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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTGTGGGCAACATGGGATCTCATTGCACTAGTTGAAAACGGAAGACATGATGGTACTCCCACACATTCAGTATGCTTTGTTTGGAACAGTGGTCGGGAGgtacattttgcctaatgcggaatgcatcaattagcagtgtactttttgtctaaaaaatcactattttagcttgatattcagtaaactgatgaagttgaattcacaatttttttctag

Basic information

species Oryza sativa
transcript LOC_Os08g29160.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g29160.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G127374_T01 (Zea mays), 5'ss of exon 7
TGTGTGGGCAACATGGGATCTCATTGCACTAGTTGAAAACGGAAGACATGATGGTACTCCCACACATTCAGTATGCTTTGTTTGGAACAGTGGTCGGGAGgtacattttgcctaatgcggaatgcatcaattagcagtgtactttttgtctaaaaaatcactattttagcttgatattcagtaaactgatgaagttgaattcacaatttttttctag---------------------------------
||| |||||||| |||||||| |||||  |||||||||| ||||| |||||||||| ||||||||||||||| || ||  |||||||||||||| |||||||   ||     ||      ||   || |   |  ||||    ||| |  ||||| || | |  ||    |   | |   |  | |  ||| | | |  || |||||   |  || |                                 
TGTTTGGGCAACTTGGGATCTTATTGCTTTAGTTGAAAATGGAAGGCATGATGGTAGTCCCACACATTCAGTTTGTTTCATTTGGAACAGTGGTAGGGAGgtgagttccttttatacaaaaaaatattacggaagagtgagtatttggcataaaagataatttgttcgagtcagtgt---gagaccccatgta-tggtcttgacaatcaataacttgagggggttaacttgcacgtgacattggctctag

upper sequence: LOC_Os08g29160.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA19G11100.1 (Glycine max), 5'ss of exon 9
---TGTGTGGGCAACATGGGATCTCATTGCACTAGTTGAAAACGGAAGACATGATGGTACTCCCACACATTCAGTATGCTTTGTTTGGAACAGTGGTCGGGAGgtacattttgcctaatgcggaatgcatcaattagcagtgtactttttgtctaaaaaatcactattttagcttgatattcagtaaactgatgaagttgaattcacaatttttttctag
   ||  ||||||||||||||||| || ||  | | |||||| ||||||||||||||  ||||||||||| | ||    ||||| |||||   |||||  ||||||        |   |  |  ||   || |||     |  | ||| || |||     | |   ||| |   |||     || |   | ||||  ||   |     || |  ||    
AATTGCATGGGCAACATGGGATCTTATAGCTATGGCTGAAAATGGAAGACATGATGGGCCTCCCACACATGCTGTCGTGTTTGTGTGGAA---TGGTCATGAGgtaag---aaaccggtcagttatagttccatt-----tccattttgtggcta---gtttatcttttgattctga-----aggagggttatgagattatttctgttatatcatttgt-
















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|29667834|gb|CB664109.1|CB664109
EST:     ATGGTACTCCCACACATTCAGTATGCTTTGTTTGGAACAGTGGTCGGGAG                         GGTGAGGATGTGGAATTGGTGGGGGATTTTACAAGTAACTGGAAAGACAAA
genomic: ATGGTACTCCCACACATTCAGTATGCTTTGTTTGGAACAGTGGTCGGGAGgtacattttg ... ttttttctagGGTGAGGATGTGGAATTGGTGGGGGATTTTACAAGTAACTGGAAAGACAAA
EST: gi|29629595|gb|CB634604.1|CB634604
EST:     ATGGTACTCCCACACATTCAGTATGCTTTGTTTGGAACAGTGGTCGGGAG                         GGTGAGGATGTGGAATTGGTGGGGGATTTTACAAGTAACTGGAAAGACAAA
genomic: ATGGTACTCCCACACATTCAGTATGCTTTGTTTGGAACAGTGGTCGGGAGgtacattttg ... ttttttctagGGTGAGGATGTGGAATTGGTGGGGGATTTTACAAGTAACTGGAAAGACAAA
EST: gi|29669707|gb|CB665982.1|CB665982
EST:     ATGGTACTCCCACACATTCAGTATGCTTTGTTTGGAACAGTGGTCGGGAG                         GGTGAGGATGTGGAATTGGTGGGGGATTTTTCAAGTAACTGGAAAGACAAA
genomic: ATGGTACTCCCACACATTCAGTATGCTTTGTTTGGAACAGTGGTCGGGAGgtacattttg ... ttttttctagGGTGAGGATGTGGAATTGGTGGGGGATTTTACAAGTAACTGGAAAGACAAA
EST: gi|86495830|gb|CI138463.1|CI138463
EST:     CAGTATGCTTTGTTTGGAACAGTGGTCGGGAG                         GGTGAGGATGTGGAATTGGTGGGGGATTTTACAAGTAACTGGAAAGACAAA
genomic: CAGTATGCTTTGTTTGGAACAGTGGTCGGGAGgtacattttg ... ttttttctagGGTGAGGATGTGGAATTGGTGGGGGATTTTACAAGTAACTGGAAAGACAAA
EST: gi|38477288|gb|CF961421.1|CF961421
EST:     ATGGTACTCCCACACATTCAGTATGCTTTGTTTGGAACAGTGGTCGGGAG                         GGTGAGGATGTGGAATTGGTGGGGGATTTTACAAGTAACTGGAAAGACAAA
genomic: ATGGTACTCCCACACATTCAGTATGCTTTGTTTGGAACAGTGGTCGGGAGgtacattttg ... ttttttctagGGTGAGGATGTGGAATTGGTGGGGGATTTTACAAGTAACTGGAAAGACAAA
EST: gi|29669705|gb|CB665980.1|CB665980
EST:     ATGGTACTCCCACACATTCAGTATGCTTTGTTTGGAACAGTGGTCGGGAG                         GGTGAGGATGTGGAATTGGTGGGGGATTTTACAAGTAACTGGAAAGACAAA
genomic: ATGGTACTCCCACACATTCAGTATGCTTTGTTTGGAACAGTGGTCGGGAGgtacattttg ... ttttttctagGGTGAGGATGTGGAATTGGTGGGGGATTTTACAAGTAACTGGAAAGACAAA
EST: gi|58681036|gb|CK069723.1|CK069723
EST:     ATGGTACTCCCACACATTCAGTATGCTTTGTTTGGAACAGTGGTCGGGAG                         GGTGAGGATGTGGAATTGGTGGGGGATTTTACAAGTAACTGGAAAGACAAA
genomic: ATGGTACTCCCACACATTCAGTATGCTTTGTTTGGAACAGTGGTCGGGAGgtacattttg ... ttttttctagGGTGAGGATGTGGAATTGGTGGGGGATTTTACAAGTAACTGGAAAGACAAA

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: 63 (upstream exon), 63 (downstream exon)
Score: 16

TGTGTGGGCAACATGGGATCTCATTGCACTAGTTGAAAACGGAAGACATGATGGTACTCCCACACATTCAGTATGCTTTGTTTGGAACAGTGGTCGGGAGgtacattttg ... ttttttctagGGTGAGGATGTGGAATTGGTGGGGGATTTTACAAGTAACTGGAAAGACAAAGTAAAGTGTGACCACAAAGGTGGGTCAAGATATGAAGCTGAAATTCGAC




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