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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattaacatttataaatggatttttggaatatttaaattgatgagatgagcttattttctagaaaggctaggcatatcttaaatgtttcattttgtgtttctgccatttgttaatgctacaacacaatcattgggcagGATATCAAAGAGAACCCAGTCTTGATCTACATGAAGGGTTTTCCTGAGTCTCCTATGTGTGGATTCAGTGCATTGGCAGTTAAAGTCCTCAAGCTATATG

Basic information

species Oryza sativa
transcript LOC_Os01g07950.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g07950.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AC208327.4_FGT002 (Zea mays), 3'ss of exon 4
gtattaacatttataaatggatttttggaatatttaaattgatga--gatgagcttattttctagaaaggctaggcatatcttaaatgtt-tcattttgtgtttctgccatttgttaatgctacaacacaatcattgggcagGATATCAAAGAGAACCCAGTCTTGATCTACATGAAGGGTTTTCCTGAGTCTCCTATGTGTGGATTCAGTGCATTGGCAGTTAAAGTCCTCAAGCTATATG
||||| ||||    | |||   ||   ||||||||| ||| |  |  || |  | ||  || | | ||  ||||||||| | | ||| || |   | | | ||| |  | |   ||    ||   | || ||  || ||||||||||||| |||||||||||||||||||||||||||||||||||||||||||| |||||||| ||||||||| |||| ||||| ||| |  ||| |||||
gtatttacatgcggagatgagattcaagaatatttatattaaacattgaagcacctaacttgtggtaaaactaggcataacctgaatcttattgatgtatctttttagcttccatt----ctttcataccattttttggcagGATATCAAGGAGAACCCAGTCTTGATCTACATGAAGGGTTTTCCTGAGTCTCCAATGTGTGGCTTCAGTGCACTGGCTGTTAAGGTCTTTCAGCAATATG

upper sequence: LOC_Os01g07950.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM5G880300_T02 (Zea mays), 3'ss of exon 3
gtattaacatttataaatggatttttggaatatttaaattgatga--gatgagcttattttctagaaaggctaggcatatcttaaatgtttcattttgtgtttctgccatttgttaatgctacaacacaatcattgggcagGATATCAAAGAGAACCCAGTCTTGATCTACATGAAGGGTTTTCCTGAGTCTCCTATGTGTGGATTCAGTGCATTGGCAGTTAAAGTCCTCAAGCTATATG
||||| ||||  | | |||   ||   ||||||||| ||| |  |  || |  | ||  || |   ||  ||||||||| | | || | ||  |  ||| | | |   |  ||  |   || |    || |   | || |||||||||| |||||||||||||||||||||||||||||||||||||||||||| |||||||| ||||||||| |||| ||||| ||| || ||| |||||
gtatttacatgcagagatgagattcaagaatatttatattaaacattgaagcacctaacttgtgataaaactaggcataacctgaa-gcttattgatgtatcttt-ttagctgccatctcttcttatcattttcttggtagGATATCAAGGAGAACCCAGTCTTGATCTACATGAAGGGTTTTCCTGAGTCTCCAATGTGTGGCTTCAGTGCACTGGCTGTTAAGGTCTTCCAGCAATATG
















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|33687689|gb|CF315928.1|CF315928
EST:     AGCCTACAAGCAAAAGTTCCAACATGTCTTTTGATGACATTGTTGCTCAG                         GATATCAAAGAGAACCCAGTCTTGATCTACATGAAGGGTTTTCCTGAGTCT
genomic: AGCCTACAAGCAAAAGTTCCAACATGTCTTTTGATGACATTGTTGCTCAGgtattaacat ... cattgggcagGATATCAAAGAGAACCCAGTCTTGATCTACATGAAGGGTTTTCCTGAGTCT
EST: gi|86595567|gb|CI264664.1|CI264664
EST:     TTTGATGACATTGTTGCTCAG                         GATATCAAAGAGAACCCAGTCTTGATCTACATGAAGGGTTTTCCTGAGTCT
genomic: TTTGATGACATTGTTGCTCAGgtattaacat ... cattgggcagGATATCAAAGAGAACCCAGTCTTGATCTACATGAAGGGTTTTCCTGAGTCT
EST: gi|88352871|gb|CI678899.1|CI678899
EST:     AGCCTACAAGCAAAAGTTCCAACATGTCTTTTGATGACATTGTTGCTCAG                         GATATCAAAGAGAACCCAGTCTTGATCTACATGAAGGGT
genomic: AGCCTACAAGCAAAAGTTCCAACATGTCTTTTGATGACATTGTTGCTCAGgtattaacat ... cattgggcagGATATCAAAGAGAACCCAGTCTTGATCTACATGAAGGGT
EST: gi|88199623|gb|CI199473.1|CI199473
EST:     CTTTTGATGACATTGTTGCTCAG                         GATATCAAAGAGAACCCAGTCTTGATCTACATGAAGGG-TTTCCTGAGTCT
genomic: CTTTTGATGACATTGTTGCTCAGgtattaacat ... cattgggcagGATATCAAAGAGAACCCAGTCTTGATCTACATGAAGGGTTTTCCTGAGTCT
EST: gi|88448599|gb|CI693990.1|CI693990
EST:     AGCCTACAAGCAAAAGTTCCAACATGTCTTTTGATGACATTGTTGCTCAG                         GATATCAAAGAGAACCCAGTCTTGATCTACATGAAGGGTTTTCCTGAGTCT
genomic: AGCCTACAAGCAAAAGTTCCAACATGTCTTTTGATGACATTGTTGCTCAGgtattaacat ... cattgggcagGATATCAAAGAGAACCCAGTCTTGATCTACATGAAGGGTTTTCCTGAGTCT
EST: gi|86545203|gb|CI185409.1|CI185409
EST:     TGATGACATTGTTGCTCAG                         GATATCAAAGAGAACCCAGTCTTGATCTACATGAAGAGTTTTCCTGAGTCT
genomic: TGATGACATTGTTGCTCAGgtattaacat ... cattgggcagGATATCAAAGAGAACCCAGTCTTGATCTACATGAAGGGTTTTCCTGAGTCT
EST: gi|88371997|gb|CI681514.1|CI681514
EST:     AGCCTACAAGCAAAAGTTCCAACATGTCTTTTGATGACATTGTTGCTCAG                         GATATCAAAGAGAACCCAGTCTTGATCTACATGAAGGGTTTTCCTGAGTCT
genomic: AGCCTACAAGCAAAAGTTCCAACATGTCTTTTGATGACATTGTTGCTCAGgtattaacat ... cattgggcagGATATCAAAGAGAACCCAGTCTTGATCTACATGAAGGGTTTTCCTGAGTCT
EST: gi|87006043|gb|CI289460.1|CI289460
EST:     AGCCTACAAGCAAAAGTTCCAACATGTCTTTTGATGACATTGTTGCTCAG                         GATATCAAAGAGAAACCAGTCTTGATCTACATGAAGGG
genomic: AGCCTACAAGCAAAAGTTCCAACATGTCTTTTGATGACATTGTTGCTCAGgtattaacat ... cattgggcagGATATCAAAGAGAACCCAGTCTTGATCTACATGAAGGG
EST: gi|88367351|gb|CI566317.1|CI566317
EST:     AGCCTACAAGCAAAAGTTCCAACATGTCTTTTGATGACATTGTTGCTCAG                         GATATCAAAGAGAACCCAGTCTTGATCTACATGAAGGGTTTTCCTGAGTCT
genomic: AGCCTACAAGCAAAAGTTCCAACATGTCTTTTGATGACATTGTTGCTCAGgtattaacat ... cattgggcagGATATCAAAGAGAACCCAGTCTTGATCTACATGAAGGGTTTTCCTGAGTCT
EST: gi|88331903|gb|CI642128.1|CI642128
EST:     AGCCTACAAGCAAAAGTTCCAACATGTCTTTTGATGACATTGTTGCTCAG                         GATATCAAAGAGAACCCAGTCTTGATCTACATGAAGGG
genomic: AGCCTACAAGCAAAAGTTCCAACATGTCTTTTGATGACATTGTTGCTCAGgtattaacat ... cattgggcagGATATCAAAGAGAACCCAGTCTTGATCTACATGAAGGG
EST: gi|88327320|gb|CI645097.1|CI645097
EST:     AGCCTACAAGCAAAAGTTCCAACATGTCTTTTGATGACATTGTTGCTCAG                         GATATCAAAGAGAACCCACTCTTGATCTACATGAAGGGTTTTCCTGAGTCT
genomic: AGCCTACAAGCAAAAGTTCCAACATGTCTTTTGATGACATTGTTGCTCAGgtattaacat ... cattgggcagGATATCAAAGAGAACCCAGTCTTGATCTACATGAAGGGTTTTCCTGAGTCT
EST: gi|33660934|gb|CF291901.1|CF291901
EST:     AAGCAAAAGTTCCAACATGTCTTTTGATGACATTGTTGCTCAG                         GATATCAAAGAGAACCCAGTCTTGATCTACATGAAGGGTTTTCCTGAGTCT
genomic: AAGCAAAAGTTCCAACATGTCTTTTGATGACATTGTTGCTCAGgtattaacat ... cattgggcagGATATCAAAGAGAACCCAGTCTTGATCTACATGAAGGGTTTTCCTGAGTCT

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: 71 (upstream exon), 69 (downstream exon)
Score: 35

CTCAAGTTCAACACGAGTAGCTGCTGATCCTGATACACATCAAGATTTCCAGCCTACAAGCAAAAGTTCCAACATGTCTTTTGATGACATTGTTGCTCAGgtattaacat ... cattgggcagGATATCAAAGAGAACCCAGTCTTGATCTACATGAAGGGTTTTCCTGAGTCTCCTATGTGTGGATTCAGTGCATTGGCAGTTAAAGTCCTCAAGCTATATG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtttcattttgtgtttctgccatttgttaatgctacaacacaatcattgggcagGATATCAAAGAGAACCCAGTCTTGATCTACATGAAGGGTTTTCCTGAGTCTCCTATGTGTGGATTCAGTGCATTGGCAGTTAAAGTCCTCAAGCTATATG
                         tgttaat  putative branch site (score: 35)
                      atttgttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattaacatttataaatggatttttggaatatttaaattgatgagatgagcttattttctagaaaggctaggcatatcttaaatgtttcattttgtgtttctgccatttgttaatgctacaacacaatcattgggcagGATATCAAAGAGAACCCAGTCTTGATCTACATGAAGGGTTTTCCTGAGTCTCCTATGTGTGGATTCAGTGCATTGGCAGTTAAAGTCCTCAAGCTATATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT