Sequence
atgc intronic sequence ATGC exonic sequencegtaactgcactttcttttcagtgtttcaagaattttttatgtttaaatcgcaattattctgaaagtgtgtttactcttatggcatcagAAAACAGGGGAGGACCATGTTGACATTATCACTTTCTACAACGAAGTATTTATTCCTACTGTGAAACCTTTGCTGGTTGAGCTAGGGTCTGGTACTAGTC
Basic information
species | Oryza sativa |
transcript | LOC_Os08g42600.2 |
intron # | 14 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os08g42600.2 (Oryza sativa), 3'ss of exon 14
lower sequence: GRMZM2G016997_T01 (Zea mays), 3'ss of exon 14
-gtaactgcactttcttttcagtgtttcaagaattttttatgtttaaatcgcaattattctgaaagtgtgtttactcttatggcatcagAAAACAGGGGAGGACCATGTTGACATTATCACTTTCTACAACGAAGTATTTATTCCTACTGTGAAACCTTTGCTGGTTGAGCTAGGGTCTGGTACTAGTC
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gttagttctgtcttgtttttagc-ttttaagaatttc--gcgatgagttggaagtttatatga-------ctgaattatatcctgccagAAAACAGGAGAAGATCATGTTGATATTATCACTTTCTACAATGAAGTATTTATTCCTGCTGTCAAGCCTTTGTTAGTGGAGGTTGGACCTGGTGCTAGTC
upper sequence: LOC_Os08g42600.2 (Oryza sativa), 3'ss of exon 14
lower sequence: GRMZM2G033828_T02 (Zea mays), 3'ss of exon 15
gtaactgcactttcttttcagtgtttcaagaattttttatgtttaaatcgcaattattctgaaagtgtgtttactcttatggcatc-----agAAAACAGGGGAGGACCATGTTGACATTATCACTTTCTACAACGAAGTATTTATTCCTACTGTGAAACCTTTGCTGGTTGAGCTAGGGTCTGGTACTAGTC
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------gtaagttcctatcttgttttcaa----cttatataagaattttggaatgagtc-gaaagtctatctgatcaaattgtatcctgccagAAAACAGGAGAAGACCACGTCGACATCATCACTTTCTACAACGAAGTATTCATTCCTGCCGTCAAGTCCTTGTTGGTGGAGGTAGGGCCTGGCGCCAGCG
upper sequence: LOC_Os08g42600.2 (Oryza sativa), 3'ss of exon 14
lower sequence: AT3G12280.2 (Arabidopsis thaliana), 3'ss of exon 14
gtaactgcactttcttttcagtgtttcaagaattttttatgtttaaatcgcaattattctgaaagtgtgtttactcttatggcatcagAAAACAGGGGAGGACCATGTTGACATTATCACTTTCTACAACGAAGTATTTATTCCTACTGTGAAACCTTTGCTGGTTGAGCTAGGGTCTGGTACTAGTC
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gtatatatacactcttaaccttatgctgaaaagtttctttactcgg-tggaga--agactaaatttgtg---acaatgacttgaacagAGAATAGGGCCAGATCATGTTGACATCATCACATTCTACAATGAAATATTTATTCCTGCCGTAAAGCCGCTGCTGGTGGAGCTAGGTCCTGTAAGAAACG
upper sequence: LOC_Os08g42600.2 (Oryza sativa), 3'ss of exon 14
lower sequence: Vv04s0008g02780.t01 (Vitis vinifera), 3'ss of exon 14
gtaactgcactttcttttcagtgtttcaagaattttttatgtttaaatcgcaattattctgaaagtgtgtttactcttatggcatcagAAAACAGGGGAGGACCATGTTGACATTATCACTTTCTACAACGAAGTATTTATTCCTACTGTGAAACCTTTGCTGGTTGAGCTAGGGTCTGGTACTAGTC
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gtatgt-tgcttaatctctattctcttagtgttagcttctgttctatgggaaatct------aagcctttcaactgattttg-aacagAAAACAGGGAAGGAACATGTTGATATTATCACATTTTACAATGAAATTTTTATTCCGGCTGTAAAGCCGCTGTTAATGGAGATTGGGCCTGGTGGTGGAAMapped 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|58675166|gb|CK063853.1|CK063853EST: AAGTTTTCCGTAGTGTTTATGTTCATTGGGCATCACGAAGCCGCAATGGG AAAACAGGGGAGGACCATGTTGACATTATCACTTTCTACAACGAAGTATTT
genomic: AAGTTTTCCGTAGTGTTTATGTTCATTGGGCATCACGAAGCCGCAATGGGgtaactgcac ... atggcatcagAAAACAGGGGAGGACCATGTTGACATTATCACTTTCTACAACGAAGTATTT
EST:
gi|58602114|gb|CK012642.1|CK012642EST: AGTTTTCCCGTAGTGTTTATGTTCATTGGGCATCACGAAGCCGCAATGGG AAAACAGGGGAGGACCATGTTGACATTATCACTTTCTACAACGAAGTATTT
genomic: AGTTTT-CCGTAGTGTTTATGTTCATTGGGCATCACGAAGCCGCAATGGGgtaactgcac ... atggcatcagAAAACAGGGGAGGACCATGTTGACATTATCACTTTCTACAACGAAGTATTT
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:
47 (upstream exon),
41 (downstream exon)
Score:
4ATTCAAGGAAATTATTTTCGGCTACAGAAAACAATCTCAGTGCAAGCCACAAGTTTTCCGTAGTGTTTATGTTCATTGGGCATCACGAAGCCGCAATGGGgtaactgcac ... atggcatcagAAAACAGGGGAGGACCATGTTGACATTATCACTTTCTACAACGAAGTATTTATTCCTACTGTGAAACCTTTGCTGGTTGAGCTAGGGTCTGGTACTAGTC
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttttatgtttaaatcgcaattattctgaaagtgtgtttactcttatggcatcagAAAACAGGGGAGGACCATGTTGACATTATCACTTTCTACAACGAAGTATTTATTCCTACTGTGAAACCTTTGCTGGTTGAGCTAGGGTCTGGTACTAGTC
ctcttat CT-rich tract
atgtttaaat TA-rich tract