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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtaactatacttattcttgtgattagctgtacttattcttttaagcaactatactttagttaacatatatccacttttgcaccattttgccacatatgcaagcatcactttctttttaattctttttatgctatggtacactggtacttttacgctatgttaatccttttatttttgtttctttagGCGGCTTAATGACAACAGTTTAAACGGTCCAATCCCGAGGGATCTGGCAAAAATATCTAGTCTCAAAGTGAT

Basic information

species Oryza sativa
transcript LOC_Os01g17250.1
intron # 3
splice site 3'
intron type U2

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|87025893|gb|CI282470.1|CI282470
EST:     ACTGGAACCATACCGAAAGAACTTGGCAAGCTGAGTTCCTTAGTATTCTT                         GCGGCTTAATGACAACAGTTTAAACGGTCCAATCCCGAGGGATCTGGCAAA
genomic: ACTGGAACCATACCGAAAGAACTTGGCAAGCTGAGTTCCTTAGTATTCTTgtgagtaact ... gtttctttagGCGGCTTAATGACAACAGTTTAAACGGTCCAATCCCGAGGGATCTGGCAAA
EST: gi|15849919|gb|BI798195.1|BI798195
EST:     AACTTGCCAAGCTGAGTTCCTTAGTATTCTT                         GCGGCTTAATGACCAACCAGTTTAAACCGGTCCAATCCCGAGGGATCTGGC
genomic: AACTTGGCAAGCTGAGTTCCTTAGTATTCTTgtgagtaact ... gtttctttagGCGGCTTAATGAC-AAC-AGTTTAAAC-GGTCCAATCCCGAGGGATCTGGC
EST: gi|86828695|gb|CI280551.1|CI280551
EST:     ACTGGAACCATACCGAAAGAACTTGGCAAGCTGAGTTCCTTAGTATTCTT                         GCGGCTTAATGACAACAGTTTAAACGGTCCAATCCCGAGGGATCTGGCAAA
genomic: ACTGGAACCATACCGAAAGAACTTGGCAAGCTGAGTTCCTTAGTATTCTTgtgagtaact ... gtttctttagGCGGCTTAATGACAACAGTTTAAACGGTCCAATCCCGAGGGATCTGGCAAA
EST: gi|29668540|gb|CB664815.1|CB664815
EST:     ACTGGAACCATACCGAAAGAACTTGGCAAGCTGAGTTCCTTAGTATTCTT                         GCGGCTTAATGACAACAGTTTAAACGGTCCAATCCCGAGGGATCTGGCAAA
genomic: ACTGGAACCATACCGAAAGAACTTGGCAAGCTGAGTTCCTTAGTATTCTTgtgagtaact ... gtttctttagGCGGCTTAATGACAACAGTTTAAACGGTCCAATCCCGAGGGATCTGGCAAA
EST: gi|88226240|gb|CI226156.1|CI226156
EST:     AACTTGGCAAGCTGAGTTCCTTAGTATTCTT                         GCGGCTTAATGACAACAGTTTAAACGGTCCAATCCCGAGGGATCTGGCAAA
genomic: AACTTGGCAAGCTGAGTTCCTTAGTATTCTTgtgagtaact ... gtttctttagGCGGCTTAATGACAACAGTTTAAACGGTCCAATCCCGAGGGATCTGGCAAA
EST: gi|58686473|gb|CK075160.1|CK075160
EST:     ACTGGAACCATACCGAAAGAACTTGGCAAGCTGAGTTCCTTAGTATTCTT                         GCGGCTTAATGACAACAGTTTAAACGGTCCAATCCCGAGGGATCTGGCAAA
genomic: ACTGGAACCATACCGAAAGAACTTGGCAAGCTGAGTTCCTTAGTATTCTTgtgagtaact ... gtttctttagGCGGCTTAATGACAACAGTTTAAACGGTCCAATCCCGAGGGATCTGGCAAA
EST: gi|7206590|gb|C97644.2|C97644
EST:     ACTGGAACCATACCGAAAGAACTTGGCAAGCTGAGTTCCTTAGTATTCTT                         GCGGCTTAATGACAACAGTTTAAACGGTCCAATCCCGAGGGATCTGGCAAA
genomic: ACTGGAACCATACCGAAAGAACTTGGCAAGCTGAGTTCCTTAGTATTCTTgtgagtaact ... gtttctttagGCGGCTTAATGACAACAGTTTAAACGGTCCAATCCCGAGGGATCTGGCAAA
EST: gi|88838832|gb|CI012708.1|CI012708
EST:     ACTGGAACCATACCGAAAGAACTTGGCAAGCTGAGTTCCTTAGTATTCTT                         GCGGCTTAATGACAACAGTTTAAACGGTCCAATCCCGAGGGATCTGGCAAA
genomic: ACTGGAACCATACCGAAAGAACTTGGCAAGCTGAGTTCCTTAGTATTCTTgtgagtaact ... gtttctttagGCGGCTTAATGACAACAGTTTAAACGGTCCAATCCCGAGGGATCTGGCAAA

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: 70 (upstream exon), 75 (downstream exon)
Score: 58

TCGGGAGTCTGAAGAACCTTATTAGCTTGGATCTGTATAACAACAACATTACTGGAACCATACCGAAAGAACTTGGCAAGCTGAGTTCCTTAGTATTCTTgtgagtaact ... gtttctttagGCGGCTTAATGACAACAGTTTAAACGGTCCAATCCCGAGGGATCTGGCAAAAATATCTAGTCTCAAAGTGAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatggtacactggtacttttacgctatgttaatccttttatttttgtttctttagGCGGCTTAATGACAACAGTTTAAACGGTCCAATCCCGAGGGATCTGGCAAAAATATCTAGTCTCAAAGTGAT
                          tgttaat  putative branch site (score: 58)
                                tccttttatttttgtt  CT-rich tract
                        tatgttaatcctttta  TA-rich tract