCAGCTAAATCAGATTGGAAG
                    gtctcac  putative branch site (score: 45)
                                       tgtcgtctctcttc  putative PPT
                                tttattgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacattttttatgccattgttaagacatccacatctagtaagtcctacctatgaagtgttttcaagttaatctacaatttagaaatctccccagttattgacaactatggcatttcacattgcgtctcacttggctttattgtgtcgtctctcttcagTCGGTGTCTGCATTCTCTCCGGTTGTCAATCCAATCAACTGCCCTTGGGGTCAGAAAGCATTCTCAAACTATTTGGGCCCAGCTAAATCAGATTGGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG