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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCGGCGGAGGGAGCATGGTGTCGCGCGTGGCCGTGCTCGCATTCTGCGTCGCCGGGATCTGGTCGGCGTACATCACCCAGGGCGTCCTCCAGGAAACCCTgtaagcgcccgcctccctccctccctccctctctctctctctctctctaatggtgctcgggagcggaggggaattgggctctgcttcggcgagtttctgaaaattgttcgccgttttctctccccgccgttcgttcag

Basic information

species Oryza sativa
transcript LOC_Os06g39260.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g39260.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G176029_T01 (Zea mays), 5'ss of exon 1
GCGGCGGAGGGAGCATGGTGTCGCGCGTGGCCGTGCTCGCATTCTGCGTCGCCGGGATCTGGTCGGCGTACATCACCCAGGGCGTCCTCCAGGAAACCCTgtaagcgcccgcctccctccctccctccctctctctctctctctctctaatggtgctcgggagcggaggggaattgggc---tctgcttcggcgagtttctgaaaattgttcgccgttttctctccccgccgttcgttcag
 |||||| |||||||||| |  |||||||||||| ||||| ||||| ||||| ||||||||||| || ||||||  |||||||||||||||||| || |||||||| ||| || | |||      |  || ||       | ||    |||    |     ||| | ||  |||| ||    | ||||     | | ||| |                                       
TCGGCGGCGGGAGCATGGCGGGGCGCGTGGCCGTCCTCGCCTTCTGTGTCGCAGGGATCTGGTCCGCCTACATCTACCAGGGCGTCCTCCAGGAGACTCTgtaagcccccccccctctctaa---ttgctgtccgaagtccgctacacaattagac----aagccggggtcaatttggtgagtttgctcgccggtggttcag---------------------------------------

upper sequence: LOC_Os06g39260.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA02G02330.1 (Glycine max), 5'ss of exon 1
GCGGCGGAGGGAGCATGGTGTCG-CGCGTGGCCGTGCTCGCATTCTGCGTCGCCGGGATCTGGTCGGCGTACATCACCCAGGGCGTCCTCCAGGAAACCCTgtaagcgcccgcctcc-ctccctccctccctctctctctctctctctctaa-tggtgctcgggagcggaggggaattgggctctgcttcggcgagtttctgaaaattgttcgccgttttctctccccgccgttcgttcag
  |||  | || | | ||   || ||| |    |||||||| |||||||||||||| |||||||| |||||||||  ||| ||||| || |||||||   ||||||   ||   ||| ||||    ||| |   ||| |  |   | || || ||  |||    |  |    |   || |  | |  ||      | ||                                          
-AGGCTCATGGCGGAGGGCTCCGTCGCATCCTTGTGCTCGCCTTCTGCGTCGCCGGAATCTGGTCCGCGTACATCTACCAAGGCGTTCTTCAGGAAAATGTgtaagaatccctatccgctccgaaactctcgagctcgcggtgaatttcgaaatgccgctactaattgctatgattttcgtttttttttttttttggtttcag--------------------------------------

upper sequence: LOC_Os06g39260.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA01G05170.1 (Glycine max), 5'ss of exon 1
GCGGCGGAGGGAGCATGGTGTCGC-GCGTGGCCGTGCTCGCATTCTGCGTCGCCGGGATCTGGTCGGCGTACATCACCCAGGGCGTCCTCCAGGAAACCCTgtaagcgcccgcctccctccctccctccctctctctctctctctctctaatggtgctcgggagcggaggggaattgggctctgcttcggcgagtttctg--aaaattgttcgccgttttctctccccgccgttcgttcag
  |||  | || |   ||   ||| | ||    || ||||| ||||||||||| || ||||||||||| ||||||  ||| ||||| || |||||||   ||||||   |||  |||   |                            |    | ||||  |   | ||||||||  |   |||  |  | | ||   |  |   || || |  | ||| | |       |||   | ||
-AGGCTCACGGCGGCGGGCTCCGCCGAGTCCTTGTTCTCGCCTTCTGCGTCGCTGGAATCTGGTCGGCATACATCTACCAAGGCGTTCTGCAGGAAAATGTgtaagaaaccgaatccgctc----------------------------agaaattctcga-attcgcggggaatttcgaaatgccgctactaattctcgctatgtttttttgttgatttttttttttttggtt---ttag

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|87006823|gb|CI285857.1|CI285857
EST:     GCCGGGATCTGGTCGGCGTACATCACCCAGTGCGTCCTCCAGGAAACCCT                         GTCGACGAAGCGGTTCGGGCCGGAG
genomic: GCCGGGATCTGGTCGGCGTACATCACCCAGGGCGTCCTCCAGGAAACCCTgtaagcgccc ... gttcgttcagGTCGACGAAGCGGTTCGGGCCGGAG
EST: gi|88386932|gb|CI629259.1|CI629259
EST:     GCCGGGATCTGGTCGGCGTACATCACCCAGGGCGTCCTCCACGAAACCCT                         GTCGACGAAGCGGTTCGGGCCGGAGGCGCGGCGGTTCGACCACCTCGCGTT
genomic: GCCGGGATCTGGTCGGCGTACATCACCCAGGGCGTCCTCCAGGAAACCCTgtaagcgccc ... gttcgttcagGTCGACGAAGCGGTTCGGGCCGGAGGCGCGGCGGTTCGACCACCTCGCGTT
EST: gi|88727081|gb|CI750736.1|CI750736
EST:     GCCGGGATCTGGTCGGCGTACATCACCCAGGGCGTCCTCCAGGAAACCCT                         GTCGAAGAAGCGGTTCGGGCCGGAGGCGCGGCGGTTCGACCACCTCGCGTT
genomic: GCCGGGATCTGGTCGGCGTACATCACCCAGGGCGTCCTCCAGGAAACCCTgtaagcgccc ... gttcgttcagGTCGACGAAGCGGTTCGGGCCGGAGGCGCGGCGGTTCGACCACCTCGCGTT
EST: gi|88400618|gb|CI596039.1|CI596039
EST:     GCCGGGATCTGGTCGGCGTACATCACCCAGGGCGTCCTCCAGGAAACCCT                         GTCGACGAAGCGGTTCGGGCCGGAGGCGCGGCGGTTCGACCACCTCGCGTT
genomic: GCCGGGATCTGGTCGGCGTACATCACCCAGGGCGTCCTCCAGGAAACCCTgtaagcgccc ... gttcgttcagGTCGACGAAGCGGTTCGGGCCGGAGGCGCGGCGGTTCGACCACCTCGCGTT
EST: gi|86832158|gb|CI305384.1|CI305384
EST:     GCCGGGATCTGGTCGGCGTACATCACCCAGGGCGTCCTCCAGGAAACCCT                         GTCGACGAAGCGGTTCGGGCCGGAGGCGCGGCGGTTCGACCACCTCGCGTT
genomic: GCCGGGATCTGGTCGGCGTACATCACCCAGGGCGTCCTCCAGGAAACCCTgtaagcgccc ... gttcgttcagGTCGACGAAGCGGTTCGGGCCGGAGGCGCGGCGGTTCGACCACCTCGCGTT
EST: gi|88574617|gb|CI666386.1|CI666386
EST:     GCCGGGATCTGGTCGGCGTACATCACCCAGGGCGTCNTCCAGGAAACCCT                         GTCGANGAAGCGGTTCGGGCCGGAGGCGCGGCGGTTCGACCACCTCGCGTT
genomic: GCCGGGATCTGGTCGGCGTACATCACCCAGGGCGTCCTCCAGGAAACCCTgtaagcgccc ... gttcgttcagGTCGACGAAGCGGTTCGGGCCGGAGGCGCGGCGGTTCGACCACCTCGCGTT

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: 56 (upstream exon), 74 (downstream exon)
Score: 5

GCGGCGGAGGGAGCATGGTGTCGCGCGTGGCCGTGCTCGCATTCTGCGTCGCCGGGATCTGGTCGGCGTACATCACCCAGGGCGTCCTCCAGGAAACCCTgtaagcgccc ... gttcgttcagGTCGACGAAGCGGTTCGGGCCGGAGGCGCGGCGGTTCGACCACCTCGCGTTCCTCAACTTCGCGCAGAACGTCGTCTGCTTCGTCTGGTCCTTCATAA




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