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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgctattatttttggacaaagaatgtcgcatgaagtttcttaagtatggagataataatttcattctaacttgattctaactttttgtcctctagACTATTAGCTATATGGCTGAACGAGTTGTTGGAACTGGATCCTTTGGTGTTGTATTCCAG

Basic information

species Oryza sativa
transcript LOC_Os06g35530.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g35530.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G043350_T02 (Zea mays), 3'ss of exon 2
gtatgctattatttttggacaaagaatgtcgcatgaagtttcttaagta--tggagataataatttcattctaacttgattct-aactttttgtcctctagACTATTAGCTATATGGCTGAACGAGTTGTTGGAACTGGATCCTTTGGTGTTGTATTCCAG
        |   ||||||| ||||||  || | | |  || || || ||  ||   ||  ||||  |||||||||||   |||  | ||  || ||| ||||| || |||||||||||||| |||||||||||||||||||| ||||| ||||| ||||||
-------gtaggttttggagaaagaaattcacttcatcttgctgaattacatgacaatgctaataacattctaacttagctcttgatttggtgccctttagACCATCAGCTATATGGCTGAGCGAGTTGTTGGAACTGGATCGTTTGGGGTTGTCTTCCAG
















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|58589448|gb|CF987756.1|CF987756
EST:     GTCATATAATTTCAACTACTATTGGAGGGCAGAACGATGAGCCCAAAAGG                         ACTATTAGCTATATGGCTGAACGAGTTGTTGGAACTGGATCCTTTGGT
genomic: GTCATATAATTTCAACTACTATTGGAGGGAAGAACGATGAGCCCAAAAGGgtatgctatt ... tgtcctctagACTATTAGCTATATGGCTGAACGAGTTGTTGGAACTGGATCCTTTGGT
EST: gi|66914786|gb|CX101634.1|CX101634
EST:     GTCATATAATTTCAACTACTATTGGAGGGAAGAACGATGAGCCCAAAAGG                         ACTATTAGCTATATGGCTGAACGAGTTGTTGGAACTGGATCCTTTGGTGTT
genomic: GTCATATAATTTCAACTACTATTGGAGGGAAGAACGATGAGCCCAAAAGGgtatgctatt ... tgtcctctagACTATTAGCTATATGGCTGAACGAGTTGTTGGAACTGGATCCTTTGGTGTT
EST: gi|33793859|gb|CF322817.1|CF322817
EST:     GTCATATAATTTCAACTACTATTGGAGGGAAGAACGATGAGCCCAAAAGG                         ACTATTAGCTATATGGCTGAACGAGTTGTTGGAACTGGATCCTTTGGTGTT
genomic: GTCATATAATTTCAACTACTATTGGAGGGAAGAACGATGAGCCCAAAAGGgtatgctatt ... tgtcctctagACTATTAGCTATATGGCTGAACGAGTTGTTGGAACTGGATCCTTTGGTGTT
EST: gi|58608373|gb|CK036406.1|CK036406
EST:     GTCATATAATTTCAACTACTATTGGAGGGAAGAACGATGAGCCCAAAAGG                         ACTATTAGCTATATGGCTGAACGAGTTGTTGGAACTGGATCCTTTGGTGTT
genomic: GTCATATAATTTCAACTACTATTGGAGGGAAGAACGATGAGCCCAAAAGGgtatgctatt ... tgtcctctagACTATTAGCTATATGGCTGAACGAGTTGTTGGAACTGGATCCTTTGGTGTT
EST: gi|29672896|gb|CB669171.1|CB669171
EST:     GTCATATAATTTCAACTACTATTGGAGGGAAGAACGATGAGCCCAAAAGG                         ACTATTAGCTATATGGCTGAACGAGTTGTTGGAACTGGATCCTTTGGTGTT
genomic: GTCATATAATTTCAACTACTATTGGAGGGAAGAACGATGAGCCCAAAAGGgtatgctatt ... tgtcctctagACTATTAGCTATATGGCTGAACGAGTTGTTGGAACTGGATCCTTTGGTGTT
EST: gi|33676536|gb|CF304775.1|CF304775
EST:     GTCATATAATTTCAACTACTATTGGAGGGAAGAACGATGAGCCCAAAAGG                         ACTATTAGCTATATGGCTGAACGAGTTGTTGGAACTGGATCCTTTGGTGTT
genomic: GTCATATAATTTCAACTACTATTGGAGGGAAGAACGATGAGCCCAAAAGGgtatgctatt ... tgtcctctagACTATTAGCTATATGGCTGAACGAGTTGTTGGAACTGGATCCTTTGGTGTT
EST: gi|58653237|gb|CK041917.1|CK041917
EST:     GTCATATAATTTCAACTACTATTGGAGGGAAGAACGATGAGCCCAAAAGG                         ACTATTAGCTATATGGCTGAACGAGTTGTTGGAACTGGATCCTTTGGTGTT
genomic: GTCATATAATTTCAACTACTATTGGAGGGAAGAACGATGAGCCCAAAAGGgtatgctatt ... tgtcctctagACTATTAGCTATATGGCTGAACGAGTTGTTGGAACTGGATCCTTTGGTGTT
EST: gi|29689142|gb|CB685417.1|CB685417
EST:     GTCATATAATTTCAACTACTATTGGAGGGAAGAACGATGAGCCCAAAAGG                         ACTATTAGCTATATGGCTGAACGAGTTGTTGGAACTGGATCCTTTGGTGTT
genomic: GTCATATAATTTCAACTACTATTGGAGGGAAGAACGATGAGCCCAAAAGGgtatgctatt ... tgtcctctagACTATTAGCTATATGGCTGAACGAGTTGTTGGAACTGGATCCTTTGGTGTT
EST: gi|29660849|gb|CB657124.1|CB657124
EST:     GTCATATAATTTCAACTACTATTGGAGGGAAGAACGATGAGCCCAAAAGG                         ACTATTAGCTATATGGCTGAACGAGTTGTTGGAACTGGATCCTTTGGTGTT
genomic: GTCATATAATTTCAACTACTATTGGAGGGAAGAACGATGAGCCCAAAAGGgtatgctatt ... tgtcctctagACTATTAGCTATATGGCTGAACGAGTTGTTGGAACTGGATCCTTTGGTGTT

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: 74 (upstream exon), 60 (downstream exon)
Score: 31

CATGGTCCCACTATAATGGGAGGAAATGATCCAGTCACAGGTCATATAATTTCAACTACTATTGGAGGGAAGAACGATGAGCCCAAAAGGgtatgctatt ... tgtcctctagACTATTAGCTATATGGCTGAACGAGTTGTTGGAACTGGATCCTTTGGTGTTGTATTCCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taagtatggagataataatttcattctaacttgattctaactttttgtcctctagACTATTAGCTATATGGCTGAACGAGTTGTTGGAACTGGATCCTTTGGTGTTGTATTCCAG
                                  ttctaac  putative branch site (score: 31)
                                        ctttttgtcctct  CT-rich tract
           ataataatttcattct  TA-rich tract